Starting phenix.real_space_refine on Thu Sep 26 17:34:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/09_2024/7m3g_23654.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/09_2024/7m3g_23654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/09_2024/7m3g_23654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/09_2024/7m3g_23654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/09_2024/7m3g_23654.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/09_2024/7m3g_23654.cif" } resolution = 2.5 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= 0.007 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 75 5.16 5 C 8616 2.51 5 N 2152 2.21 5 O 2449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13298 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6485 Classifications: {'peptide': 821} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 31, 'TRANS': 789} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6375 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 31, 'TRANS': 772} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Modifications used: {'PEPT-D': 7} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Modifications used: {'PEPT-D': 7} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} 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: "F" 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: "G" 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: "H" 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: "I" 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: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 93 Unusual residues: {' CA': 3, 'H43': 1, 'NAG': 3, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 905 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Unusual residues: {' CA': 1, 'H43': 1, 'NAG': 2, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B 904 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.76, per 1000 atoms: 0.66 Number of scatterers: 13298 At special positions: 0 Unit cell: (99.9, 92.13, 192.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 75 16.00 P 2 15.00 O 2449 8.00 N 2152 7.00 C 8616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.04 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG DCY C 2 " distance=2.04 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.04 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG DCY D 2 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.04 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 902 " - " ASN A 468 " " NAG A 903 " - " ASN A 488 " " NAG A 904 " - " ASN A 594 " " NAG B 902 " - " ASN B 468 " " NAG B 903 " - " ASN B 594 " " NAG E 1 " - " ASN A 261 " " NAG F 1 " - " ASN A 541 " " NAG G 1 " - " ASN B 261 " " NAG H 1 " - " ASN B 488 " " NAG I 1 " - " ASN B 541 " Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DCY C 2 " pdb=" CB DAL C 3 " pdb=" CB DAR C 4 " pdb=" CB DAR C 5 " pdb=" CB DAR C 6 " pdb=" CB DAL C 7 " pdb=" CB DAR C 8 " pdb=" CB DCY D 2 " pdb=" CB DAL D 3 " pdb=" CB DAR D 4 " pdb=" CB DAR D 5 " pdb=" CB DAR D 6 " pdb=" CB DAL D 7 " pdb=" CB DAR D 8 " Number of C-beta restraints generated: 3064 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 47.3% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.535A pdb=" N PHE A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.502A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.605A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.658A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.681A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.810A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.513A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.594A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 Processing helix chain 'A' and resid 640 through 646 Processing helix chain 'A' and resid 649 through 664 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.700A pdb=" N PHE A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 680 through 697 removed outlier: 4.144A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.715A pdb=" N VAL A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 4.000A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.890A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 removed outlier: 3.510A pdb=" N SER A 827 " --> pdb=" O PRO A 823 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 853 removed outlier: 3.506A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 863 removed outlier: 3.725A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 873 removed outlier: 3.700A pdb=" N VAL A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 886 removed outlier: 3.757A pdb=" N VAL A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 83 removed outlier: 3.748A pdb=" N MET B 74 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.546A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.650A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.781A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.544A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.674A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.715A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 272 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.620A pdb=" N VAL B 404 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.536A pdb=" N ASN B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.072A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.589A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.799A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 668 removed outlier: 3.785A pdb=" N PHE B 668 " --> pdb=" O SER B 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 668' Processing helix chain 'B' and resid 680 through 698 removed outlier: 4.038A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 4.156A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 793 removed outlier: 3.936A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 821 removed outlier: 4.059A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 825 Processing helix chain 'B' and resid 831 through 854 removed outlier: 3.829A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 836 " --> pdb=" O PHE B 832 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 861 Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.763A pdb=" N DAL D 7 " --> pdb=" O DAL D 3 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.299A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.151A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 267 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 320 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AA5, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.442A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE B 33 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VAL B 142 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 35 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 41 through 44 removed outlier: 7.345A pdb=" N ARG B 62 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 44 " --> pdb=" O CYS B 60 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS B 60 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.043A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 320 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB2, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.616A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N CYS B 765 " --> pdb=" O GLU B 604 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1626 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: 4.75 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4047 1.34 - 1.46: 3424 1.46 - 1.58: 6061 1.58 - 1.71: 2 1.71 - 1.83: 89 Bond restraints: 13623 Sorted by residual: bond pdb=" C11 H43 A 901 " pdb=" N12 H43 A 901 " ideal model delta sigma weight residual 1.454 1.574 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C13 H43 A 901 " pdb=" N12 H43 A 901 " ideal model delta sigma weight residual 1.459 1.563 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C11 H43 B 901 " pdb=" N12 H43 B 901 " ideal model delta sigma weight residual 1.454 1.553 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C8 H43 A 901 " pdb=" N9 H43 A 901 " ideal model delta sigma weight residual 1.367 1.465 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C8 H43 B 901 " pdb=" N9 H43 B 901 " ideal model delta sigma weight residual 1.367 1.464 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 13618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 18091 2.83 - 5.67: 335 5.67 - 8.50: 48 8.50 - 11.34: 7 11.34 - 14.17: 1 Bond angle restraints: 18482 Sorted by residual: angle pdb=" CA PRO B 641 " pdb=" N PRO B 641 " pdb=" CD PRO B 641 " ideal model delta sigma weight residual 112.00 104.81 7.19 1.40e+00 5.10e-01 2.64e+01 angle pdb=" CB MET B 734 " pdb=" CG MET B 734 " pdb=" SD MET B 734 " ideal model delta sigma weight residual 112.70 126.87 -14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" CA PRO B 748 " pdb=" N PRO B 748 " pdb=" CD PRO B 748 " ideal model delta sigma weight residual 112.00 105.43 6.57 1.40e+00 5.10e-01 2.20e+01 angle pdb=" CB ILE B 603 " pdb=" CG1 ILE B 603 " pdb=" CD1 ILE B 603 " ideal model delta sigma weight residual 113.80 123.60 -9.80 2.10e+00 2.27e-01 2.18e+01 angle pdb=" N GLU B 759 " pdb=" CA GLU B 759 " pdb=" C GLU B 759 " ideal model delta sigma weight residual 114.62 109.48 5.14 1.14e+00 7.69e-01 2.03e+01 ... (remaining 18477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 7931 35.99 - 71.98: 244 71.98 - 107.98: 18 107.98 - 143.97: 1 143.97 - 179.96: 4 Dihedral angle restraints: 8198 sinusoidal: 3451 harmonic: 4747 Sorted by residual: dihedral pdb=" CD DAR D 4 " pdb=" NE DAR D 4 " pdb=" CZ DAR D 4 " pdb=" NH1 DAR D 4 " ideal model delta sinusoidal sigma weight residual 0.00 179.96 -179.96 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD DAR C 8 " pdb=" NE DAR C 8 " pdb=" CZ DAR C 8 " pdb=" NH1 DAR C 8 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD DAR D 5 " pdb=" NE DAR D 5 " pdb=" CZ DAR D 5 " pdb=" NH1 DAR D 5 " ideal model delta sinusoidal sigma weight residual 0.00 -179.70 179.70 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 8195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1678 0.069 - 0.138: 368 0.138 - 0.207: 42 0.207 - 0.276: 3 0.276 - 0.345: 4 Chirality restraints: 2095 Sorted by residual: chirality pdb=" C13 H43 A 901 " pdb=" C14 H43 A 901 " pdb=" C24 H43 A 901 " pdb=" N12 H43 A 901 " both_signs ideal model delta sigma weight residual False -2.34 -2.68 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE A 61 " pdb=" CA ILE A 61 " pdb=" CG1 ILE A 61 " pdb=" CG2 ILE A 61 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C13 H43 B 901 " pdb=" C14 H43 B 901 " pdb=" C24 H43 B 901 " pdb=" N12 H43 B 901 " both_signs ideal model delta sigma weight residual False -2.34 -2.67 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 2092 not shown) Planarity restraints: 2332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 747 " -0.098 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO B 748 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO B 748 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 748 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 640 " -0.096 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO B 641 " 0.244 5.00e-02 4.00e+02 pdb=" CA PRO B 641 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO B 641 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 789 " 0.034 2.00e-02 2.50e+03 2.79e-02 1.36e+01 pdb=" CG PHE A 789 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 789 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 789 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 789 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 789 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 789 " 0.006 2.00e-02 2.50e+03 ... (remaining 2329 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3499 2.80 - 3.33: 11058 3.33 - 3.85: 21208 3.85 - 4.38: 24712 4.38 - 4.90: 42544 Nonbonded interactions: 103021 Sorted by model distance: nonbonded pdb=" O ALA A 548 " pdb=" OG SER A 574 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASP A 480 " pdb=" N ASP A 484 " model vdw 2.290 3.120 nonbonded pdb=" OD2 ASP B 238 " pdb=" OG SER B 262 " model vdw 2.299 3.040 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.312 3.040 nonbonded pdb=" O GLY A 613 " pdb=" OG1 THR A 617 " model vdw 2.322 3.040 ... (remaining 103016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 125 or resid 131 through 566 or (resid 567 and \ (name N or name CA or name C or name O or name CB )) or resid 568 through 704 or \ (resid 705 and (name N or name CA or name C or name O or name CB )) or resid 70 \ 6 through 862 or (resid 863 and (name N or name CA or name C or name O or name C \ B )) or resid 864 through 865 or (resid 866 and (name N or name CA or name C or \ name O or name CB )) or resid 867 through 870 or resid 903 through 906)) selection = (chain 'B' and (resid 20 through 48 or (resid 49 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 362 or resid 391 throug \ h 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) or \ resid 501 through 555 or (resid 556 and (name N or name CA or name C or name O o \ r name CB )) or resid 557 through 725 or (resid 726 and (name N or name CA or na \ me C or name O or name CB )) or resid 727 through 870 or resid 902 through 905)) \ } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.390 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.440 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.007 0.120 13623 Z= 0.459 Angle : 0.961 14.174 18482 Z= 0.527 Chirality : 0.058 0.345 2095 Planarity : 0.008 0.145 2322 Dihedral : 17.275 179.960 5077 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.93 % Allowed : 18.54 % Favored : 80.53 % 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: -2.02 (0.18), residues: 1609 helix: -0.94 (0.17), residues: 686 sheet: -1.14 (0.32), residues: 223 loop : -1.70 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 675 HIS 0.006 0.002 HIS B 338 PHE 0.063 0.003 PHE A 789 TYR 0.021 0.003 TYR A 421 ARG 0.011 0.001 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.585 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 170 average time/residue: 0.9966 time to fit residues: 190.4817 Evaluate side-chains 163 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 697 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 647 ASN A 673 GLN A 724 GLN A 753 ASN B 253 GLN B 583 ASN B 595 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13623 Z= 0.232 Angle : 0.601 7.416 18482 Z= 0.320 Chirality : 0.045 0.189 2095 Planarity : 0.005 0.088 2322 Dihedral : 11.581 179.422 2159 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.15 % Allowed : 16.32 % Favored : 80.53 % 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: -0.80 (0.20), residues: 1609 helix: 0.58 (0.19), residues: 694 sheet: -1.05 (0.32), residues: 223 loop : -1.47 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.044 0.002 PHE A 789 TYR 0.019 0.002 TYR A 421 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: B 399 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: B 517 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8538 (tmmm) outliers start: 44 outliers final: 16 residues processed: 193 average time/residue: 0.8376 time to fit residues: 183.7887 Evaluate side-chains 180 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 147 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 253 GLN B 463 HIS B 583 ASN B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13623 Z= 0.250 Angle : 0.590 7.221 18482 Z= 0.314 Chirality : 0.046 0.205 2095 Planarity : 0.005 0.070 2322 Dihedral : 10.767 179.785 2146 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.22 % Allowed : 16.82 % Favored : 79.96 % 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: -0.37 (0.20), residues: 1609 helix: 1.11 (0.20), residues: 695 sheet: -0.99 (0.33), residues: 223 loop : -1.38 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.023 0.002 PHE A 832 TYR 0.020 0.002 TYR A 421 ARG 0.003 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: A 575 ASP cc_start: 0.8052 (p0) cc_final: 0.7661 (p0) REVERT: A 576 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: A 793 LYS cc_start: 0.8879 (tppp) cc_final: 0.8394 (tppt) REVERT: B 270 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: B 399 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: B 441 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6935 (mpp-170) REVERT: B 507 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: B 790 PHE cc_start: 0.8946 (m-80) cc_final: 0.8555 (m-80) outliers start: 45 outliers final: 21 residues processed: 189 average time/residue: 0.8504 time to fit residues: 182.7229 Evaluate side-chains 186 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 253 GLN B 583 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13623 Z= 0.332 Angle : 0.629 9.778 18482 Z= 0.333 Chirality : 0.048 0.220 2095 Planarity : 0.005 0.074 2322 Dihedral : 10.615 179.737 2146 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.79 % Allowed : 16.54 % Favored : 79.67 % 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: -0.37 (0.20), residues: 1609 helix: 1.12 (0.19), residues: 712 sheet: -1.04 (0.33), residues: 224 loop : -1.45 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 299 HIS 0.005 0.001 HIS A 429 PHE 0.025 0.002 PHE B 729 TYR 0.023 0.002 TYR A 421 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 165 time to evaluate : 1.715 Fit side-chains REVERT: A 499 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 576 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: B 270 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: B 399 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: B 441 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6918 (mpp-170) REVERT: B 507 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7679 (tm-30) outliers start: 53 outliers final: 29 residues processed: 197 average time/residue: 0.9289 time to fit residues: 207.1474 Evaluate side-chains 191 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 116 optimal weight: 0.0470 chunk 64 optimal weight: 0.2980 chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 253 GLN B 583 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13623 Z= 0.197 Angle : 0.579 8.702 18482 Z= 0.309 Chirality : 0.049 0.782 2095 Planarity : 0.005 0.069 2322 Dihedral : 10.455 179.781 2146 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.65 % Allowed : 17.39 % Favored : 78.95 % 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: -0.11 (0.21), residues: 1609 helix: 1.45 (0.20), residues: 698 sheet: -0.94 (0.33), residues: 223 loop : -1.37 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.025 0.001 PHE B 729 TYR 0.019 0.002 TYR A 421 ARG 0.002 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 161 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: A 576 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7405 (pm20) REVERT: A 583 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8184 (m110) REVERT: A 794 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 270 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: B 399 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: B 507 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: B 604 GLU cc_start: 0.7954 (tt0) cc_final: 0.7741 (tt0) outliers start: 51 outliers final: 24 residues processed: 195 average time/residue: 0.8316 time to fit residues: 184.7922 Evaluate side-chains 185 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13623 Z= 0.362 Angle : 0.658 9.474 18482 Z= 0.345 Chirality : 0.050 0.521 2095 Planarity : 0.005 0.074 2322 Dihedral : 10.527 179.444 2146 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.79 % Allowed : 17.47 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.22 (0.20), residues: 1609 helix: 1.31 (0.19), residues: 710 sheet: -1.03 (0.32), residues: 232 loop : -1.42 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 299 HIS 0.006 0.001 HIS A 429 PHE 0.026 0.002 PHE B 729 TYR 0.024 0.002 TYR A 421 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 158 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: A 249 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6376 (tp30) REVERT: A 499 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: A 583 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8216 (m110) REVERT: A 794 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8377 (p) REVERT: B 270 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: B 399 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: B 507 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: B 604 GLU cc_start: 0.7970 (tt0) cc_final: 0.7746 (tt0) outliers start: 53 outliers final: 33 residues processed: 195 average time/residue: 0.8270 time to fit residues: 183.8617 Evaluate side-chains 201 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 161 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13623 Z= 0.225 Angle : 0.589 8.271 18482 Z= 0.310 Chirality : 0.046 0.381 2095 Planarity : 0.005 0.071 2322 Dihedral : 10.542 179.818 2146 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.44 % Allowed : 17.90 % Favored : 78.67 % 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: -0.00 (0.21), residues: 1609 helix: 1.50 (0.20), residues: 700 sheet: -0.86 (0.34), residues: 222 loop : -1.29 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 299 HIS 0.005 0.001 HIS A 595 PHE 0.030 0.001 PHE B 789 TYR 0.020 0.002 TYR A 421 ARG 0.002 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: A 583 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8212 (m110) REVERT: A 794 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8488 (p) REVERT: B 399 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: B 507 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: B 604 GLU cc_start: 0.7873 (tt0) cc_final: 0.7663 (tt0) outliers start: 48 outliers final: 31 residues processed: 193 average time/residue: 0.8403 time to fit residues: 184.4933 Evaluate side-chains 191 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.0020 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13623 Z= 0.210 Angle : 0.571 8.604 18482 Z= 0.300 Chirality : 0.045 0.311 2095 Planarity : 0.004 0.069 2322 Dihedral : 10.510 179.600 2146 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.58 % Allowed : 17.97 % Favored : 78.45 % 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: 0.09 (0.21), residues: 1609 helix: 1.59 (0.20), residues: 707 sheet: -0.80 (0.35), residues: 210 loop : -1.28 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.029 0.001 PHE B 729 TYR 0.019 0.002 TYR A 421 ARG 0.002 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 157 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: A 583 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8190 (m110) REVERT: A 794 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 270 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: B 399 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: B 507 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: B 517 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8425 (ttmm) outliers start: 50 outliers final: 28 residues processed: 192 average time/residue: 0.8595 time to fit residues: 188.0426 Evaluate side-chains 190 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN B 463 HIS B 583 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13623 Z= 0.265 Angle : 0.605 9.018 18482 Z= 0.316 Chirality : 0.046 0.287 2095 Planarity : 0.005 0.071 2322 Dihedral : 10.427 179.779 2146 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.58 % Allowed : 18.47 % Favored : 78.95 % 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: 0.00 (0.21), residues: 1609 helix: 1.51 (0.19), residues: 713 sheet: -0.84 (0.35), residues: 210 loop : -1.35 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 299 HIS 0.005 0.001 HIS A 463 PHE 0.029 0.002 PHE B 729 TYR 0.021 0.002 TYR A 421 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: A 583 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8216 (m110) REVERT: B 270 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: B 399 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: B 507 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7644 (tm-30) outliers start: 36 outliers final: 29 residues processed: 181 average time/residue: 0.8633 time to fit residues: 177.4491 Evaluate side-chains 185 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 128 optimal weight: 0.0470 chunk 13 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13623 Z= 0.279 Angle : 0.619 9.513 18482 Z= 0.324 Chirality : 0.047 0.282 2095 Planarity : 0.005 0.071 2322 Dihedral : 10.400 179.633 2146 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.58 % Allowed : 18.54 % Favored : 78.88 % 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: 0.01 (0.21), residues: 1609 helix: 1.50 (0.19), residues: 713 sheet: -0.85 (0.34), residues: 210 loop : -1.34 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 299 HIS 0.005 0.001 HIS A 463 PHE 0.029 0.002 PHE B 729 TYR 0.021 0.002 TYR A 421 ARG 0.003 0.000 ARG A 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: A 583 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8214 (m110) REVERT: B 399 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: B 507 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7646 (tm-30) outliers start: 36 outliers final: 29 residues processed: 176 average time/residue: 0.9027 time to fit residues: 179.3745 Evaluate side-chains 183 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 128 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 0.0370 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088617 restraints weight = 19417.230| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.58 r_work: 0.2993 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13623 Z= 0.186 Angle : 0.563 9.634 18482 Z= 0.294 Chirality : 0.044 0.259 2095 Planarity : 0.004 0.069 2322 Dihedral : 10.255 179.556 2146 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.29 % Allowed : 18.97 % Favored : 78.74 % 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: 0.14 (0.21), residues: 1609 helix: 1.61 (0.19), residues: 715 sheet: -0.77 (0.35), residues: 209 loop : -1.29 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 299 HIS 0.003 0.001 HIS A 463 PHE 0.029 0.001 PHE B 729 TYR 0.018 0.001 TYR A 421 ARG 0.002 0.000 ARG A 648 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4499.66 seconds wall clock time: 79 minutes 30.36 seconds (4770.36 seconds total)