Starting phenix.real_space_refine on Sun May 19 16:32:00 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.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=3.0 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.pdb" } resolution = 3.0 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= 0.069 sd= 0.195 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 42 5.16 5 C 4311 2.51 5 N 1096 2.21 5 O 1269 1.98 5 H 6701 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 138": "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 ASP 190": "OD1" <-> "OD2" 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" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 13419 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6914 Inner-chain residues flagged as termini: ['pdbres="GLY A 238 "', 'pdbres="CYS A 284 "', 'pdbres="PRO A 397 "', 'pdbres="PRO A 451 "'] Classifications: {'peptide': 445} Modifications used: {'COO': 3, 'NH2': 1, 'NH3': 2} Link IDs: {'PTRANS': 11, 'TRANS': 433} Chain breaks: 2 Chain: "C" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3220 Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "D" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3285 Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 204} Time building chain proxies: 4.19, per 1000 atoms: 0.31 Number of scatterers: 13419 At special positions: 0 Unit cell: (73.44, 76.68, 147.96, 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 42 16.00 O 1269 8.00 N 1096 7.00 C 4311 6.00 H 6701 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 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 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: 5.85 Conformation dependent library (CDL) restraints added in 799.2 milliseconds Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 45.2% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 24 through 53 Processing helix chain 'A' and resid 58 through 84 removed outlier: 5.330A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 127 through 155 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 167 through 198 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 201 through 229 Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.693A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 285 through 304 removed outlier: 4.662A pdb=" N GLU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.639A pdb=" N TYR A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 369 through 391 Processing helix chain 'A' and resid 452 through 482 Processing helix chain 'A' and resid 489 through 513 Processing helix chain 'A' and resid 517 through 546 removed outlier: 4.412A pdb=" N GLY A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 203 through 207 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 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing sheet with id= A, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.546A pdb=" N LYS C 123 " --> pdb=" O MET C 31 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR C 33 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 6.117A 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: 3.698A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 105 through 110 removed outlier: 3.590A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 135 through 138 removed outlier: 3.567A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 165 through 170 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: 3.583A pdb=" N GLY D 68 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LYS D 57 " --> pdb=" O TRP D 66 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP D 66 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ARG D 59 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.482A 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 149 removed outlier: 3.636A pdb=" N LEU D 166 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR D 200 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 175 through 179 removed outlier: 4.928A pdb=" N ILE D 218 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 194 through 196 403 hydrogen bonds defined for protein. 1077 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: 5.02 Time building geometry restraints manager: 6.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 6692 1.14 - 1.31: 1079 1.31 - 1.48: 2839 1.48 - 1.65: 2896 1.65 - 1.82: 65 Bond restraints: 13571 Sorted by residual: bond pdb=" N ALA C 150 " pdb=" H ALA C 150 " ideal model delta sigma weight residual 0.860 1.034 -0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" N THR D 209 " pdb=" H THR D 209 " ideal model delta sigma weight residual 0.860 1.028 -0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N GLY C 149 " pdb=" H GLY C 149 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N SER C 72 " pdb=" H SER C 72 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N VAL D 161 " pdb=" H VAL D 161 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.75e+01 ... (remaining 13566 not shown) Histogram of bond angle deviations from ideal: 95.82 - 103.54: 76 103.54 - 111.25: 15074 111.25 - 118.97: 3530 118.97 - 126.68: 5708 126.68 - 134.40: 120 Bond angle restraints: 24508 Sorted by residual: angle pdb=" N GLY D 169 " pdb=" CA GLY D 169 " pdb=" C GLY D 169 " ideal model delta sigma weight residual 113.76 105.99 7.77 1.80e+00 3.09e-01 1.86e+01 angle pdb=" N THR D 209 " pdb=" CA THR D 209 " pdb=" C THR D 209 " ideal model delta sigma weight residual 111.07 114.52 -3.45 1.07e+00 8.73e-01 1.04e+01 angle pdb=" CB THR D 142 " pdb=" CG2 THR D 142 " pdb="HG22 THR D 142 " ideal model delta sigma weight residual 110.00 101.72 8.28 3.00e+00 1.11e-01 7.61e+00 angle pdb=" N PRO D 172 " pdb=" CA PRO D 172 " pdb=" C PRO D 172 " ideal model delta sigma weight residual 112.47 117.64 -5.17 2.06e+00 2.36e-01 6.29e+00 angle pdb=" CA TYR D 170 " pdb=" CB TYR D 170 " pdb=" CG TYR D 170 " ideal model delta sigma weight residual 113.90 118.38 -4.48 1.80e+00 3.09e-01 6.18e+00 ... (remaining 24503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4081 17.39 - 34.78: 489 34.78 - 52.17: 196 52.17 - 69.56: 59 69.56 - 86.95: 5 Dihedral angle restraints: 4830 sinusoidal: 3443 harmonic: 1387 Sorted by residual: dihedral pdb=" CA GLY D 169 " pdb=" C GLY D 169 " pdb=" N TYR D 170 " pdb=" CA TYR D 170 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER C 194 " pdb=" C SER C 194 " pdb=" N MET C 195 " pdb=" CA MET C 195 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER C 228 " pdb=" C SER C 228 " pdb=" N PHE C 229 " pdb=" CA PHE C 229 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 756 0.036 - 0.071: 236 0.071 - 0.107: 69 0.107 - 0.143: 26 0.143 - 0.179: 3 Chirality restraints: 1090 Sorted by residual: chirality pdb=" CA ILE C 164 " pdb=" N ILE C 164 " pdb=" C ILE C 164 " pdb=" CB ILE C 164 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA PRO D 172 " pdb=" N PRO D 172 " pdb=" C PRO D 172 " pdb=" CB PRO D 172 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CB ILE D 235 " pdb=" CA ILE D 235 " pdb=" CG1 ILE D 235 " pdb=" CG2 ILE D 235 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1087 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 143 " -0.042 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO D 144 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 516 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO A 517 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 213 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 214 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 214 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 214 " -0.029 5.00e-02 4.00e+02 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 230 1.95 - 2.61: 14140 2.61 - 3.28: 40360 3.28 - 3.94: 52198 3.94 - 4.60: 77635 Nonbonded interactions: 184563 Sorted by model distance: nonbonded pdb=" O SER C 141 " pdb=" H LEU C 145 " model vdw 1.288 1.850 nonbonded pdb=" HG1 THR C 184 " pdb=" O SER C 194 " model vdw 1.375 1.850 nonbonded pdb=" OG SER C 141 " pdb=" H GLN C 144 " model vdw 1.457 1.850 nonbonded pdb=" O GLY A 368 " pdb=" HG1 THR A 372 " model vdw 1.520 1.850 nonbonded pdb=" O ILE A 354 " pdb=" HG1 THR A 357 " model vdw 1.556 1.850 ... (remaining 184558 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=0.47 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: 0.020 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: 0.150 Extract box with map and model: 0.650 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 26.230 Find NCS groups from input model: 0.160 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:18.030 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.003 0.053 6870 Z= 0.214 Angle : 0.586 7.768 9354 Z= 0.316 Chirality : 0.041 0.179 1090 Planarity : 0.006 0.065 1166 Dihedral : 14.872 86.950 2413 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Rotamer: Outliers : 2.15 % Allowed : 19.92 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.69 (0.29), residues: 867 helix: 1.66 (0.25), residues: 394 sheet: 0.46 (0.38), residues: 207 loop : -1.38 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 74 TYR 0.014 0.001 TYR D 170 PHE 0.019 0.002 PHE D 191 TRP 0.015 0.001 TRP D 213 HIS 0.007 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6870 Z= 0.278 Angle : 0.511 6.213 9354 Z= 0.277 Chirality : 0.050 0.189 1090 Planarity : 0.004 0.060 1166 Dihedral : 13.154 83.410 2413 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.34 % Favored : 93.19 % Rotamer: Outliers : 1.48 % Allowed : 11.31 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.69 (0.27), residues: 867 helix: 0.47 (0.24), residues: 390 sheet: -0.01 (0.36), residues: 208 loop : -2.14 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 365 TYR 0.010 0.001 TYR D 113 PHE 0.009 0.001 PHE A 324 TRP 0.012 0.001 TRP C 183 HIS 0.007 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 20.0000 chunk 64 optimal weight: 50.0000 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6870 Z= 0.357 Angle : 0.531 6.495 9354 Z= 0.293 Chirality : 0.051 0.181 1090 Planarity : 0.004 0.042 1166 Dihedral : 12.335 85.078 2413 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 1.38 % Allowed : 9.23 % Favored : 89.39 % Rotamer: Outliers : 2.02 % Allowed : 10.09 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.02 (0.25), residues: 867 helix: -0.39 (0.23), residues: 387 sheet: -0.71 (0.36), residues: 208 loop : -3.13 (0.29), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 117 TYR 0.012 0.001 TYR C 193 PHE 0.009 0.001 PHE C 107 TRP 0.008 0.001 TRP D 69 HIS 0.004 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6870 Z= 0.308 Angle : 0.486 6.193 9354 Z= 0.268 Chirality : 0.050 0.175 1090 Planarity : 0.004 0.054 1166 Dihedral : 11.729 81.705 2413 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 1.50 % Allowed : 9.00 % Favored : 89.50 % Rotamer: Outliers : 1.75 % Allowed : 8.61 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.11 (0.25), residues: 867 helix: -0.09 (0.23), residues: 389 sheet: -1.10 (0.33), residues: 206 loop : -3.51 (0.29), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.010 0.001 TYR A 64 PHE 0.009 0.001 PHE A 324 TRP 0.007 0.001 TRP D 69 HIS 0.003 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 56 optimal weight: 60.0000 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6870 Z= 0.352 Angle : 0.501 6.580 9354 Z= 0.277 Chirality : 0.050 0.172 1090 Planarity : 0.004 0.046 1166 Dihedral : 11.540 85.340 2413 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 1.96 % Allowed : 9.80 % Favored : 88.24 % Rotamer: Outliers : 2.02 % Allowed : 8.21 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.56 (0.25), residues: 867 helix: -0.43 (0.22), residues: 387 sheet: -1.43 (0.33), residues: 209 loop : -3.69 (0.29), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 117 TYR 0.011 0.001 TYR A 64 PHE 0.007 0.001 PHE A 324 TRP 0.008 0.001 TRP D 69 HIS 0.003 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 chunk 63 optimal weight: 60.0000 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6870 Z= 0.313 Angle : 0.484 6.245 9354 Z= 0.268 Chirality : 0.050 0.166 1090 Planarity : 0.004 0.057 1166 Dihedral : 11.303 81.424 2413 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 2.08 % Allowed : 8.88 % Favored : 89.04 % Rotamer: Outliers : 2.15 % Allowed : 7.94 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.53 (0.25), residues: 867 helix: -0.23 (0.23), residues: 387 sheet: -1.65 (0.31), residues: 213 loop : -3.77 (0.29), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.011 0.001 TYR A 64 PHE 0.007 0.001 PHE A 541 TRP 0.007 0.001 TRP D 69 HIS 0.004 0.001 HIS D 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 297.33 seconds wall clock time: 5 minutes 52.63 seconds (352.63 seconds total)