Starting phenix.real_space_refine on Sun May 19 16:30:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.4 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.pdb" } resolution = 3.4 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 39 5.16 5 C 4253 2.51 5 N 1077 2.21 5 O 1247 1.98 5 H 6614 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 13230 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3225 Inner-chain residues flagged as termini: ['pdbres="ALA C 131 "', 'pdbres="ALA C 132 "', 'pdbres="GLY C 148 "'] Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "D" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3286 Inner-chain residues flagged as termini: ['pdbres="THR D 142 "', 'pdbres="ALA D 143 "'] Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 3} Link IDs: {'PTRANS': 14, 'TRANS': 204} Chain: "A" Number of atoms: 6719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6719 Inner-chain residues flagged as termini: ['pdbres="ALA A 237 "', 'pdbres="ALA A 289 "', 'pdbres="GLY A 395 "', 'pdbres="ILE A 453 "'] Classifications: {'peptide': 427} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 8, 'TRANS': 418} Chain breaks: 2 Time building chain proxies: 2.05, per 1000 atoms: 0.15 Number of scatterers: 13230 At special positions: 0 Unit cell: (129.47, 117.7, 85.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 O 1247 8.00 N 1077 7.00 C 4253 6.00 H 6614 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 165 " - pdb=" SG CYS D 220 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 435.6 milliseconds 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1582 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 43.1% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 205 through 208 No H-bonds generated for 'chain 'C' and resid 205 through 208' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 24 through 53 removed outlier: 3.514A pdb=" N TYR A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 85 removed outlier: 3.676A pdb=" N LEU A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 114 Processing helix chain 'A' and resid 128 through 152 Processing helix chain 'A' and resid 155 through 163 removed outlier: 3.521A pdb=" N ALA A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 199 Proline residue: A 189 - end of helix removed outlier: 3.954A pdb=" N TYR A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 229 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 290 through 304 Processing helix chain 'A' and resid 306 through 319 removed outlier: 4.159A pdb=" N LEU A 309 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.825A pdb=" N GLN A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.897A pdb=" N SER A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 392 removed outlier: 3.602A pdb=" N GLY A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 483 Processing helix chain 'A' and resid 488 through 511 removed outlier: 4.535A pdb=" N GLY A 491 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 492 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 493 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 507 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 544 Processing sheet with id= A, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.776A pdb=" N LYS C 123 " --> pdb=" O MET C 31 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR C 33 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU C 125 " --> pdb=" O THR C 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.954A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 87 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 105 through 109 removed outlier: 3.635A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 211 through 216 removed outlier: 3.785A pdb=" N TYR C 212 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 149 through 159 removed outlier: 5.817A pdb=" N TYR C 193 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 22 through 25 Processing sheet with id= G, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.585A pdb=" N GLY D 68 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS D 57 " --> pdb=" O TRP D 66 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP D 66 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ARG D 59 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU D 64 " --> pdb=" O ARG D 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= I, first strand: chain 'D' and resid 188 through 191 removed outlier: 4.144A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 194 through 196 Processing sheet with id= K, first strand: chain 'D' and resid 219 through 224 344 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.24: 7507 1.24 - 1.51: 3191 1.51 - 1.78: 2617 1.78 - 2.05: 63 2.05 - 2.32: 2 Bond restraints: 13380 Sorted by residual: bond pdb=" CD1 TYR C 160 " pdb=" CE1 TYR C 160 " ideal model delta sigma weight residual 1.382 2.321 -0.939 3.00e-02 1.11e+03 9.80e+02 bond pdb=" CD2 TYR C 160 " pdb=" CE2 TYR C 160 " ideal model delta sigma weight residual 1.382 2.221 -0.839 3.00e-02 1.11e+03 7.81e+02 bond pdb=" CE1 TYR C 160 " pdb=" CZ TYR C 160 " ideal model delta sigma weight residual 1.378 1.964 -0.586 2.40e-02 1.74e+03 5.97e+02 bond pdb=" CE2 TYR C 160 " pdb=" CZ TYR C 160 " ideal model delta sigma weight residual 1.378 1.865 -0.487 2.40e-02 1.74e+03 4.12e+02 bond pdb=" N ALA C 131 " pdb=" CA ALA C 131 " ideal model delta sigma weight residual 1.459 1.710 -0.251 1.27e-02 6.20e+03 3.89e+02 ... (remaining 13375 not shown) Histogram of bond angle deviations from ideal: 55.91 - 74.88: 1 74.88 - 93.84: 7 93.84 - 112.81: 15788 112.81 - 131.77: 8339 131.77 - 150.73: 23 Bond angle restraints: 24158 Sorted by residual: angle pdb=" C GLU C 130 " pdb=" N ALA C 131 " pdb=" CA ALA C 131 " ideal model delta sigma weight residual 123.11 150.73 -27.62 1.42e+00 4.96e-01 3.78e+02 angle pdb=" CB ALA C 131 " pdb=" CA ALA C 131 " pdb=" HA ALA C 131 " ideal model delta sigma weight residual 109.00 55.91 53.09 3.00e+00 1.11e-01 3.13e+02 angle pdb=" CG2 THR D 142 " pdb=" CB THR D 142 " pdb=" HB THR D 142 " ideal model delta sigma weight residual 108.00 75.17 32.83 3.00e+00 1.11e-01 1.20e+02 angle pdb=" H2 ALA C 131 " pdb=" N ALA C 131 " pdb=" H3 ALA C 131 " ideal model delta sigma weight residual 109.47 79.24 30.23 3.00e+00 1.11e-01 1.02e+02 angle pdb=" H1 ALA C 131 " pdb=" N ALA C 131 " pdb=" H2 ALA C 131 " ideal model delta sigma weight residual 109.47 79.59 29.88 3.00e+00 1.11e-01 9.92e+01 ... (remaining 24153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 5699 16.87 - 33.75: 385 33.75 - 50.62: 167 50.62 - 67.49: 70 67.49 - 84.37: 10 Dihedral angle restraints: 6331 sinusoidal: 3376 harmonic: 2955 Sorted by residual: dihedral pdb=" N ALA C 131 " pdb=" C ALA C 131 " pdb=" CA ALA C 131 " pdb=" CB ALA C 131 " ideal model delta harmonic sigma weight residual 122.90 143.55 -20.65 0 2.50e+00 1.60e-01 6.82e+01 dihedral pdb=" CB CYS D 165 " pdb=" SG CYS D 165 " pdb=" SG CYS D 220 " pdb=" CB CYS D 220 " ideal model delta sinusoidal sigma weight residual -86.00 -134.77 48.77 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA TRP D 213 " pdb=" C TRP D 213 " pdb=" N PRO D 214 " pdb=" CA PRO D 214 " ideal model delta harmonic sigma weight residual -180.00 -152.32 -27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 6328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 1071 0.234 - 0.468: 2 0.468 - 0.702: 0 0.702 - 0.936: 0 0.936 - 1.170: 1 Chirality restraints: 1074 Sorted by residual: chirality pdb=" CB THR D 142 " pdb=" CA THR D 142 " pdb=" OG1 THR D 142 " pdb=" CG2 THR D 142 " both_signs ideal model delta sigma weight residual False 2.55 1.38 1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" CA ALA C 131 " pdb=" N ALA C 131 " pdb=" C ALA C 131 " pdb=" CB ALA C 131 " both_signs ideal model delta sigma weight residual False 2.54 2.08 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CA PRO D 144 " pdb=" N PRO D 144 " pdb=" C PRO D 144 " pdb=" CB PRO D 144 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1071 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 171 " 0.118 5.00e-02 4.00e+02 1.82e-01 5.33e+01 pdb=" N PRO D 172 " -0.316 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " 0.105 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " 0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 143 " 0.106 5.00e-02 4.00e+02 1.60e-01 4.08e+01 pdb=" N PRO D 144 " -0.276 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 147 " 0.085 5.00e-02 4.00e+02 1.30e-01 2.68e+01 pdb=" N PRO D 148 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO D 148 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO D 148 " 0.067 5.00e-02 4.00e+02 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 285 1.92 - 2.59: 13622 2.59 - 3.26: 40671 3.26 - 3.93: 51251 3.93 - 4.60: 77264 Nonbonded interactions: 183093 Sorted by model distance: nonbonded pdb=" HA ALA C 131 " pdb=" HB3 ALA C 131 " model vdw 1.253 1.952 nonbonded pdb=" O THR D 142 " pdb=" H2 ALA D 143 " model vdw 1.342 1.960 nonbonded pdb=" O TRP D 213 " pdb=" H SER D 215 " model vdw 1.352 1.850 nonbonded pdb=" O GLU C 130 " pdb=" H2 ALA C 131 " model vdw 1.398 1.960 nonbonded pdb=" HZ3 LYS D 140 " pdb=" O SER D 197 " model vdw 1.418 1.850 ... (remaining 183088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.46 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.370 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.420 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:10.090 Internal consistency checks: 0.000 Total: 26.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.939 6766 Z= 1.156 Angle : 0.926 27.623 9214 Z= 0.515 Chirality : 0.059 1.170 1074 Planarity : 0.011 0.182 1145 Dihedral : 13.250 84.365 2375 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 2.71 % Allowed : 8.83 % Favored : 88.46 % Rotamer: Outliers : 2.60 % Allowed : 8.88 % Favored : 88.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.25), residues: 849 helix: -1.30 (0.24), residues: 359 sheet: -1.75 (0.34), residues: 190 loop : -3.55 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 59 TYR 0.043 0.002 TYR C 160 PHE 0.026 0.002 PHE D 171 TRP 0.022 0.002 TRP D 179 HIS 0.019 0.003 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 191 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue TYR 206 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 346 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8957 (t0) cc_final: 0.8733 (t0) REVERT: A 106 CYS cc_start: 0.8603 (t) cc_final: 0.8362 (t) REVERT: A 112 MET cc_start: 0.8170 (mmm) cc_final: 0.7926 (tmm) REVERT: A 159 ILE cc_start: 0.8538 (mm) cc_final: 0.8177 (mm) REVERT: A 170 LEU cc_start: 0.8143 (tt) cc_final: 0.7668 (tp) REVERT: A 190 MET cc_start: 0.7725 (ttt) cc_final: 0.7491 (ttt) REVERT: A 297 ASP cc_start: 0.9196 (m-30) cc_final: 0.8734 (m-30) REVERT: A 366 LYS cc_start: 0.8480 (tttt) cc_final: 0.7964 (tptt) REVERT: A 474 ASP cc_start: 0.8835 (t0) cc_final: 0.8512 (t0) REVERT: A 478 THR cc_start: 0.8902 (m) cc_final: 0.8530 (m) outliers start: 19 outliers final: 7 residues processed: 354 average time/residue: 0.3085 time to fit residues: 145.1268 Evaluate side-chains 254 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 247 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 547 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 GLN C 57 GLN C 186 GLN D 76 ASN D 216 GLN ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 125 HIS A 185 ASN A 194 GLN A 494 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.960 6766 Z= 1.180 Angle : 0.845 24.469 9214 Z= 0.464 Chirality : 0.064 1.548 1074 Planarity : 0.010 0.178 1145 Dihedral : 6.635 74.189 934 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.94 % Allowed : 8.48 % Favored : 90.58 % Rotamer: Outliers : 3.96 % Allowed : 22.13 % Favored : 73.91 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.27), residues: 849 helix: -0.47 (0.25), residues: 371 sheet: -1.10 (0.35), residues: 187 loop : -3.33 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.040 0.002 TYR C 160 PHE 0.012 0.002 PHE D 126 TRP 0.014 0.002 TRP C 168 HIS 0.011 0.003 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 191 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue TYR 206 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 267 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8960 (t0) cc_final: 0.8671 (t0) REVERT: A 109 ILE cc_start: 0.8540 (mm) cc_final: 0.8275 (mm) REVERT: A 112 MET cc_start: 0.8199 (mmm) cc_final: 0.7903 (tmm) REVERT: A 187 LEU cc_start: 0.8401 (mm) cc_final: 0.7928 (tp) REVERT: A 312 MET cc_start: 0.8311 (mmm) cc_final: 0.8042 (mmm) REVERT: A 366 LYS cc_start: 0.8425 (tttt) cc_final: 0.7979 (tptt) REVERT: A 474 ASP cc_start: 0.8869 (t0) cc_final: 0.8550 (t0) REVERT: A 478 THR cc_start: 0.8740 (m) cc_final: 0.8524 (m) REVERT: A 538 MET cc_start: 0.8839 (ttp) cc_final: 0.8513 (tmm) outliers start: 29 outliers final: 20 residues processed: 281 average time/residue: 0.2450 time to fit residues: 92.2117 Evaluate side-chains 245 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 529 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.968 6766 Z= 1.182 Angle : 0.810 24.048 9214 Z= 0.456 Chirality : 0.064 1.597 1074 Planarity : 0.008 0.164 1145 Dihedral : 6.288 70.820 928 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 1.18 % Allowed : 7.54 % Favored : 91.28 % Rotamer: Outliers : 4.78 % Allowed : 25.68 % Favored : 69.54 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.28), residues: 849 helix: 0.04 (0.26), residues: 371 sheet: -0.79 (0.37), residues: 186 loop : -3.15 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 119 TYR 0.037 0.002 TYR C 160 PHE 0.021 0.001 PHE C 155 TRP 0.014 0.002 TRP D 213 HIS 0.033 0.004 HIS A 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 191 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue TYR 206 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 225 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8949 (t0) cc_final: 0.8672 (t0) REVERT: A 109 ILE cc_start: 0.8538 (mm) cc_final: 0.8338 (mm) REVERT: A 112 MET cc_start: 0.8145 (mmm) cc_final: 0.7862 (tmm) REVERT: A 312 MET cc_start: 0.8295 (mmm) cc_final: 0.7707 (mmm) REVERT: A 366 LYS cc_start: 0.8416 (tttt) cc_final: 0.7967 (tptt) REVERT: A 474 ASP cc_start: 0.8849 (t0) cc_final: 0.8574 (t0) REVERT: A 478 THR cc_start: 0.8833 (m) cc_final: 0.8628 (m) REVERT: A 511 MET cc_start: 0.8572 (mmm) cc_final: 0.7984 (mmm) REVERT: A 538 MET cc_start: 0.8850 (ttp) cc_final: 0.8485 (tmm) outliers start: 35 outliers final: 29 residues processed: 242 average time/residue: 0.1903 time to fit residues: 61.4078 Evaluate side-chains 242 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 547 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 81 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 GLN A 100 ASN A 125 HIS A 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.963 6766 Z= 1.169 Angle : 0.788 23.658 9214 Z= 0.439 Chirality : 0.064 1.597 1074 Planarity : 0.007 0.161 1145 Dihedral : 5.899 67.682 925 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.77 % Favored : 91.40 % Rotamer: Outliers : 5.33 % Allowed : 27.19 % Favored : 67.49 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.29), residues: 849 helix: 0.41 (0.27), residues: 372 sheet: -0.70 (0.37), residues: 197 loop : -2.87 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.032 0.002 TYR C 160 PHE 0.018 0.001 PHE C 155 TRP 0.017 0.001 TRP D 213 HIS 0.009 0.002 HIS A 536 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 191 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue TYR 206 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 231 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8956 (t0) cc_final: 0.8667 (t0) REVERT: A 109 ILE cc_start: 0.8544 (mm) cc_final: 0.8319 (mm) REVERT: A 112 MET cc_start: 0.8227 (mmm) cc_final: 0.7961 (tmm) REVERT: A 187 LEU cc_start: 0.8413 (mm) cc_final: 0.7934 (tp) REVERT: A 312 MET cc_start: 0.8265 (mmm) cc_final: 0.7696 (mmm) REVERT: A 366 LYS cc_start: 0.8436 (tttt) cc_final: 0.7913 (tptt) REVERT: A 474 ASP cc_start: 0.8836 (t0) cc_final: 0.8556 (t0) REVERT: A 478 THR cc_start: 0.8832 (m) cc_final: 0.8626 (m) REVERT: A 511 MET cc_start: 0.8624 (mmm) cc_final: 0.8060 (mmm) REVERT: A 538 MET cc_start: 0.8826 (ttp) cc_final: 0.8458 (tmm) outliers start: 39 outliers final: 34 residues processed: 245 average time/residue: 0.1785 time to fit residues: 58.5582 Evaluate side-chains 252 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 547 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN A 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.953 6766 Z= 1.184 Angle : 0.789 24.451 9214 Z= 0.445 Chirality : 0.064 1.593 1074 Planarity : 0.008 0.160 1145 Dihedral : 5.853 62.930 925 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.48 % Favored : 90.93 % Rotamer: Outliers : 4.78 % Allowed : 29.37 % Favored : 65.85 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.29), residues: 849 helix: 0.34 (0.27), residues: 373 sheet: -0.58 (0.37), residues: 195 loop : -2.93 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 175 TYR 0.028 0.002 TYR C 160 PHE 0.016 0.001 PHE C 159 TRP 0.017 0.002 TRP D 213 HIS 0.009 0.002 HIS A 536 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 191 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue TYR 206 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8973 (t0) cc_final: 0.8671 (t0) REVERT: A 109 ILE cc_start: 0.8543 (mm) cc_final: 0.8322 (mm) REVERT: A 112 MET cc_start: 0.8265 (mmm) cc_final: 0.8019 (tmm) REVERT: A 312 MET cc_start: 0.8280 (mmm) cc_final: 0.7725 (mmm) REVERT: A 366 LYS cc_start: 0.8422 (tttt) cc_final: 0.7919 (tptt) REVERT: A 474 ASP cc_start: 0.8843 (t0) cc_final: 0.8573 (t0) REVERT: A 478 THR cc_start: 0.8847 (m) cc_final: 0.8640 (m) REVERT: A 511 MET cc_start: 0.8697 (mmm) cc_final: 0.8231 (mmm) REVERT: A 538 MET cc_start: 0.8734 (ttp) cc_final: 0.8472 (tmm) outliers start: 35 outliers final: 29 residues processed: 225 average time/residue: 0.1747 time to fit residues: 52.6600 Evaluate side-chains 233 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 547 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.959 6766 Z= 1.174 Angle : 0.788 24.011 9214 Z= 0.441 Chirality : 0.064 1.600 1074 Planarity : 0.008 0.158 1145 Dihedral : 5.772 56.611 925 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.13 % Favored : 91.28 % Rotamer: Outliers : 4.37 % Allowed : 29.78 % Favored : 65.85 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.29), residues: 849 helix: 0.55 (0.27), residues: 373 sheet: -0.56 (0.36), residues: 195 loop : -2.79 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 467 TYR 0.029 0.002 TYR C 160 PHE 0.028 0.002 PHE A 460 TRP 0.026 0.002 TRP A 158 HIS 0.009 0.001 HIS A 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 941.12 seconds wall clock time: 16 minutes 45.66 seconds (1005.66 seconds total)