Starting phenix.real_space_refine on Sun May 19 16:32:01 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 c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.4 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } resolution = 3.4 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { c_beta_restraints = False ramachandran_plot_restraints { enabled = False } } 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: 3.71, per 1000 atoms: 0.28 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: 5.56 Conformation dependent library (CDL) restraints added in 871.5 milliseconds 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: 0.64 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: 4.52 Time building geometry restraints manager: 5.91 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: 4118 16.87 - 33.75: 384 33.75 - 50.62: 167 50.62 - 67.49: 70 67.49 - 84.37: 10 Dihedral angle restraints: 4749 sinusoidal: 3376 harmonic: 1373 Sorted by residual: 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 dihedral pdb=" CA PHE D 171 " pdb=" C PHE D 171 " pdb=" N PRO D 172 " pdb=" CA PRO D 172 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 4746 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: 0.140 Extract box with map and model: 0.690 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 25.210 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:18.530 Internal consistency checks: 0.000 Total: 44.890 ------------------------------------------------------------------------------- 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 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.982 6766 Z= 1.149 Angle : 0.774 25.258 9214 Z= 0.443 Chirality : 0.080 1.453 1074 Planarity : 0.008 0.134 1145 Dihedral : 12.367 84.731 2375 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 3.18 % Allowed : 10.95 % Favored : 85.87 % Rotamer: Outliers : 2.32 % Allowed : 7.51 % Favored : 90.16 % 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: -4.05 (0.24), residues: 849 helix: -2.12 (0.22), residues: 363 sheet: -1.61 (0.34), residues: 200 loop : -4.06 (0.30), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 467 TYR 0.039 0.002 TYR C 160 PHE 0.015 0.001 PHE D 126 TRP 0.008 0.001 TRP A 471 HIS 0.004 0.002 HIS A 536 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 40.0000 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.962 6766 Z= 1.171 Angle : 0.794 24.635 9214 Z= 0.456 Chirality : 0.082 1.570 1074 Planarity : 0.008 0.122 1145 Dihedral : 12.339 78.765 2375 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 5.30 % Allowed : 13.90 % Favored : 80.80 % Rotamer: Outliers : 3.01 % Allowed : 9.15 % Favored : 87.84 % 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: -4.89 (0.23), residues: 849 helix: -2.70 (0.20), residues: 368 sheet: -1.97 (0.35), residues: 206 loop : -4.80 (0.25), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.036 0.002 TYR C 160 PHE 0.015 0.002 PHE D 126 TRP 0.012 0.002 TRP D 213 HIS 0.009 0.002 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 81 optimal weight: 40.0000 chunk 26 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3828 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= 1.172 Angle : 0.726 24.327 9214 Z= 0.421 Chirality : 0.083 1.590 1074 Planarity : 0.006 0.110 1145 Dihedral : 12.095 76.524 2375 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 4.59 % Allowed : 13.31 % Favored : 82.10 % Rotamer: Outliers : 3.01 % Allowed : 8.61 % Favored : 88.39 % 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: -4.86 (0.23), residues: 849 helix: -2.54 (0.20), residues: 364 sheet: -2.30 (0.33), residues: 200 loop : -4.63 (0.27), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.041 0.002 TYR C 160 PHE 0.012 0.001 PHE D 126 TRP 0.009 0.001 TRP D 179 HIS 0.004 0.001 HIS A 536 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 9.5998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.991 6766 Z= 1.153 Angle : 0.730 24.954 9214 Z= 0.426 Chirality : 0.082 1.567 1074 Planarity : 0.006 0.106 1145 Dihedral : 12.286 79.581 2375 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 5.54 % Allowed : 14.13 % Favored : 80.33 % Rotamer: Outliers : 3.69 % Allowed : 9.02 % Favored : 87.30 % 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: -5.06 (0.23), residues: 849 helix: -2.45 (0.21), residues: 368 sheet: -2.76 (0.32), residues: 198 loop : -4.83 (0.25), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.039 0.002 TYR C 160 PHE 0.012 0.002 PHE D 126 TRP 0.011 0.001 TRP D 179 HIS 0.008 0.002 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 overall best weight: 9.5998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.975 6766 Z= 1.159 Angle : 0.708 24.451 9214 Z= 0.412 Chirality : 0.082 1.547 1074 Planarity : 0.006 0.103 1145 Dihedral : 12.274 81.706 2375 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 5.18 % Allowed : 14.96 % Favored : 79.86 % Rotamer: Outliers : 3.69 % Allowed : 9.15 % Favored : 87.16 % 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: -5.06 (0.23), residues: 849 helix: -2.44 (0.21), residues: 364 sheet: -2.94 (0.31), residues: 199 loop : -4.67 (0.28), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.042 0.002 TYR C 160 PHE 0.011 0.001 PHE D 126 TRP 0.010 0.001 TRP D 179 HIS 0.004 0.002 HIS A 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 323.17 seconds wall clock time: 6 minutes 21.09 seconds (381.09 seconds total)