Starting phenix.real_space_refine on Thu Feb 15 21:30:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7air_11803/02_2024/7air_11803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7air_11803/02_2024/7air_11803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7air_11803/02_2024/7air_11803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7air_11803/02_2024/7air_11803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7air_11803/02_2024/7air_11803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7air_11803/02_2024/7air_11803_updated.pdb" } resolution = 3.66 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= 0.005 sd= 0.038 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 5 5.49 5 S 96 5.16 5 C 8760 2.51 5 N 2221 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A GLU 909": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B GLU 843": "OE1" <-> "OE2" Residue "B GLU 909": "OE1" <-> "OE2" Residue "B GLU 924": "OE1" <-> "OE2" Residue "B GLU 1051": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13504 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 6707 Classifications: {'peptide': 885} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 38, 'TRANS': 846} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 866, 6623 Classifications: {'peptide': 866} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 37, 'TRANS': 828} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.68, per 1000 atoms: 0.57 Number of scatterers: 13504 At special positions: 0 Unit cell: (108.8, 110.5, 159.8, 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 96 16.00 P 5 15.00 O 2422 8.00 N 2221 7.00 C 8760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.05 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.04 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1101 " - " ASN B 361 " " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG E 1 " - " ASN B 312 " Time building additional restraints: 5.55 Conformation dependent library (CDL) restraints added in 2.4 seconds 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3222 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 10 sheets defined 55.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 121 through 132 removed outlier: 5.842A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 142 through 176 removed outlier: 6.509A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 226 Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'A' and resid 270 through 300 removed outlier: 5.535A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 421 through 430 Proline residue: A 429 - end of helix Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 447 through 476 Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 505 through 536 removed outlier: 3.696A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 558 through 571 removed outlier: 4.525A pdb=" N ILE A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 601 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 616 through 633 Processing helix chain 'A' and resid 635 through 660 Processing helix chain 'A' and resid 665 through 681 Processing helix chain 'A' and resid 710 through 719 Processing helix chain 'A' and resid 739 through 755 Processing helix chain 'A' and resid 770 through 779 Processing helix chain 'A' and resid 806 through 819 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 855 through 866 Proline residue: A 862 - end of helix Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 888 through 902 removed outlier: 3.792A pdb=" N HIS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 1012 through 1032 removed outlier: 4.114A pdb=" N ARG A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A1019 " --> pdb=" O ASN A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'B' and resid 121 through 132 removed outlier: 5.930A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 142 through 176 removed outlier: 6.862A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 193 Processing helix chain 'B' and resid 195 through 226 removed outlier: 3.559A pdb=" N LEU B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 268 Processing helix chain 'B' and resid 270 through 300 removed outlier: 5.575A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 420 through 430 Proline residue: B 429 - end of helix Processing helix chain 'B' and resid 447 through 476 Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 505 through 535 removed outlier: 3.658A pdb=" N ILE B 509 " --> pdb=" O TRP B 505 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 558 through 571 removed outlier: 4.398A pdb=" N ILE B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 601 Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 616 through 633 Processing helix chain 'B' and resid 635 through 660 Processing helix chain 'B' and resid 665 through 681 Processing helix chain 'B' and resid 710 through 719 Processing helix chain 'B' and resid 739 through 755 Processing helix chain 'B' and resid 770 through 779 Processing helix chain 'B' and resid 806 through 819 Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 855 through 866 Proline residue: B 862 - end of helix Processing helix chain 'B' and resid 869 through 871 No H-bonds generated for 'chain 'B' and resid 869 through 871' Processing helix chain 'B' and resid 888 through 902 removed outlier: 3.587A pdb=" N HIS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 925 removed outlier: 5.324A pdb=" N ALA B 920 " --> pdb=" O SER B 916 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR B 921 " --> pdb=" O ASP B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1032 removed outlier: 3.548A pdb=" N MET B1019 " --> pdb=" O ASN B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1063 Processing sheet with id= A, first strand: chain 'A' and resid 306 through 310 Processing sheet with id= B, first strand: chain 'A' and resid 326 through 329 Processing sheet with id= C, first strand: chain 'A' and resid 694 through 697 removed outlier: 6.868A pdb=" N SER A 790 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU A 697 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 792 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 824 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 793 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 826 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A1072 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A1039 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL A1073 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A1041 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 726 through 732 removed outlier: 6.988A pdb=" N PHE A 761 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N SER A 729 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN A 763 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE A 731 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 765 " --> pdb=" O ILE A 731 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 845 through 848 removed outlier: 6.378A pdb=" N ARG A 875 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 848 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG A 877 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU A 907 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR A 880 " --> pdb=" O GLU A 907 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 909 " --> pdb=" O THR A 880 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 306 through 309 removed outlier: 3.546A pdb=" N VAL B 307 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 326 through 329 Processing sheet with id= H, first strand: chain 'B' and resid 725 through 728 removed outlier: 6.711A pdb=" N LEU B 694 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY B 728 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 696 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER B 790 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 697 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 792 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 824 " --> pdb=" O VAL B 791 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B1072 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B1039 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL B1073 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B1041 " --> pdb=" O VAL B1073 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 730 through 732 removed outlier: 6.789A pdb=" N VAL B 765 " --> pdb=" O ILE B 731 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 845 through 848 removed outlier: 6.055A pdb=" N ARG B 875 " --> pdb=" O ILE B 846 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 848 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG B 877 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU B 907 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR B 880 " --> pdb=" O GLU B 907 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU B 909 " --> pdb=" O THR B 880 " (cutoff:3.500A) No H-bonds generated for sheet with id= J 661 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4231 1.35 - 1.47: 3518 1.47 - 1.60: 5903 1.60 - 1.72: 12 1.72 - 1.85: 152 Bond restraints: 13816 Sorted by residual: bond pdb=" C4 ATP A1201 " pdb=" C5 ATP A1201 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C4 ATP B1102 " pdb=" C5 ATP B1102 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C5 ATP A1201 " pdb=" C6 ATP A1201 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.80e+01 bond pdb=" O1B ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 1.477 1.610 -0.133 2.20e-02 2.07e+03 3.66e+01 bond pdb=" O1B ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 1.477 1.608 -0.131 2.20e-02 2.07e+03 3.52e+01 ... (remaining 13811 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.28: 388 106.28 - 113.54: 8095 113.54 - 120.80: 6388 120.80 - 128.05: 3812 128.05 - 135.31: 146 Bond angle restraints: 18829 Sorted by residual: angle pdb=" PA ATP B1102 " pdb=" O3A ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 136.83 123.96 12.87 1.00e+00 1.00e+00 1.66e+02 angle pdb=" PA ATP A1201 " pdb=" O3A ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 136.83 125.68 11.15 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C5 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N3 ATP A1201 " ideal model delta sigma weight residual 126.80 118.27 8.53 1.00e+00 1.00e+00 7.28e+01 angle pdb=" C5 ATP B1102 " pdb=" C4 ATP B1102 " pdb=" N3 ATP B1102 " ideal model delta sigma weight residual 126.80 118.82 7.98 1.00e+00 1.00e+00 6.38e+01 angle pdb=" N3 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N9 ATP A1201 " ideal model delta sigma weight residual 127.04 135.13 -8.09 1.15e+00 7.59e-01 4.96e+01 ... (remaining 18824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 7419 21.80 - 43.61: 691 43.61 - 65.41: 115 65.41 - 87.22: 22 87.22 - 109.02: 13 Dihedral angle restraints: 8260 sinusoidal: 3235 harmonic: 5025 Sorted by residual: dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 353 " pdb=" CB CYS B 353 " ideal model delta sinusoidal sigma weight residual 93.00 142.37 -49.37 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 353 " pdb=" CB CYS A 353 " ideal model delta sinusoidal sigma weight residual 93.00 136.22 -43.22 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.69 109.02 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1615 0.053 - 0.105: 512 0.105 - 0.158: 103 0.158 - 0.211: 7 0.211 - 0.263: 2 Chirality restraints: 2239 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" N2 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.30 -0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 2236 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 137 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LEU A 137 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 137 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 138 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A1026 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ASN A1026 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN A1026 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU A1027 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 121 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C LEU A 121 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 121 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 122 " -0.013 2.00e-02 2.50e+03 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2715 2.76 - 3.30: 13156 3.30 - 3.83: 21325 3.83 - 4.37: 22800 4.37 - 4.90: 41610 Nonbonded interactions: 101606 Sorted by model distance: nonbonded pdb=" OG1 THR A 120 " pdb=" OG SER A 450 " model vdw 2.231 2.440 nonbonded pdb=" OG SER A 430 " pdb=" OH TYR A 466 " model vdw 2.235 2.440 nonbonded pdb=" O PRO B 605 " pdb=" NH2 ARG B 608 " model vdw 2.251 2.520 nonbonded pdb=" O SER B 780 " pdb=" OG SER B 780 " model vdw 2.260 2.440 nonbonded pdb=" O GLY A 479 " pdb=" NH2 ARG A 483 " model vdw 2.262 2.520 ... (remaining 101601 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 116 through 233 or resid 244 through 444 or (resid 445 and \ (name N or name CA or name C or name O or name CB )) or resid 446 through 611 o \ r (resid 612 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 13 through 733 or resid 735 through 926 or resid 1014 through 1015 or (resid 101 \ 6 through 1017 and (name N or name CA or name C or name O or name CB )) or resid \ 1018 through 1081)) selection = (chain 'B' and (resid 116 through 733 or resid 735 through 881 or resid 887 thro \ ugh 899 or (resid 900 through 901 and (name N or name CA or name C or name O or \ name CB )) or resid 902 through 914 or (resid 915 through 926 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1014 through 1081)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.300 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 37.730 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.008 0.133 13816 Z= 0.550 Angle : 0.968 13.073 18829 Z= 0.529 Chirality : 0.051 0.263 2239 Planarity : 0.005 0.045 2322 Dihedral : 17.147 109.020 5020 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.14 % Allowed : 20.74 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1732 helix: 0.45 (0.16), residues: 971 sheet: -2.20 (0.39), residues: 136 loop : -2.70 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 381 HIS 0.011 0.002 HIS A 853 PHE 0.024 0.002 PHE A 611 TYR 0.035 0.002 TYR A 356 ARG 0.004 0.001 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 322 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 CYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7616 (m) REVERT: A 704 LEU cc_start: 0.8446 (mt) cc_final: 0.8093 (tt) REVERT: A 777 LEU cc_start: 0.8123 (tp) cc_final: 0.7788 (tp) REVERT: A 879 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.5772 (t80) REVERT: B 879 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6841 (m-80) outliers start: 16 outliers final: 3 residues processed: 334 average time/residue: 0.2649 time to fit residues: 127.3430 Evaluate side-chains 166 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 879 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 177 ASN A 344 HIS A 615 HIS A 655 GLN A 717 GLN A 732 GLN A 747 GLN A 751 ASN A 853 HIS A 868 HIS B 131 ASN B 152 GLN B 250 ASN B 344 HIS B 521 GLN B 655 GLN B 732 GLN B 751 ASN B 853 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13816 Z= 0.270 Angle : 0.679 9.536 18829 Z= 0.334 Chirality : 0.044 0.310 2239 Planarity : 0.004 0.053 2322 Dihedral : 9.948 85.628 2134 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.65 % Allowed : 23.82 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1732 helix: 1.47 (0.17), residues: 964 sheet: -1.51 (0.43), residues: 134 loop : -2.39 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 849 HIS 0.006 0.001 HIS A 845 PHE 0.017 0.002 PHE A 714 TYR 0.012 0.001 TYR B 292 ARG 0.008 0.001 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 190 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7790 (pp) REVERT: A 704 LEU cc_start: 0.8326 (mt) cc_final: 0.8010 (tt) REVERT: A 879 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.6101 (t80) REVERT: B 165 LEU cc_start: 0.8477 (tp) cc_final: 0.8008 (tt) REVERT: B 879 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6755 (m-80) outliers start: 65 outliers final: 35 residues processed: 234 average time/residue: 0.2086 time to fit residues: 75.4866 Evaluate side-chains 193 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 155 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 879 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 107 optimal weight: 50.0000 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 171 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13816 Z= 0.201 Angle : 0.623 9.924 18829 Z= 0.301 Chirality : 0.042 0.310 2239 Planarity : 0.004 0.049 2322 Dihedral : 8.468 78.192 2132 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.29 % Allowed : 25.89 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1732 helix: 1.83 (0.17), residues: 972 sheet: -1.19 (0.43), residues: 134 loop : -1.99 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 143 HIS 0.005 0.001 HIS B 394 PHE 0.017 0.001 PHE B 280 TYR 0.009 0.001 TYR B 292 ARG 0.005 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 171 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7768 (pp) REVERT: A 879 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5932 (t80) REVERT: B 165 LEU cc_start: 0.8511 (tp) cc_final: 0.8054 (tt) outliers start: 60 outliers final: 37 residues processed: 214 average time/residue: 0.1987 time to fit residues: 67.4647 Evaluate side-chains 195 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 152 GLN A 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13816 Z= 0.173 Angle : 0.587 9.946 18829 Z= 0.282 Chirality : 0.041 0.269 2239 Planarity : 0.003 0.039 2322 Dihedral : 7.547 88.920 2128 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.22 % Allowed : 25.89 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1732 helix: 2.11 (0.17), residues: 962 sheet: -1.05 (0.43), residues: 136 loop : -1.77 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 501 HIS 0.004 0.001 HIS B 394 PHE 0.017 0.001 PHE B 280 TYR 0.009 0.001 TYR B 466 ARG 0.004 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 168 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7746 (pp) REVERT: B 165 LEU cc_start: 0.8473 (tp) cc_final: 0.8057 (tt) outliers start: 59 outliers final: 40 residues processed: 209 average time/residue: 0.2006 time to fit residues: 66.5144 Evaluate side-chains 193 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 152 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 1073 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13816 Z= 0.229 Angle : 0.608 16.192 18829 Z= 0.293 Chirality : 0.041 0.275 2239 Planarity : 0.003 0.036 2322 Dihedral : 7.191 79.870 2124 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.08 % Allowed : 24.82 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1732 helix: 2.17 (0.17), residues: 961 sheet: -0.96 (0.47), residues: 124 loop : -1.65 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 143 HIS 0.005 0.001 HIS B 845 PHE 0.017 0.001 PHE A 541 TYR 0.010 0.001 TYR B 292 ARG 0.003 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 161 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7777 (pp) REVERT: A 809 LYS cc_start: 0.7953 (pttt) cc_final: 0.7724 (pttt) REVERT: A 891 MET cc_start: 0.8133 (mmm) cc_final: 0.7565 (mmm) REVERT: B 165 LEU cc_start: 0.8498 (tp) cc_final: 0.8052 (tt) REVERT: B 591 PHE cc_start: 0.7045 (m-80) cc_final: 0.6781 (m-80) outliers start: 71 outliers final: 54 residues processed: 211 average time/residue: 0.2014 time to fit residues: 66.4920 Evaluate side-chains 208 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 153 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13816 Z= 0.285 Angle : 0.639 17.101 18829 Z= 0.310 Chirality : 0.042 0.279 2239 Planarity : 0.004 0.036 2322 Dihedral : 7.128 71.469 2124 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 6.37 % Allowed : 24.68 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.21), residues: 1732 helix: 2.21 (0.17), residues: 952 sheet: -0.93 (0.47), residues: 124 loop : -1.56 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 143 HIS 0.004 0.001 HIS B 776 PHE 0.017 0.001 PHE A 714 TYR 0.011 0.001 TYR B 292 ARG 0.003 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 152 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7342 (tt) REVERT: A 542 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7825 (pp) REVERT: A 891 MET cc_start: 0.8210 (mmm) cc_final: 0.7648 (mmm) REVERT: B 165 LEU cc_start: 0.8517 (tp) cc_final: 0.8105 (tt) REVERT: B 623 MET cc_start: 0.7292 (ttp) cc_final: 0.6948 (ttm) outliers start: 89 outliers final: 64 residues processed: 222 average time/residue: 0.2028 time to fit residues: 70.8610 Evaluate side-chains 218 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 152 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1073 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13816 Z= 0.348 Angle : 0.695 16.011 18829 Z= 0.338 Chirality : 0.044 0.276 2239 Planarity : 0.004 0.037 2322 Dihedral : 7.251 75.381 2124 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.08 % Allowed : 25.68 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1732 helix: 2.02 (0.17), residues: 957 sheet: -1.07 (0.47), residues: 124 loop : -1.52 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 143 HIS 0.005 0.001 HIS A 788 PHE 0.018 0.002 PHE A 541 TYR 0.013 0.001 TYR B 411 ARG 0.003 0.000 ARG A 877 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 151 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7427 (tt) REVERT: A 542 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7864 (pp) REVERT: A 809 LYS cc_start: 0.7999 (pttt) cc_final: 0.7790 (pttt) REVERT: A 891 MET cc_start: 0.8229 (mmm) cc_final: 0.7625 (mmm) REVERT: B 165 LEU cc_start: 0.8606 (tp) cc_final: 0.8167 (tt) REVERT: B 623 MET cc_start: 0.7216 (ttp) cc_final: 0.6945 (ttm) outliers start: 85 outliers final: 66 residues processed: 216 average time/residue: 0.2048 time to fit residues: 69.4224 Evaluate side-chains 216 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 148 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 861 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13816 Z= 0.174 Angle : 0.603 16.067 18829 Z= 0.287 Chirality : 0.041 0.274 2239 Planarity : 0.003 0.038 2322 Dihedral : 6.949 74.892 2124 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.58 % Allowed : 27.97 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1732 helix: 2.23 (0.17), residues: 958 sheet: -0.66 (0.50), residues: 122 loop : -1.36 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 808 HIS 0.006 0.001 HIS B 776 PHE 0.020 0.001 PHE B 280 TYR 0.008 0.001 TYR A 649 ARG 0.005 0.000 ARG A1032 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 160 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7337 (tt) REVERT: A 542 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7786 (pp) REVERT: A 891 MET cc_start: 0.8160 (mmm) cc_final: 0.7589 (mmm) REVERT: B 165 LEU cc_start: 0.8484 (tp) cc_final: 0.8077 (tt) outliers start: 50 outliers final: 42 residues processed: 196 average time/residue: 0.2047 time to fit residues: 63.1323 Evaluate side-chains 200 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 94 optimal weight: 0.0980 chunk 68 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13816 Z= 0.163 Angle : 0.608 15.716 18829 Z= 0.287 Chirality : 0.040 0.268 2239 Planarity : 0.003 0.040 2322 Dihedral : 6.783 73.317 2124 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.43 % Allowed : 28.54 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1732 helix: 2.25 (0.17), residues: 956 sheet: -0.50 (0.50), residues: 123 loop : -1.26 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 808 HIS 0.010 0.001 HIS B 776 PHE 0.018 0.001 PHE B 280 TYR 0.008 0.001 TYR A 649 ARG 0.003 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 170 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7335 (tt) REVERT: A 542 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7772 (pp) REVERT: A 623 MET cc_start: 0.7727 (tmm) cc_final: 0.7482 (tmm) REVERT: A 891 MET cc_start: 0.8133 (mmm) cc_final: 0.7563 (mmm) REVERT: B 165 LEU cc_start: 0.8468 (tp) cc_final: 0.8072 (tt) REVERT: B 642 MET cc_start: 0.6363 (mtp) cc_final: 0.6127 (ttp) outliers start: 48 outliers final: 41 residues processed: 205 average time/residue: 0.2081 time to fit residues: 66.5026 Evaluate side-chains 200 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 157 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 114 optimal weight: 20.0000 chunk 173 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 106 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 109 optimal weight: 0.0010 chunk 147 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A1026 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13816 Z= 0.154 Angle : 0.624 15.551 18829 Z= 0.290 Chirality : 0.041 0.267 2239 Planarity : 0.004 0.041 2322 Dihedral : 6.676 73.269 2124 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.72 % Allowed : 29.47 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1732 helix: 2.23 (0.17), residues: 953 sheet: -0.32 (0.51), residues: 123 loop : -1.25 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP A 808 HIS 0.003 0.000 HIS B 394 PHE 0.012 0.001 PHE B 280 TYR 0.007 0.001 TYR A 649 ARG 0.003 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 169 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7754 (pp) REVERT: A 891 MET cc_start: 0.8067 (mmm) cc_final: 0.7518 (mmm) REVERT: B 165 LEU cc_start: 0.8467 (tp) cc_final: 0.8082 (tt) outliers start: 38 outliers final: 32 residues processed: 196 average time/residue: 0.2152 time to fit residues: 66.4614 Evaluate side-chains 196 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 0.1980 chunk 138 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 141 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074332 restraints weight = 37504.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077149 restraints weight = 17753.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079054 restraints weight = 11003.154| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13816 Z= 0.162 Angle : 0.615 15.592 18829 Z= 0.285 Chirality : 0.040 0.265 2239 Planarity : 0.003 0.044 2322 Dihedral : 6.608 74.189 2124 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.93 % Allowed : 29.47 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1732 helix: 2.24 (0.17), residues: 953 sheet: -0.21 (0.52), residues: 123 loop : -1.22 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 808 HIS 0.003 0.001 HIS B 776 PHE 0.012 0.001 PHE B 280 TYR 0.007 0.001 TYR A 649 ARG 0.003 0.000 ARG A 610 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2475.80 seconds wall clock time: 46 minutes 4.15 seconds (2764.15 seconds total)