Starting phenix.real_space_refine on Tue Apr 9 10:34:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/04_2024/8otx_17186_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/04_2024/8otx_17186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/04_2024/8otx_17186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/04_2024/8otx_17186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/04_2024/8otx_17186_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/04_2024/8otx_17186_trim_updated.pdb" } resolution = 3.08 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= 0.016 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 P 4 5.49 5 S 74 5.16 5 C 10344 2.51 5 N 2668 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 354": "OE1" <-> "OE2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15966 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7889 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 195 Conformer: "B" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 195 bond proxies already assigned to first conformer: 8013 Chain: "A" Number of atoms: 7889 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 195 Conformer: "B" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 195 bond proxies already assigned to first conformer: 8013 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 16.60, per 1000 atoms: 1.04 Number of scatterers: 15966 At special positions: 0 Unit cell: (150.76, 106.903, 123.349, 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 74 16.00 P 4 15.00 O 2876 8.00 N 2668 7.00 C 10344 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: 7.87 Conformation dependent library (CDL) restraints added in 6.0 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 6 sheets defined 66.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'B' and resid 77 through 94 Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.846A pdb=" N ASN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 removed outlier: 3.588A pdb=" N GLU B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 156 through 188 removed outlier: 3.626A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 224 through 253 Processing helix chain 'B' and resid 261 through 292 removed outlier: 4.549A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix removed outlier: 3.794A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 316 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 343 through 378 removed outlier: 3.704A pdb=" N ARG B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 369 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 370 " --> pdb=" O MET B 366 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL B 378 " --> pdb=" O GLN B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 412 removed outlier: 4.211A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 449 through 480 removed outlier: 5.407A pdb=" N LYS B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 514 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 574 through 600 Processing helix chain 'B' and resid 606 through 620 Processing helix chain 'B' and resid 635 through 638 No H-bonds generated for 'chain 'B' and resid 635 through 638' Processing helix chain 'B' and resid 642 through 653 Processing helix chain 'B' and resid 669 through 676 Processing helix chain 'B' and resid 678 through 703 removed outlier: 3.570A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 724 through 749 Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'B' and resid 762 through 782 removed outlier: 3.791A pdb=" N PHE B 766 " --> pdb=" O HIS B 762 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 767 " --> pdb=" O TRP B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 802 No H-bonds generated for 'chain 'B' and resid 800 through 802' Processing helix chain 'B' and resid 804 through 856 removed outlier: 3.807A pdb=" N LYS B 815 " --> pdb=" O ARG B 812 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 818 " --> pdb=" O LYS B 815 " (cutoff:3.500A) Proline residue: B 819 - end of helix Processing helix chain 'B' and resid 864 through 888 removed outlier: 4.003A pdb=" N ILE B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 918 removed outlier: 4.062A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 942 Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 967 through 975 Processing helix chain 'B' and resid 1044 through 1049 Processing helix chain 'B' and resid 1070 through 1079 Processing helix chain 'B' and resid 1086 through 1106 removed outlier: 3.696A pdb=" N THR B1100 " --> pdb=" O ILE B1096 " (cutoff:3.500A) Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1116 through 1122 Processing helix chain 'A' and resid 77 through 94 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.845A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.588A pdb=" N GLU A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 156 through 188 removed outlier: 3.628A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 224 through 253 Processing helix chain 'A' and resid 261 through 292 removed outlier: 4.550A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix removed outlier: 3.793A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 343 through 378 removed outlier: 3.706A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 412 removed outlier: 4.247A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 433 through 444 Processing helix chain 'A' and resid 449 through 480 removed outlier: 5.406A pdb=" N LYS A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 455 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 574 through 600 Processing helix chain 'A' and resid 606 through 620 Processing helix chain 'A' and resid 635 through 638 No H-bonds generated for 'chain 'A' and resid 635 through 638' Processing helix chain 'A' and resid 642 through 653 Processing helix chain 'A' and resid 669 through 676 Processing helix chain 'A' and resid 678 through 703 removed outlier: 3.518A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 724 through 749 Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 762 through 782 removed outlier: 3.816A pdb=" N PHE A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 767 " --> pdb=" O TRP A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 802 No H-bonds generated for 'chain 'A' and resid 800 through 802' Processing helix chain 'A' and resid 804 through 856 removed outlier: 3.847A pdb=" N LYS A 815 " --> pdb=" O ARG A 812 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 818 " --> pdb=" O LYS A 815 " (cutoff:3.500A) Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 864 through 888 removed outlier: 4.047A pdb=" N ILE A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 918 removed outlier: 4.073A pdb=" N VAL A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 942 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 967 through 975 Processing helix chain 'A' and resid 1044 through 1049 Processing helix chain 'A' and resid 1070 through 1079 Processing helix chain 'A' and resid 1086 through 1106 removed outlier: 3.698A pdb=" N THR A1100 " --> pdb=" O ILE A1096 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1116 through 1122 Processing sheet with id= A, first strand: chain 'B' and resid 979 through 982 removed outlier: 3.659A pdb=" N SER B1003 " --> pdb=" O GLN B1064 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR B1066 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE B1001 " --> pdb=" O TYR B1066 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 1032 through 1036 Processing sheet with id= C, first strand: chain 'B' and resid 1145 through 1149 removed outlier: 6.819A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 979 through 982 removed outlier: 3.652A pdb=" N SER A1003 " --> pdb=" O GLN A1064 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A1066 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A1001 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1033 through 1036 Processing sheet with id= F, first strand: chain 'A' and resid 1145 through 1149 removed outlier: 6.747A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) 1035 hydrogen bonds defined for protein. 2778 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: 5.24 Time building geometry restraints manager: 8.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2812 1.33 - 1.45: 3843 1.45 - 1.57: 9448 1.57 - 1.69: 1 1.69 - 1.81: 140 Bond restraints: 16244 Sorted by residual: bond pdb=" N PRO A1184 " pdb=" CD PRO A1184 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.11e+01 bond pdb=" N PRO A1184 " pdb=" CA PRO A1184 " ideal model delta sigma weight residual 1.470 1.421 0.050 1.23e-02 6.61e+03 1.62e+01 bond pdb=" CB PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 1.492 1.688 -0.196 5.00e-02 4.00e+02 1.54e+01 bond pdb=" CG PRO A1184 " pdb=" CD PRO A1184 " ideal model delta sigma weight residual 1.503 1.371 0.132 3.40e-02 8.65e+02 1.50e+01 bond pdb=" N GLY A 836 " pdb=" CA GLY A 836 " ideal model delta sigma weight residual 1.454 1.444 0.010 1.22e-02 6.72e+03 6.79e-01 ... (remaining 16239 not shown) Histogram of bond angle deviations from ideal: 91.29 - 99.83: 3 99.83 - 108.37: 558 108.37 - 116.92: 10935 116.92 - 125.46: 10340 125.46 - 134.00: 218 Bond angle restraints: 22054 Sorted by residual: angle pdb=" CA PRO A1184 " pdb=" N PRO A1184 " pdb=" CD PRO A1184 " ideal model delta sigma weight residual 112.00 91.29 20.71 1.40e+00 5.10e-01 2.19e+02 angle pdb=" N PRO A1184 " pdb=" CD PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 103.20 93.22 9.98 1.50e+00 4.44e-01 4.42e+01 angle pdb=" CA PRO A1184 " pdb=" CB PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 104.50 95.15 9.35 1.90e+00 2.77e-01 2.42e+01 angle pdb=" N PRO A1184 " pdb=" CA PRO A1184 " pdb=" CB PRO A1184 " ideal model delta sigma weight residual 103.36 100.30 3.06 8.30e-01 1.45e+00 1.36e+01 angle pdb=" N PRO A1184 " pdb=" CA PRO A1184 " pdb=" C PRO A1184 " ideal model delta sigma weight residual 110.55 116.16 -5.61 1.63e+00 3.76e-01 1.19e+01 ... (remaining 22049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.08: 9278 33.08 - 66.17: 438 66.17 - 99.25: 28 99.25 - 132.34: 0 132.34 - 165.42: 2 Dihedral angle restraints: 9746 sinusoidal: 3612 harmonic: 6134 Sorted by residual: dihedral pdb=" C21 3PH A1402 " pdb=" C2 3PH A1402 " pdb=" O21 3PH A1402 " pdb=" C3 3PH A1402 " ideal model delta sinusoidal sigma weight residual 147.58 -17.84 165.42 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C21 3PH B1402 " pdb=" C2 3PH B1402 " pdb=" O21 3PH B1402 " pdb=" C3 3PH B1402 " ideal model delta sinusoidal sigma weight residual 147.58 -17.67 165.25 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA VAL B1171 " pdb=" C VAL B1171 " pdb=" N HIS B1172 " pdb=" CA HIS B1172 " ideal model delta harmonic sigma weight residual 180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2235 0.052 - 0.104: 400 0.104 - 0.156: 22 0.156 - 0.208: 0 0.208 - 0.259: 1 Chirality restraints: 2658 Sorted by residual: chirality pdb=" CA PRO A1184 " pdb=" N PRO A1184 " pdb=" C PRO A1184 " pdb=" CB PRO A1184 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL B 321 " pdb=" N VAL B 321 " pdb=" C VAL B 321 " pdb=" CB VAL B 321 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA VAL A 321 " pdb=" N VAL A 321 " pdb=" C VAL A 321 " pdb=" CB VAL A 321 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 2655 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1183 " -0.115 5.00e-02 4.00e+02 1.54e-01 3.77e+01 pdb=" N PRO A1184 " 0.264 5.00e-02 4.00e+02 pdb=" CA PRO A1184 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A1184 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 642 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 642 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.023 5.00e-02 4.00e+02 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 212 2.63 - 3.19: 16484 3.19 - 3.76: 24710 3.76 - 4.33: 31209 4.33 - 4.90: 52528 Nonbonded interactions: 125143 Sorted by model distance: nonbonded pdb=" OD1 ASP B1139 " pdb=" OG1 THR B1141 " model vdw 2.057 2.440 nonbonded pdb=" N GLU B 924 " pdb=" OE1 GLU B 924 " model vdw 2.083 2.520 nonbonded pdb=" OE1 GLU A 590 " pdb=" OH TYR A 594 " model vdw 2.104 2.440 nonbonded pdb=" OE1 GLU B 590 " pdb=" OH TYR B 594 " model vdw 2.106 2.440 nonbonded pdb=" O PRO A 952 " pdb=" ND2 ASN A 955 " model vdw 2.134 2.520 ... (remaining 125138 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 68 through 131 or resid 133 through 1190 or resid 1401 thr \ ough 1402)) selection = (chain 'B' and (resid 68 through 131 or resid 133 through 1190 or resid 1401 thr \ ough 1402)) } 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=0.36 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 21.800 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 58.420 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.130 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 0.196 16244 Z= 0.188 Angle : 0.444 20.712 22054 Z= 0.258 Chirality : 0.035 0.259 2658 Planarity : 0.004 0.154 2754 Dihedral : 17.926 165.422 5766 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 35.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 34.19 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.35 (0.20), residues: 2094 helix: 2.80 (0.14), residues: 1426 sheet: -0.01 (0.56), residues: 76 loop : -1.50 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 278 HIS 0.007 0.001 HIS B1172 PHE 0.011 0.001 PHE A1134 TYR 0.008 0.001 TYR B 309 ARG 0.006 0.000 ARG A1185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.776 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2419 time to fit residues: 51.6826 Evaluate side-chains 129 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 0.0070 chunk 164 optimal weight: 50.0000 chunk 63 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 overall best weight: 0.9538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16244 Z= 0.207 Angle : 0.574 11.103 22054 Z= 0.287 Chirality : 0.039 0.178 2658 Planarity : 0.004 0.064 2754 Dihedral : 9.331 158.987 2404 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 1.79 % Allowed : 32.59 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.93 (0.19), residues: 2094 helix: 2.48 (0.14), residues: 1410 sheet: 0.30 (0.63), residues: 68 loop : -1.61 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 635 HIS 0.009 0.001 HIS A1172 PHE 0.012 0.001 PHE B1134 TYR 0.010 0.001 TYR B 641 ARG 0.005 0.001 ARG B1185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 1.737 Fit side-chains REVERT: B 483 MET cc_start: 0.9114 (mtp) cc_final: 0.8871 (mtp) REVERT: B 532 ILE cc_start: 0.9283 (mm) cc_final: 0.9080 (mp) REVERT: B 609 ARG cc_start: 0.9406 (tpt90) cc_final: 0.9073 (tmm-80) REVERT: B 967 MET cc_start: 0.8177 (mmm) cc_final: 0.7914 (tmm) REVERT: B 976 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.6383 (ttm110) REVERT: B 1066 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 1107 MET cc_start: 0.7241 (tmm) cc_final: 0.7038 (tmm) REVERT: A 532 ILE cc_start: 0.9150 (mm) cc_final: 0.8918 (mp) REVERT: A 609 ARG cc_start: 0.9567 (tpt90) cc_final: 0.9137 (ptm160) REVERT: A 976 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6365 (ttm110) REVERT: A 1107 MET cc_start: 0.7357 (tmm) cc_final: 0.7131 (tmm) outliers start: 28 outliers final: 9 residues processed: 180 average time/residue: 0.2870 time to fit residues: 77.9338 Evaluate side-chains 151 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.2980 chunk 59 optimal weight: 50.0000 chunk 158 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 170 optimal weight: 50.0000 chunk 189 optimal weight: 4.9990 chunk 65 optimal weight: 50.0000 chunk 153 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16244 Z= 0.256 Angle : 0.571 12.929 22054 Z= 0.287 Chirality : 0.039 0.176 2658 Planarity : 0.004 0.071 2754 Dihedral : 9.035 150.572 2404 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.78 % Favored : 95.17 % Rotamer: Outliers : 2.37 % Allowed : 31.56 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.66 (0.19), residues: 2094 helix: 2.31 (0.14), residues: 1408 sheet: -0.85 (0.59), residues: 82 loop : -1.69 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 635 HIS 0.009 0.001 HIS A1172 PHE 0.024 0.001 PHE B 598 TYR 0.020 0.001 TYR B 641 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.709 Fit side-chains revert: symmetry clash REVERT: B 483 MET cc_start: 0.9175 (mtp) cc_final: 0.8914 (mtp) REVERT: B 532 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9092 (mp) REVERT: B 609 ARG cc_start: 0.9438 (tpt90) cc_final: 0.9103 (tmm-80) REVERT: B 837 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: B 976 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6330 (ttm110) REVERT: B 1009 TYR cc_start: 0.8398 (t80) cc_final: 0.8187 (t80) REVERT: B 1066 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: B 1107 MET cc_start: 0.7209 (tmm) cc_final: 0.6769 (tmm) REVERT: B 1166 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6120 (tt) REVERT: A 532 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8888 (mp) REVERT: A 602 MET cc_start: 0.6629 (mmp) cc_final: 0.6304 (mmp) REVERT: A 849 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: A 976 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.6304 (ttm110) REVERT: A 1009 TYR cc_start: 0.8184 (t80) cc_final: 0.7952 (t80) REVERT: A 1107 MET cc_start: 0.7363 (tmm) cc_final: 0.6929 (tmm) outliers start: 37 outliers final: 17 residues processed: 175 average time/residue: 0.2655 time to fit residues: 70.4210 Evaluate side-chains 165 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 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 614 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16244 Z= 0.189 Angle : 0.531 11.031 22054 Z= 0.269 Chirality : 0.038 0.159 2658 Planarity : 0.004 0.071 2754 Dihedral : 8.742 140.876 2404 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 2.75 % Allowed : 31.31 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.74 (0.19), residues: 2094 helix: 2.39 (0.14), residues: 1396 sheet: -0.79 (0.59), residues: 82 loop : -1.60 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 635 HIS 0.008 0.001 HIS A1172 PHE 0.025 0.001 PHE B 598 TYR 0.016 0.001 TYR B 641 ARG 0.003 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.923 Fit side-chains revert: symmetry clash REVERT: B 483 MET cc_start: 0.9165 (mtp) cc_final: 0.8933 (mtp) REVERT: B 512 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.8996 (mm) REVERT: B 609 ARG cc_start: 0.9400 (tpt90) cc_final: 0.9077 (tmm-80) REVERT: B 837 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.6850 (m-80) REVERT: B 849 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: B 900 GLN cc_start: 0.8480 (tp40) cc_final: 0.8017 (tp40) REVERT: B 967 MET cc_start: 0.8544 (tpp) cc_final: 0.8291 (tmm) REVERT: B 976 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.6414 (ttm110) REVERT: B 1066 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: B 1107 MET cc_start: 0.7373 (tmm) cc_final: 0.6890 (tmm) REVERT: B 1166 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6104 (tt) REVERT: A 532 ILE cc_start: 0.9115 (mm) cc_final: 0.8893 (mp) REVERT: A 602 MET cc_start: 0.6575 (mmp) cc_final: 0.6217 (mmp) REVERT: A 976 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6347 (ttm110) REVERT: A 1107 MET cc_start: 0.7408 (tmm) cc_final: 0.6930 (tmm) outliers start: 43 outliers final: 22 residues processed: 182 average time/residue: 0.2806 time to fit residues: 78.5899 Evaluate side-chains 168 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.0670 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 151 optimal weight: 0.0070 chunk 83 optimal weight: 0.0040 chunk 173 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 182 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16244 Z= 0.142 Angle : 0.519 12.451 22054 Z= 0.261 Chirality : 0.037 0.152 2658 Planarity : 0.004 0.068 2754 Dihedral : 8.406 130.488 2404 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.01 % Allowed : 30.47 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.87 (0.19), residues: 2094 helix: 2.46 (0.14), residues: 1394 sheet: -0.61 (0.59), residues: 82 loop : -1.49 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 635 HIS 0.006 0.000 HIS A1172 PHE 0.016 0.001 PHE B 598 TYR 0.015 0.001 TYR B 641 ARG 0.003 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 1.871 Fit side-chains REVERT: B 220 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7911 (mp) REVERT: B 512 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9067 (mm) REVERT: B 609 ARG cc_start: 0.9362 (tpt90) cc_final: 0.9071 (tmm-80) REVERT: B 849 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: B 924 GLU cc_start: 0.7478 (mp0) cc_final: 0.6664 (mp0) REVERT: B 967 MET cc_start: 0.8525 (tpp) cc_final: 0.8202 (tmm) REVERT: B 976 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6516 (ttm110) REVERT: B 1066 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: B 1073 MET cc_start: 0.8340 (mmm) cc_final: 0.8133 (mmt) REVERT: B 1107 MET cc_start: 0.7447 (tmm) cc_final: 0.6914 (tmm) REVERT: B 1166 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.6066 (tt) REVERT: A 129 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7680 (t0) REVERT: A 220 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7840 (mp) REVERT: A 595 TRP cc_start: 0.8519 (OUTLIER) cc_final: 0.7694 (m100) REVERT: A 609 ARG cc_start: 0.9544 (tpt90) cc_final: 0.9220 (ptt180) REVERT: A 900 GLN cc_start: 0.8228 (tp40) cc_final: 0.7972 (tp40) REVERT: A 976 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6602 (ttm110) REVERT: A 1066 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: A 1107 MET cc_start: 0.7503 (tmm) cc_final: 0.7012 (tmm) outliers start: 47 outliers final: 23 residues processed: 187 average time/residue: 0.2701 time to fit residues: 77.5880 Evaluate side-chains 174 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 168 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 40.0000 chunk 106 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16244 Z= 0.175 Angle : 0.533 15.872 22054 Z= 0.264 Chirality : 0.037 0.200 2658 Planarity : 0.004 0.066 2754 Dihedral : 8.386 124.195 2404 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.27 % Allowed : 30.35 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.00 (0.19), residues: 2094 helix: 2.47 (0.14), residues: 1396 sheet: 0.61 (0.62), residues: 68 loop : -1.35 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 635 HIS 0.013 0.001 HIS A1172 PHE 0.032 0.001 PHE B 598 TYR 0.013 0.001 TYR B 641 ARG 0.003 0.000 ARG A 856 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 143 time to evaluate : 1.698 Fit side-chains REVERT: B 512 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9031 (mm) REVERT: B 579 MET cc_start: 0.7322 (mmm) cc_final: 0.6852 (mmp) REVERT: B 609 ARG cc_start: 0.9376 (tpt90) cc_final: 0.9055 (tmm-80) REVERT: B 837 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: B 849 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: B 924 GLU cc_start: 0.7536 (mp0) cc_final: 0.6754 (mp0) REVERT: B 935 GLU cc_start: 0.8728 (tp30) cc_final: 0.8461 (tp30) REVERT: B 967 MET cc_start: 0.8630 (tpp) cc_final: 0.8310 (tmm) REVERT: B 976 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6540 (ttm110) REVERT: B 1066 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: B 1107 MET cc_start: 0.7419 (tmm) cc_final: 0.7096 (tmm) REVERT: B 1166 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5988 (tt) REVERT: A 129 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7728 (t0) REVERT: A 595 TRP cc_start: 0.8529 (OUTLIER) cc_final: 0.7670 (m100) REVERT: A 609 ARG cc_start: 0.9556 (tpt90) cc_final: 0.9230 (ptt180) REVERT: A 900 GLN cc_start: 0.8338 (tp40) cc_final: 0.8113 (tp40) REVERT: A 976 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6518 (ttm110) REVERT: A 1066 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: A 1107 MET cc_start: 0.7489 (tmm) cc_final: 0.7019 (tmm) outliers start: 51 outliers final: 31 residues processed: 185 average time/residue: 0.2621 time to fit residues: 74.4885 Evaluate side-chains 179 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 138 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 50.0000 chunk 113 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16244 Z= 0.218 Angle : 0.543 15.644 22054 Z= 0.272 Chirality : 0.038 0.158 2658 Planarity : 0.004 0.066 2754 Dihedral : 8.570 122.875 2404 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 3.65 % Allowed : 29.45 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.95 (0.19), residues: 2094 helix: 2.43 (0.14), residues: 1394 sheet: 1.12 (0.66), residues: 58 loop : -1.37 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 635 HIS 0.010 0.001 HIS A1172 PHE 0.026 0.001 PHE B 598 TYR 0.012 0.001 TYR B 641 ARG 0.002 0.000 ARG B1185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 141 time to evaluate : 1.977 Fit side-chains revert: symmetry clash REVERT: B 512 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.8979 (mm) REVERT: B 579 MET cc_start: 0.7395 (mmm) cc_final: 0.7020 (mmp) REVERT: B 609 ARG cc_start: 0.9388 (tpt90) cc_final: 0.9060 (tmm-80) REVERT: B 837 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: B 849 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: B 924 GLU cc_start: 0.7584 (mp0) cc_final: 0.6934 (mp0) REVERT: B 967 MET cc_start: 0.8659 (tpp) cc_final: 0.8304 (tmm) REVERT: B 976 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6429 (ttm110) REVERT: B 1066 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: B 1107 MET cc_start: 0.7377 (tmm) cc_final: 0.7143 (tmm) REVERT: B 1166 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6008 (tt) REVERT: A 129 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7771 (t0) REVERT: A 595 TRP cc_start: 0.8541 (OUTLIER) cc_final: 0.7536 (m100) REVERT: A 900 GLN cc_start: 0.8331 (tp40) cc_final: 0.8061 (tp40) REVERT: A 976 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6406 (ttm110) REVERT: A 1066 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: A 1107 MET cc_start: 0.7452 (tmm) cc_final: 0.7004 (tmm) outliers start: 57 outliers final: 34 residues processed: 190 average time/residue: 0.2865 time to fit residues: 82.0876 Evaluate side-chains 183 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 139 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 120 optimal weight: 7.9990 chunk 60 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16244 Z= 0.165 Angle : 0.533 15.243 22054 Z= 0.265 Chirality : 0.038 0.201 2658 Planarity : 0.004 0.066 2754 Dihedral : 8.459 117.122 2404 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.17 % Rotamer: Outliers : 2.88 % Allowed : 29.83 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.98 (0.19), residues: 2094 helix: 2.43 (0.14), residues: 1394 sheet: 1.19 (0.65), residues: 58 loop : -1.33 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 595 HIS 0.008 0.001 HIS A1172 PHE 0.038 0.001 PHE B 598 TYR 0.011 0.001 TYR B 641 ARG 0.003 0.000 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 1.915 Fit side-chains REVERT: B 512 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9052 (mm) REVERT: B 579 MET cc_start: 0.7496 (mmm) cc_final: 0.7137 (mmp) REVERT: B 586 MET cc_start: 0.7927 (tpp) cc_final: 0.7686 (tpp) REVERT: B 609 ARG cc_start: 0.9354 (tpt90) cc_final: 0.9045 (tmm-80) REVERT: B 837 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: B 849 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: B 976 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6535 (ttm110) REVERT: B 1066 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: B 1166 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5980 (tt) REVERT: A 129 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7736 (t0) REVERT: A 579 MET cc_start: 0.7185 (mmm) cc_final: 0.6799 (mmp) REVERT: A 595 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.8086 (m100) REVERT: A 609 ARG cc_start: 0.9557 (tpt90) cc_final: 0.9251 (ptt180) REVERT: A 900 GLN cc_start: 0.8351 (tp40) cc_final: 0.8063 (tp40) REVERT: A 976 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6436 (ttm110) REVERT: A 1066 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: A 1107 MET cc_start: 0.7362 (tmm) cc_final: 0.7150 (tmm) outliers start: 45 outliers final: 25 residues processed: 185 average time/residue: 0.2629 time to fit residues: 75.5445 Evaluate side-chains 175 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 170 optimal weight: 50.0000 chunk 178 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16244 Z= 0.218 Angle : 0.548 15.211 22054 Z= 0.274 Chirality : 0.038 0.163 2658 Planarity : 0.004 0.065 2754 Dihedral : 8.447 114.514 2404 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 2.75 % Allowed : 29.96 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.92 (0.19), residues: 2094 helix: 2.40 (0.14), residues: 1394 sheet: 1.06 (0.64), residues: 58 loop : -1.35 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 635 HIS 0.007 0.001 HIS A1172 PHE 0.032 0.001 PHE B 598 TYR 0.011 0.001 TYR B 641 ARG 0.004 0.000 ARG B 856 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 140 time to evaluate : 2.202 Fit side-chains REVERT: B 512 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.8984 (mm) REVERT: B 579 MET cc_start: 0.7489 (mmm) cc_final: 0.7145 (mmp) REVERT: B 586 MET cc_start: 0.7947 (tpp) cc_final: 0.7680 (tpp) REVERT: B 609 ARG cc_start: 0.9386 (tpt90) cc_final: 0.9065 (tmm-80) REVERT: B 837 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.6937 (m-80) REVERT: B 849 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: B 900 GLN cc_start: 0.8309 (tp40) cc_final: 0.7827 (tp-100) REVERT: B 967 MET cc_start: 0.8750 (tpp) cc_final: 0.8314 (tmm) REVERT: B 976 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.6459 (ttm110) REVERT: B 1066 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: B 1166 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5989 (tt) REVERT: A 129 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7772 (t0) REVERT: A 579 MET cc_start: 0.7148 (mmm) cc_final: 0.6755 (mmp) REVERT: A 586 MET cc_start: 0.7932 (tpp) cc_final: 0.7700 (tpp) REVERT: A 595 TRP cc_start: 0.8868 (OUTLIER) cc_final: 0.8072 (m100) REVERT: A 609 ARG cc_start: 0.9570 (tpt90) cc_final: 0.9253 (ptt180) REVERT: A 900 GLN cc_start: 0.8375 (tp40) cc_final: 0.8081 (tp40) REVERT: A 976 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6415 (ttm110) REVERT: A 1107 MET cc_start: 0.7318 (tmm) cc_final: 0.7098 (tmm) outliers start: 43 outliers final: 28 residues processed: 177 average time/residue: 0.2751 time to fit residues: 76.1855 Evaluate side-chains 174 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 209 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 166 optimal weight: 50.0000 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 132 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16244 Z= 0.152 Angle : 0.529 14.946 22054 Z= 0.262 Chirality : 0.037 0.153 2658 Planarity : 0.004 0.065 2754 Dihedral : 8.114 111.225 2404 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 2.11 % Allowed : 30.47 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.91 (0.19), residues: 2094 helix: 2.46 (0.14), residues: 1390 sheet: -0.49 (0.59), residues: 82 loop : -1.37 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 635 HIS 0.007 0.001 HIS A1172 PHE 0.030 0.001 PHE B 598 TYR 0.011 0.001 TYR B 641 ARG 0.003 0.000 ARG A 865 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.866 Fit side-chains REVERT: B 512 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9095 (mm) REVERT: B 586 MET cc_start: 0.7928 (tpp) cc_final: 0.7669 (tpp) REVERT: B 609 ARG cc_start: 0.9355 (tpt90) cc_final: 0.9042 (tmm-80) REVERT: B 837 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.6850 (m-80) REVERT: B 849 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: B 900 GLN cc_start: 0.8262 (tp40) cc_final: 0.7757 (tp-100) REVERT: B 967 MET cc_start: 0.8746 (tpp) cc_final: 0.8310 (tmm) REVERT: B 976 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6568 (ttm110) REVERT: B 1066 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: B 1166 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5964 (tt) REVERT: A 129 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7757 (t0) REVERT: A 199 MET cc_start: 0.9016 (mmm) cc_final: 0.8813 (mmt) REVERT: A 579 MET cc_start: 0.7248 (mmm) cc_final: 0.6880 (mmp) REVERT: A 586 MET cc_start: 0.7908 (tpp) cc_final: 0.7684 (tpp) REVERT: A 595 TRP cc_start: 0.8830 (OUTLIER) cc_final: 0.8084 (m100) REVERT: A 609 ARG cc_start: 0.9556 (tpt90) cc_final: 0.9231 (ptt180) REVERT: A 900 GLN cc_start: 0.8388 (tp40) cc_final: 0.8088 (tp40) REVERT: A 976 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6443 (ttm110) REVERT: A 1066 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: A 1107 MET cc_start: 0.7339 (tmm) cc_final: 0.7113 (tmm) outliers start: 33 outliers final: 21 residues processed: 171 average time/residue: 0.2706 time to fit residues: 71.2980 Evaluate side-chains 170 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 50.0000 chunk 69 optimal weight: 0.2980 chunk 171 optimal weight: 40.0000 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.116828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075412 restraints weight = 59717.005| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.81 r_work: 0.3011 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16244 Z= 0.147 Angle : 0.536 14.986 22054 Z= 0.266 Chirality : 0.037 0.188 2658 Planarity : 0.004 0.065 2754 Dihedral : 7.960 109.555 2404 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 2.50 % Allowed : 30.15 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.04 (0.19), residues: 2094 helix: 2.50 (0.14), residues: 1390 sheet: 1.21 (0.65), residues: 58 loop : -1.32 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 962 HIS 0.006 0.001 HIS A1172 PHE 0.029 0.001 PHE B 598 TYR 0.019 0.001 TYR B 641 ARG 0.002 0.000 ARG A 865 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3538.40 seconds wall clock time: 65 minutes 50.13 seconds (3950.13 seconds total)