Starting phenix.real_space_refine on Sat Dec 9 11:52:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/12_2023/7xy9_33514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/12_2023/7xy9_33514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/12_2023/7xy9_33514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/12_2023/7xy9_33514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/12_2023/7xy9_33514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/12_2023/7xy9_33514.pdb" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.110 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 Mg 8 5.21 5 S 72 5.16 5 C 6640 2.51 5 N 1808 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D ASP 247": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10962 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "D" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 146 Classifications: {'water': 146} Link IDs: {None: 145} Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Classifications: {'water': 150} Link IDs: {None: 149} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 286 SG CYS A 37 70.821 60.293 24.390 1.00 40.90 S ATOM 2132 SG CYS A 295 64.935 51.850 36.905 1.00 39.55 S ATOM 4726 SG CYS B 295 43.904 51.877 46.832 1.00 35.49 S ATOM 2880 SG CYS B 37 38.029 60.293 59.329 1.00 38.05 S ATOM 7320 SG CYS C 295 65.020 30.263 46.889 1.00 36.74 S ATOM 5474 SG CYS C 37 70.759 21.742 59.360 1.00 40.13 S ATOM 9914 SG CYS D 295 43.871 30.247 36.849 1.00 37.58 S ATOM 8068 SG CYS D 37 38.064 21.769 24.366 1.00 40.89 S Time building chain proxies: 5.89, per 1000 atoms: 0.54 Number of scatterers: 10962 At special positions: 0 Unit cell: (109.699, 82.9026, 84.5774, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 72 16.00 Mg 8 11.99 O 2430 8.00 N 1808 7.00 C 6640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.59 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 59 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 37 " pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS B 59 " pdb="ZN ZN B 503 " - pdb=" SG CYS B 37 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 37 " pdb=" ZN D 503 " pdb="ZN ZN D 503 " - pdb=" NE2 HIS D 59 " pdb="ZN ZN D 503 " - pdb=" SG CYS D 37 " 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 14 sheets defined 35.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.601A pdb=" N ILE A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.708A pdb=" N GLY A 221 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.924A pdb=" N MET A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.925A pdb=" N LYS A 318 " --> pdb=" O ASP A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'B' and resid 37 through 47 removed outlier: 3.588A pdb=" N ILE B 41 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.726A pdb=" N GLY B 221 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.584A pdb=" N MET B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 315 through 318 removed outlier: 3.931A pdb=" N LYS B 318 " --> pdb=" O ASP B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 315 through 318' Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'C' and resid 37 through 47 removed outlier: 3.629A pdb=" N ILE C 41 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 176 through 189 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 217 through 221 removed outlier: 3.702A pdb=" N GLY C 221 " --> pdb=" O TYR C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 245 through 255 removed outlier: 3.912A pdb=" N MET C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 315 through 318 removed outlier: 3.942A pdb=" N LYS C 318 " --> pdb=" O ASP C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 315 through 318' Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.592A pdb=" N ILE D 41 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 150 through 162 Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 200 through 211 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 245 through 255 removed outlier: 3.921A pdb=" N MET D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 315 through 318 removed outlier: 3.960A pdb=" N LYS D 318 " --> pdb=" O ASP D 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 315 through 318' Processing helix chain 'D' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 removed outlier: 6.544A pdb=" N LYS A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.598A pdb=" N ILE A 28 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 62 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA A 61 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 83 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 126 removed outlier: 4.355A pdb=" N VAL A 320 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 348 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS A 322 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 350 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE A 324 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 216 removed outlier: 8.908A pdb=" N ASP A 237 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 261 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N ASP B 237 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 261 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 17 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 126 removed outlier: 6.596A pdb=" N ILE B 28 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 62 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA B 61 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 83 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126 removed outlier: 4.344A pdb=" N VAL B 320 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 348 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS B 322 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 350 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE B 324 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 17 removed outlier: 6.574A pdb=" N LYS C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 126 removed outlier: 6.596A pdb=" N ILE C 28 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 62 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA C 61 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 124 through 126 removed outlier: 4.378A pdb=" N VAL C 320 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL C 348 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS C 322 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE C 350 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE C 324 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 214 through 216 removed outlier: 8.902A pdb=" N ASP C 237 " --> pdb=" O GLY C 259 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 261 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N ASP D 237 " --> pdb=" O GLY D 259 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR D 261 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 17 removed outlier: 6.566A pdb=" N LYS D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 124 through 126 removed outlier: 6.520A pdb=" N ILE D 28 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 62 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA D 61 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 124 through 126 removed outlier: 4.336A pdb=" N VAL D 320 " --> pdb=" O LYS D 346 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 348 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N HIS D 322 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE D 350 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE D 324 " --> pdb=" O ILE D 350 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1203 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: 3.56 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3426 1.34 - 1.46: 2195 1.46 - 1.58: 4859 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 10608 Sorted by residual: bond pdb=" C CYS D 295 " pdb=" N PRO D 296 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.01e-02 9.80e+03 1.32e+00 bond pdb=" C CYS C 295 " pdb=" N PRO C 296 " ideal model delta sigma weight residual 1.333 1.345 -0.011 1.01e-02 9.80e+03 1.19e+00 bond pdb=" N CYS D 295 " pdb=" CA CYS D 295 " ideal model delta sigma weight residual 1.463 1.457 0.007 6.90e-03 2.10e+04 9.23e-01 bond pdb=" C LEU D 294 " pdb=" N CYS D 295 " ideal model delta sigma weight residual 1.341 1.327 0.013 1.65e-02 3.67e+03 6.53e-01 bond pdb=" CA TYR D 218 " pdb=" CB TYR D 218 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 ... (remaining 10603 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 423 107.08 - 113.80: 5923 113.80 - 120.53: 3877 120.53 - 127.25: 3986 127.25 - 133.98: 135 Bond angle restraints: 14344 Sorted by residual: angle pdb=" CG1 ILE A 175 " pdb=" CB ILE A 175 " pdb=" CG2 ILE A 175 " ideal model delta sigma weight residual 110.70 100.70 10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N LEU B 294 " pdb=" CA LEU B 294 " pdb=" C LEU B 294 " ideal model delta sigma weight residual 110.65 106.59 4.06 1.26e+00 6.30e-01 1.04e+01 angle pdb=" C MET B 147 " pdb=" N ILE B 148 " pdb=" CA ILE B 148 " ideal model delta sigma weight residual 120.33 122.90 -2.57 8.00e-01 1.56e+00 1.03e+01 angle pdb=" N LEU A 294 " pdb=" CA LEU A 294 " pdb=" C LEU A 294 " ideal model delta sigma weight residual 110.65 106.62 4.03 1.26e+00 6.30e-01 1.03e+01 angle pdb=" N PRO C 296 " pdb=" CA PRO C 296 " pdb=" C PRO C 296 " ideal model delta sigma weight residual 110.50 115.01 -4.51 1.57e+00 4.06e-01 8.25e+00 ... (remaining 14339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 5471 17.42 - 34.84: 580 34.84 - 52.26: 168 52.26 - 69.68: 65 69.68 - 87.10: 24 Dihedral angle restraints: 6308 sinusoidal: 2492 harmonic: 3816 Sorted by residual: dihedral pdb=" CA CYS A 295 " pdb=" C CYS A 295 " pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA CYS B 295 " pdb=" C CYS B 295 " pdb=" N PRO B 296 " pdb=" CA PRO B 296 " ideal model delta harmonic sigma weight residual -180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA CYS D 295 " pdb=" C CYS D 295 " pdb=" N PRO D 296 " pdb=" CA PRO D 296 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 6305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1231 0.049 - 0.097: 258 0.097 - 0.146: 102 0.146 - 0.194: 0 0.194 - 0.243: 1 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CB ILE A 175 " pdb=" CA ILE A 175 " pdb=" CG1 ILE A 175 " pdb=" CG2 ILE A 175 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA VAL B 62 " pdb=" N VAL B 62 " pdb=" C VAL B 62 " pdb=" CB VAL B 62 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL A 62 " pdb=" N VAL A 62 " pdb=" C VAL A 62 " pdb=" CB VAL A 62 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1589 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 200 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO A 201 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 200 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 201 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 200 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO B 201 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " 0.029 5.00e-02 4.00e+02 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 145 2.57 - 3.15: 8664 3.15 - 3.74: 18347 3.74 - 4.32: 27448 4.32 - 4.90: 42748 Nonbonded interactions: 97352 Sorted by model distance: nonbonded pdb=" OD2 ASP C 150 " pdb="ZN ZN C 503 " model vdw 1.988 2.230 nonbonded pdb=" OD2 ASP D 150 " pdb="ZN ZN D 503 " model vdw 1.996 2.230 nonbonded pdb=" NE2 HIS A 157 " pdb="MG MG A 403 " model vdw 2.038 2.250 nonbonded pdb=" NE2 HIS B 157 " pdb="MG MG B 502 " model vdw 2.039 2.250 nonbonded pdb=" NE2 HIS C 157 " pdb="MG MG C 502 " model vdw 2.040 2.250 ... (remaining 97347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 351 or resid 402)) selection = (chain 'B' and (resid 0 through 351 or resid 502)) selection = (chain 'C' and (resid 0 through 351 or resid 502)) selection = (chain 'D' and (resid 0 through 351 or resid 502)) } 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: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.860 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: 0.010 Extract box with map and model: 6.490 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 34.390 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 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 : 0.002 0.022 10608 Z= 0.152 Angle : 0.544 10.000 14344 Z= 0.292 Chirality : 0.046 0.243 1592 Planarity : 0.004 0.056 1856 Dihedral : 17.431 87.100 3884 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.67 % Allowed : 19.80 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.23), residues: 1360 helix: 1.10 (0.25), residues: 452 sheet: 0.81 (0.31), residues: 304 loop : -0.56 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.004 0.001 HIS D 157 PHE 0.008 0.001 PHE C 124 TYR 0.008 0.001 TYR D 311 ARG 0.001 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.221 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 140 average time/residue: 1.5977 time to fit residues: 238.4338 Evaluate side-chains 140 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 1.6591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.8724 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10608 Z= 0.460 Angle : 0.774 9.316 14344 Z= 0.421 Chirality : 0.056 0.169 1592 Planarity : 0.006 0.065 1856 Dihedral : 5.782 32.221 1448 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.72 % Allowed : 16.45 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.24 (0.22), residues: 1360 helix: 0.47 (0.23), residues: 452 sheet: 0.22 (0.27), residues: 332 loop : -0.81 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 110 HIS 0.006 0.002 HIS A 102 PHE 0.016 0.002 PHE D 124 TYR 0.014 0.003 TYR B 311 ARG 0.006 0.001 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 1.290 Fit side-chains outliers start: 40 outliers final: 24 residues processed: 165 average time/residue: 1.4541 time to fit residues: 256.5082 Evaluate side-chains 158 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 1.0169 time to fit residues: 9.3008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 54 ASN D 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10608 Z= 0.338 Angle : 0.689 9.030 14344 Z= 0.374 Chirality : 0.052 0.180 1592 Planarity : 0.006 0.065 1856 Dihedral : 5.705 30.852 1448 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.72 % Allowed : 16.08 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -0.37 (0.21), residues: 1360 helix: 0.45 (0.23), residues: 452 sheet: 0.19 (0.28), residues: 308 loop : -0.95 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 90 HIS 0.006 0.002 HIS A 157 PHE 0.014 0.002 PHE A 124 TYR 0.013 0.003 TYR A 311 ARG 0.005 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 1.166 Fit side-chains outliers start: 40 outliers final: 23 residues processed: 163 average time/residue: 1.5558 time to fit residues: 270.6032 Evaluate side-chains 160 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.7312 time to fit residues: 5.4244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 54 ASN D 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10608 Z= 0.152 Angle : 0.542 8.927 14344 Z= 0.290 Chirality : 0.046 0.226 1592 Planarity : 0.004 0.059 1856 Dihedral : 5.155 29.241 1448 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.88 % Allowed : 16.64 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.22), residues: 1360 helix: 0.99 (0.24), residues: 452 sheet: 0.49 (0.29), residues: 304 loop : -0.87 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.006 0.001 HIS D 157 PHE 0.010 0.001 PHE D 124 TYR 0.010 0.001 TYR D 311 ARG 0.001 0.000 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.437 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 158 average time/residue: 1.4163 time to fit residues: 239.9500 Evaluate side-chains 148 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.7080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 0.0670 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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: 0.8654 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10608 Z= 0.159 Angle : 0.544 9.213 14344 Z= 0.290 Chirality : 0.047 0.229 1592 Planarity : 0.004 0.057 1856 Dihedral : 5.056 29.689 1448 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.07 % Allowed : 17.38 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.22), residues: 1360 helix: 1.10 (0.24), residues: 452 sheet: 0.57 (0.29), residues: 304 loop : -0.81 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.004 0.001 HIS D 157 PHE 0.011 0.001 PHE A 124 TYR 0.010 0.001 TYR D 311 ARG 0.001 0.000 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.602 Fit side-chains outliers start: 33 outliers final: 20 residues processed: 160 average time/residue: 1.5157 time to fit residues: 259.5524 Evaluate side-chains 150 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.7960 time to fit residues: 3.4624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN C 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10608 Z= 0.344 Angle : 0.679 9.634 14344 Z= 0.368 Chirality : 0.052 0.187 1592 Planarity : 0.005 0.062 1856 Dihedral : 5.595 33.556 1448 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.25 % Allowed : 17.10 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.21 (0.22), residues: 1360 helix: 0.66 (0.24), residues: 452 sheet: 0.19 (0.28), residues: 308 loop : -0.87 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS A 102 PHE 0.015 0.002 PHE B 124 TYR 0.013 0.003 TYR B 311 ARG 0.005 0.001 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.355 Fit side-chains outliers start: 35 outliers final: 24 residues processed: 158 average time/residue: 1.5328 time to fit residues: 258.6831 Evaluate side-chains 160 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 1.2201 time to fit residues: 9.5963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 54 ASN D 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10608 Z= 0.148 Angle : 0.547 9.899 14344 Z= 0.289 Chirality : 0.046 0.240 1592 Planarity : 0.004 0.059 1856 Dihedral : 5.099 29.449 1448 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.42 % Allowed : 18.22 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.22), residues: 1360 helix: 0.96 (0.24), residues: 452 sheet: 0.53 (0.29), residues: 304 loop : -0.86 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS D 157 PHE 0.010 0.001 PHE A 124 TYR 0.009 0.001 TYR D 311 ARG 0.001 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.284 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 149 average time/residue: 1.4990 time to fit residues: 239.0604 Evaluate side-chains 145 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.7479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 54 ASN C 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10608 Z= 0.392 Angle : 0.717 9.570 14344 Z= 0.388 Chirality : 0.054 0.197 1592 Planarity : 0.006 0.062 1856 Dihedral : 5.709 37.647 1448 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.15 % Rotamer: Outliers : 2.97 % Allowed : 17.75 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.31 (0.21), residues: 1360 helix: 0.53 (0.23), residues: 452 sheet: 0.14 (0.28), residues: 308 loop : -0.89 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 90 HIS 0.005 0.002 HIS A 102 PHE 0.015 0.002 PHE C 124 TYR 0.014 0.003 TYR B 311 ARG 0.005 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.319 Fit side-chains outliers start: 32 outliers final: 24 residues processed: 157 average time/residue: 1.5141 time to fit residues: 254.2175 Evaluate side-chains 158 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 1.0502 time to fit residues: 9.6854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 54 ASN C 54 ASN D 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10608 Z= 0.234 Angle : 0.619 9.959 14344 Z= 0.331 Chirality : 0.049 0.213 1592 Planarity : 0.005 0.061 1856 Dihedral : 5.461 32.916 1448 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.51 % Allowed : 18.31 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -0.20 (0.22), residues: 1360 helix: 0.68 (0.24), residues: 452 sheet: 0.20 (0.28), residues: 308 loop : -0.88 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS C 102 PHE 0.013 0.001 PHE D 124 TYR 0.011 0.002 TYR D 311 ARG 0.003 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.230 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 149 average time/residue: 1.4163 time to fit residues: 225.3269 Evaluate side-chains 151 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 5 average time/residue: 0.9467 time to fit residues: 6.3372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN C 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10608 Z= 0.162 Angle : 0.565 10.306 14344 Z= 0.298 Chirality : 0.047 0.239 1592 Planarity : 0.005 0.061 1856 Dihedral : 5.147 30.183 1448 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.86 % Allowed : 18.87 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % 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: 0.06 (0.22), residues: 1360 helix: 0.93 (0.24), residues: 452 sheet: 0.49 (0.29), residues: 304 loop : -0.85 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS D 157 PHE 0.011 0.001 PHE A 124 TYR 0.010 0.001 TYR D 311 ARG 0.002 0.000 ARG C 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.314 Fit side-chains outliers start: 20 outliers final: 17 residues processed: 150 average time/residue: 1.5026 time to fit residues: 240.8682 Evaluate side-chains 146 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.7308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 108 optimal weight: 0.0570 chunk 45 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 54 ASN C 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108024 restraints weight = 8766.428| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.32 r_work: 0.3131 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10608 Z= 0.261 Angle : 0.642 9.873 14344 Z= 0.341 Chirality : 0.049 0.203 1592 Planarity : 0.005 0.062 1856 Dihedral : 5.439 33.443 1448 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.04 % Allowed : 18.40 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.10 (0.22), residues: 1360 helix: 0.78 (0.24), residues: 452 sheet: 0.28 (0.28), residues: 308 loop : -0.85 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS C 102 PHE 0.013 0.001 PHE B 124 TYR 0.012 0.002 TYR B 311 ARG 0.004 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4489.07 seconds wall clock time: 82 minutes 23.54 seconds (4943.54 seconds total)