Starting phenix.real_space_refine on Mon Dec 30 20:44:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qhh_13972/12_2024/7qhh_13972.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qhh_13972/12_2024/7qhh_13972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qhh_13972/12_2024/7qhh_13972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qhh_13972/12_2024/7qhh_13972.map" model { file = "/net/cci-nas-00/data/ceres_data/7qhh_13972/12_2024/7qhh_13972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qhh_13972/12_2024/7qhh_13972.cif" } resolution = 3.6 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= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8884 2.51 5 N 2202 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13626 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2682 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 17, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 223 Chain: "B" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2691 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Chain: "C" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2682 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 17, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 223 Chain: "D" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2691 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Chain: "J" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1282 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "I" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1282 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'OLC': 1, 'PAM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'79N': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'OLC': 1, 'PAM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'79N': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PAM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PAM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.10, per 1000 atoms: 0.67 Number of scatterers: 13626 At special positions: 0 Unit cell: (124.02, 109.18, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2478 8.00 N 2202 7.00 C 8884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.04 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.06 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.06 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 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 22 sheets defined 57.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.715A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 591 through 626 removed outlier: 3.512A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.562A pdb=" N LYS A 671 " --> pdb=" O TRP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 738 through 753 removed outlier: 3.659A pdb=" N LEU A 747 " --> pdb=" O ASN A 743 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 767 Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.711A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.792A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.704A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.545A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.702A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 478 through 484 removed outlier: 3.715A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 582 Processing helix chain 'C' and resid 591 through 626 removed outlier: 3.512A pdb=" N VAL C 597 " --> pdb=" O SER C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 658 Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.561A pdb=" N LYS C 671 " --> pdb=" O TRP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 693 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 753 removed outlier: 3.659A pdb=" N LEU C 747 " --> pdb=" O ASN C 743 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 767 Processing helix chain 'C' and resid 788 through 815 removed outlier: 3.710A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.792A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.703A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.544A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.703A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 41 removed outlier: 3.554A pdb=" N VAL J 21 " --> pdb=" O LYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 128 Processing helix chain 'J' and resid 128 through 151 removed outlier: 3.652A pdb=" N ALA J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG J 149 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL J 150 " --> pdb=" O ALA J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 185 removed outlier: 3.579A pdb=" N LEU J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 234 removed outlier: 3.775A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 41 removed outlier: 3.555A pdb=" N VAL I 21 " --> pdb=" O LYS I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 128 through 151 removed outlier: 3.652A pdb=" N ALA I 146 " --> pdb=" O GLY I 142 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 185 removed outlier: 3.579A pdb=" N LEU I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 234 removed outlier: 3.775A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 394 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.012A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.012A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 395 through 398 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.917A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.917A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 391 through 394 Processing sheet with id=AB3, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB4, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB5, first strand: chain 'C' and resid 642 through 645 removed outlier: 6.013A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 642 through 645 removed outlier: 6.013A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 395 through 398 Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 5.917A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 5.917A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 100 through 102 Processing sheet with id=AC4, first strand: chain 'I' and resid 100 through 102 936 hydrogen bonds defined for protein. 2766 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: 4.88 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2224 1.32 - 1.45: 3822 1.45 - 1.57: 7764 1.57 - 1.70: 0 1.70 - 1.83: 90 Bond restraints: 13900 Sorted by residual: bond pdb=" C LYS A 726 " pdb=" O LYS A 726 " ideal model delta sigma weight residual 1.234 1.282 -0.048 1.26e-02 6.30e+03 1.45e+01 bond pdb=" C LYS C 726 " pdb=" O LYS C 726 " ideal model delta sigma weight residual 1.234 1.282 -0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" CA SER C 512 " pdb=" CB SER C 512 " ideal model delta sigma weight residual 1.532 1.472 0.060 1.65e-02 3.67e+03 1.33e+01 bond pdb=" N ILE A 485 " pdb=" CA ILE A 485 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" CA SER A 512 " pdb=" CB SER A 512 " ideal model delta sigma weight residual 1.532 1.472 0.060 1.65e-02 3.67e+03 1.31e+01 ... (remaining 13895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 9961 1.29 - 2.57: 5760 2.57 - 3.86: 2617 3.86 - 5.15: 579 5.15 - 6.43: 55 Bond angle restraints: 18972 Sorted by residual: angle pdb=" CA GLY B 465 " pdb=" C GLY B 465 " pdb=" O GLY B 465 " ideal model delta sigma weight residual 120.75 114.86 5.89 1.03e+00 9.43e-01 3.27e+01 angle pdb=" CA GLY D 465 " pdb=" C GLY D 465 " pdb=" O GLY D 465 " ideal model delta sigma weight residual 120.75 114.88 5.87 1.03e+00 9.43e-01 3.24e+01 angle pdb=" C VAL B 464 " pdb=" N GLY B 465 " pdb=" CA GLY B 465 " ideal model delta sigma weight residual 119.98 125.83 -5.85 1.11e+00 8.12e-01 2.78e+01 angle pdb=" C VAL D 464 " pdb=" N GLY D 465 " pdb=" CA GLY D 465 " ideal model delta sigma weight residual 119.98 125.82 -5.84 1.11e+00 8.12e-01 2.76e+01 angle pdb=" CA GLY C 495 " pdb=" C GLY C 495 " pdb=" O GLY C 495 " ideal model delta sigma weight residual 121.19 116.63 4.56 9.10e-01 1.21e+00 2.52e+01 ... (remaining 18967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 7674 25.86 - 51.72: 228 51.72 - 77.58: 26 77.58 - 103.45: 4 103.45 - 129.31: 4 Dihedral angle restraints: 7936 sinusoidal: 2280 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 156.94 -63.94 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" C24 OLC A 903 " pdb=" C21 OLC A 903 " pdb=" C22 OLC A 903 " pdb=" O20 OLC A 903 " ideal model delta sinusoidal sigma weight residual 182.78 53.47 129.31 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 7933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 966 0.060 - 0.119: 858 0.119 - 0.178: 362 0.178 - 0.238: 50 0.238 - 0.297: 10 Chirality restraints: 2246 Sorted by residual: chirality pdb=" CA VAL D 626 " pdb=" N VAL D 626 " pdb=" C VAL D 626 " pdb=" CB VAL D 626 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA VAL B 626 " pdb=" N VAL B 626 " pdb=" C VAL B 626 " pdb=" CB VAL B 626 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ILE C 587 " pdb=" N ILE C 587 " pdb=" C ILE C 587 " pdb=" CB ILE C 587 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2243 not shown) Planarity restraints: 2414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 79N D 902 " 0.138 2.00e-02 2.50e+03 1.40e-01 1.95e+02 pdb=" C7 79N D 902 " 0.141 2.00e-02 2.50e+03 pdb=" C8 79N D 902 " -0.148 2.00e-02 2.50e+03 pdb=" C9 79N D 902 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 79N B 902 " -0.137 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C7 79N B 902 " -0.141 2.00e-02 2.50e+03 pdb=" C8 79N B 902 " 0.148 2.00e-02 2.50e+03 pdb=" C9 79N B 902 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM I1502 " 0.143 2.00e-02 2.50e+03 1.09e-01 1.18e+02 pdb=" C11 PAM I1502 " -0.057 2.00e-02 2.50e+03 pdb=" C8 PAM I1502 " 0.057 2.00e-02 2.50e+03 pdb=" C9 PAM I1502 " -0.143 2.00e-02 2.50e+03 ... (remaining 2411 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 7267 3.02 - 3.49: 15140 3.49 - 3.96: 21572 3.96 - 4.43: 24524 4.43 - 4.90: 39208 Nonbonded interactions: 107711 Sorted by model distance: nonbonded pdb=" O TRP D 606 " pdb=" OG1 THR D 609 " model vdw 2.546 3.040 nonbonded pdb=" O TRP B 606 " pdb=" OG1 THR B 609 " model vdw 2.546 3.040 nonbonded pdb=" O GLN J 20 " pdb=" OG1 THR J 24 " model vdw 2.569 3.040 nonbonded pdb=" O GLN I 20 " pdb=" OG1 THR I 24 " model vdw 2.569 3.040 nonbonded pdb=" N ILE A 587 " pdb=" O ILE A 587 " model vdw 2.569 2.496 ... (remaining 107706 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 390 or resid 393 through 394 or (resid 395 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 400 or (resid 401 \ and (name N or name CA or name C or name O or name CB )) or resid 402 through 4 \ 03 or resid 405 through 407 or resid 412 through 414 or (resid 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 422 or (resid 4 \ 24 through 426 and (name N or name CA or name C or name O or name CB )) or resid \ 427 through 431 or resid 433 or resid 436 or resid 438 or resid 440 or (resid 4 \ 41 and (name N or name CA or name C or name O or name CB )) or (resid 443 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 444 through 446 and \ (name N or name CA or name C or name O or name CB )) or (resid 447 through 450 \ and (name N or name CA or name C or name O or name CB )) or (resid 452 through 4 \ 54 and (name N or name CA or name C or name O or name CB )) or (resid 456 throug \ h 460 and (name N or name CA or name C or name O or name CB )) or (resid 461 thr \ ough 465 and (name N or name CA or name C or name O or name CB )) or resid 466 o \ r resid 468 through 469 or resid 471 or resid 473 through 478 or (resid 479 thro \ ugh 486 and (name N or name CA or name C or name O or name CB )) or resid 487 th \ rough 540 or (resid 541 through 543 and (name N or name CA or name C or name O o \ r name CB )) or resid 544 through 545 or (resid 566 and (name N or name CA or na \ me C or name O or name CB )) or resid 567 through 568 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 581 or resid 5 \ 83 through 625 or (resid 626 and (name N or name CA or name C or name O or name \ CB )) or resid 627 through 633 or (resid 634 through 635 and (name N or name CA \ or name C or name O or name CB )) or resid 637 through 644 or (resid 645 and (na \ me N or name CA or name C or name O or name CB )) or resid 646 or resid 649 thro \ ugh 652 or (resid 653 and (name N or name CA or name C or name O or name CB )) o \ r resid 654 or (resid 655 through 659 and (name N or name CA or name C or name O \ or name CB )) or resid 660 through 661 or (resid 662 and (name N or name CA or \ name C or name O or name CB )) or resid 663 or (resid 665 through 668 and (name \ N or name CA or name C or name O or name CB )) or resid 669 through 670 or (resi \ d 672 through 674 and (name N or name CA or name C or name O or name CB )) or re \ sid 675 through 678 or (resid 679 through 680 and (name N or name CA or name C o \ r name O or name CB )) or resid 681 through 682 or (resid 684 and (name N or nam \ e CA or name C or name O or name CB )) or resid 685 or resid 688 through 698 or \ (resid 699 and (name N or name CA or name C or name O or name CB )) or resid 700 \ through 701 or (resid 702 and (name N or name CA or name C or name O or name CB \ )) or resid 703 through 707 or (resid 708 through 712 and (name N or name CA or \ name C or name O or name CB )) or resid 713 through 717 or (resid 718 and (name \ N or name CA or name C or name O or name CB )) or resid 719 through 722 or (res \ id 723 and (name N or name CA or name C or name O or name CB )) or resid 724 thr \ ough 735 or (resid 736 and (name N or name CA or name C or name O or name CB )) \ or resid 738 or resid 741 or (resid 742 through 752 and (name N or name CA or na \ me C or name O or name CB )) or resid 753 through 759 or resid 761 through 795 o \ r resid 797 through 815 or resid 901)) selection = (chain 'B' and ((resid 394 and (name N or name CA or name C or name O or name CB \ )) or resid 397 through 399 or (resid 400 through 402 and (name N or name CA or \ name C or name O or name CB )) or resid 404 through 407 or resid 409 through 41 \ 1 or resid 416 through 418 or resid 420 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )) or resid 423 through 426 or resid 428 \ through 434 or (resid 435 and (name N or name CA or name C or name O or name CB \ )) or resid 437 or resid 440 or (resid 442 and (name N or name CA or name C or \ name O or name CB )) or resid 444 through 445 or resid 447 through 454 or resid \ 456 through 458 or (resid 460 through 461 and (name N or name CA or name C or na \ me O or name CB )) or (resid 462 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 470 or resid 472 through 473 or resid 475 or resi \ d 477 through 478 or (resid 479 and (name N or name CA or name C or name O or na \ me CB )) or resid 480 or (resid 481 and (name N or name CA or name C or name O o \ r name CB )) or resid 482 through 483 or (resid 484 through 490 and (name N or n \ ame CA or name C or name O or name CB )) or resid 491 through 492 or (resid 493 \ and (name N or name CA or name C or name O or name CB )) or resid 494 through 50 \ 0 or (resid 501 through 503 and (name N or name CA or name C or name O or name C \ B )) or resid 504 through 545 or (resid 546 through 547 and (name N or name CA o \ r name C or name O or name CB )) or resid 548 through 585 or resid 587 through 6 \ 33 or (resid 634 and (name N or name CA or name C or name O or name CB )) or res \ id 635 through 638 or (resid 639 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 641 through 642 and (name N or name CA or name C or name O o \ r name CB )) or resid 643 through 650 or resid 653 through 654 or (resid 655 thr \ ough 657 and (name N or name CA or name C or name O or name CB )) or resid 658 t \ hrough 660 or (resid 661 through 663 and (name N or name CA or name C or name O \ or name CB )) or resid 664 through 667 or resid 669 through 674 or resid 676 thr \ ough 679 or (resid 680 through 681 and (name N or name CA or name C or name O or \ name CB )) or resid 682 through 685 or (resid 686 and (name N or name CA or nam \ e C or name O or name CB )) or resid 688 through 689 or resid 692 through 718 or \ (resid 719 through 722 and (name N or name CA or name C or name O or name CB )) \ or resid 723 through 725 or (resid 726 through 727 and (name N or name CA or na \ me C or name O or name CB )) or resid 728 through 729 or (resid 730 and (name N \ or name CA or name C or name O or name CB )) or resid 731 through 733 or (resid \ 734 through 736 and (name N or name CA or name C or name O or name CB )) or resi \ d 737 through 740 or resid 742 or resid 745 through 746 or (resid 747 through 75 \ 6 and (name N or name CA or name C or name O or name CB )) or (resid 757 through \ 763 and (name N or name CA or name C or name O or name CB )) or resid 765 throu \ gh 767 or (resid 768 through 770 and (name N or name CA or name C or name O or n \ ame CB )) or resid 771 through 774 or resid 777 through 781 or resid 784 through \ 799 or resid 801 through 813 or (resid 814 and (name N or name CA or name C or \ name O or name CB )) or resid 815 through 817 or (resid 818 through 819 and (nam \ e N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'C' and (resid 390 or resid 393 through 394 or (resid 395 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 400 or (resid 401 \ and (name N or name CA or name C or name O or name CB )) or resid 402 through 4 \ 03 or resid 405 through 407 or resid 412 through 414 or (resid 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 422 or (resid 4 \ 24 through 426 and (name N or name CA or name C or name O or name CB )) or resid \ 427 through 431 or resid 433 or resid 436 or resid 438 or resid 440 or (resid 4 \ 41 and (name N or name CA or name C or name O or name CB )) or (resid 443 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 444 through 446 and \ (name N or name CA or name C or name O or name CB )) or (resid 447 through 450 \ and (name N or name CA or name C or name O or name CB )) or (resid 452 through 4 \ 54 and (name N or name CA or name C or name O or name CB )) or (resid 456 throug \ h 460 and (name N or name CA or name C or name O or name CB )) or (resid 461 thr \ ough 465 and (name N or name CA or name C or name O or name CB )) or resid 466 o \ r resid 468 through 469 or resid 471 or resid 473 through 478 or (resid 479 thro \ ugh 486 and (name N or name CA or name C or name O or name CB )) or resid 487 th \ rough 540 or (resid 541 through 543 and (name N or name CA or name C or name O o \ r name CB )) or resid 544 through 545 or (resid 566 and (name N or name CA or na \ me C or name O or name CB )) or resid 567 through 568 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 581 or resid 5 \ 83 through 625 or (resid 626 and (name N or name CA or name C or name O or name \ CB )) or resid 627 through 633 or (resid 634 through 635 and (name N or name CA \ or name C or name O or name CB )) or resid 637 through 644 or (resid 645 and (na \ me N or name CA or name C or name O or name CB )) or resid 646 or resid 649 thro \ ugh 652 or (resid 653 and (name N or name CA or name C or name O or name CB )) o \ r resid 654 or (resid 655 through 659 and (name N or name CA or name C or name O \ or name CB )) or resid 660 through 661 or (resid 662 and (name N or name CA or \ name C or name O or name CB )) or resid 663 or (resid 665 through 668 and (name \ N or name CA or name C or name O or name CB )) or resid 669 through 670 or (resi \ d 672 through 674 and (name N or name CA or name C or name O or name CB )) or re \ sid 675 through 678 or (resid 679 through 680 and (name N or name CA or name C o \ r name O or name CB )) or resid 681 through 682 or (resid 684 and (name N or nam \ e CA or name C or name O or name CB )) or resid 685 or resid 688 through 698 or \ (resid 699 and (name N or name CA or name C or name O or name CB )) or resid 700 \ through 701 or (resid 702 and (name N or name CA or name C or name O or name CB \ )) or resid 703 through 707 or (resid 708 through 712 and (name N or name CA or \ name C or name O or name CB )) or resid 713 through 717 or (resid 718 and (name \ N or name CA or name C or name O or name CB )) or resid 719 through 722 or (res \ id 723 and (name N or name CA or name C or name O or name CB )) or resid 724 thr \ ough 735 or (resid 736 and (name N or name CA or name C or name O or name CB )) \ or resid 738 or resid 741 or (resid 742 through 752 and (name N or name CA or na \ me C or name O or name CB )) or resid 753 through 759 or resid 761 through 795 o \ r resid 797 through 815 or resid 901)) selection = (chain 'D' and ((resid 394 and (name N or name CA or name C or name O or name CB \ )) or resid 397 through 399 or (resid 400 through 402 and (name N or name CA or \ name C or name O or name CB )) or resid 404 through 407 or resid 409 through 41 \ 1 or resid 416 through 418 or resid 420 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )) or resid 423 through 426 or resid 428 \ through 434 or (resid 435 and (name N or name CA or name C or name O or name CB \ )) or resid 437 or resid 440 or (resid 442 and (name N or name CA or name C or \ name O or name CB )) or resid 444 through 445 or resid 447 through 454 or resid \ 456 through 458 or (resid 460 through 461 and (name N or name CA or name C or na \ me O or name CB )) or (resid 462 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 470 or resid 472 through 473 or resid 475 or resi \ d 477 through 478 or (resid 479 and (name N or name CA or name C or name O or na \ me CB )) or resid 480 or (resid 481 and (name N or name CA or name C or name O o \ r name CB )) or resid 482 through 483 or (resid 484 through 490 and (name N or n \ ame CA or name C or name O or name CB )) or resid 491 through 492 or (resid 493 \ and (name N or name CA or name C or name O or name CB )) or resid 494 through 50 \ 0 or (resid 501 through 503 and (name N or name CA or name C or name O or name C \ B )) or resid 504 through 545 or (resid 546 through 547 and (name N or name CA o \ r name C or name O or name CB )) or resid 548 through 585 or resid 587 through 6 \ 33 or (resid 634 and (name N or name CA or name C or name O or name CB )) or res \ id 635 through 638 or (resid 639 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 641 through 642 and (name N or name CA or name C or name O o \ r name CB )) or resid 643 through 650 or resid 653 through 654 or (resid 655 thr \ ough 657 and (name N or name CA or name C or name O or name CB )) or resid 658 t \ hrough 660 or (resid 661 through 663 and (name N or name CA or name C or name O \ or name CB )) or resid 664 through 667 or resid 669 through 674 or resid 676 thr \ ough 679 or (resid 680 through 681 and (name N or name CA or name C or name O or \ name CB )) or resid 682 through 685 or (resid 686 and (name N or name CA or nam \ e C or name O or name CB )) or resid 688 through 689 or resid 692 through 718 or \ (resid 719 through 722 and (name N or name CA or name C or name O or name CB )) \ or resid 723 through 725 or (resid 726 through 727 and (name N or name CA or na \ me C or name O or name CB )) or resid 728 through 729 or (resid 730 and (name N \ or name CA or name C or name O or name CB )) or resid 731 through 733 or (resid \ 734 through 736 and (name N or name CA or name C or name O or name CB )) or resi \ d 737 through 740 or resid 742 or resid 745 through 746 or (resid 747 through 75 \ 6 and (name N or name CA or name C or name O or name CB )) or (resid 757 through \ 763 and (name N or name CA or name C or name O or name CB )) or resid 765 throu \ gh 767 or (resid 768 through 770 and (name N or name CA or name C or name O or n \ ame CB )) or resid 771 through 774 or resid 777 through 781 or resid 784 through \ 799 or resid 801 through 813 or (resid 814 and (name N or name CA or name C or \ name O or name CB )) or resid 815 through 817 or (resid 818 through 819 and (nam \ e N or name CA or name C or name O or name CB )) or resid 901)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 1.800 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 35.280 Find NCS groups from input model: 0.980 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: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.014 0.060 13900 Z= 0.946 Angle : 1.829 6.433 18972 Z= 1.429 Chirality : 0.090 0.297 2246 Planarity : 0.010 0.140 2414 Dihedral : 13.085 129.307 4300 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.59 % Rotamer: Outliers : 0.19 % Allowed : 2.64 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: -0.83 (0.17), residues: 1942 helix: -0.13 (0.14), residues: 1094 sheet: -0.52 (0.39), residues: 168 loop : -1.05 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP B 766 HIS 0.004 0.002 HIS J 198 PHE 0.036 0.005 PHE A 537 TYR 0.046 0.006 TYR B 732 ARG 0.014 0.001 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 THR cc_start: 0.6900 (p) cc_final: 0.6577 (t) REVERT: A 581 MET cc_start: 0.8199 (mmt) cc_final: 0.7845 (mmt) REVERT: A 646 LEU cc_start: 0.8022 (tp) cc_final: 0.7560 (mt) REVERT: A 663 PHE cc_start: 0.8822 (m-80) cc_final: 0.8581 (m-80) REVERT: A 678 PHE cc_start: 0.7432 (m-80) cc_final: 0.7151 (m-80) REVERT: A 705 ASN cc_start: 0.7677 (t0) cc_final: 0.6989 (t0) REVERT: B 661 ARG cc_start: 0.8634 (ptt180) cc_final: 0.8370 (ptt90) REVERT: B 704 LEU cc_start: 0.8572 (pt) cc_final: 0.8111 (tp) REVERT: B 764 ASN cc_start: 0.7113 (m-40) cc_final: 0.6598 (m-40) REVERT: B 769 ASP cc_start: 0.8477 (m-30) cc_final: 0.7694 (m-30) REVERT: C 416 ARG cc_start: 0.6802 (ttp-170) cc_final: 0.5770 (tpt90) REVERT: C 478 THR cc_start: 0.6917 (p) cc_final: 0.6598 (t) REVERT: C 581 MET cc_start: 0.8198 (mmt) cc_final: 0.7857 (mmt) REVERT: C 646 LEU cc_start: 0.8087 (tp) cc_final: 0.7656 (mt) REVERT: C 663 PHE cc_start: 0.8807 (m-80) cc_final: 0.8558 (m-80) REVERT: C 678 PHE cc_start: 0.7512 (m-80) cc_final: 0.7199 (m-80) REVERT: C 705 ASN cc_start: 0.7573 (t0) cc_final: 0.6767 (t0) REVERT: D 661 ARG cc_start: 0.8645 (ptt180) cc_final: 0.8440 (ptt90) REVERT: D 704 LEU cc_start: 0.8567 (pt) cc_final: 0.8080 (tp) REVERT: D 764 ASN cc_start: 0.7028 (m-40) cc_final: 0.6542 (m-40) REVERT: D 769 ASP cc_start: 0.8467 (m-30) cc_final: 0.7707 (m-30) outliers start: 2 outliers final: 0 residues processed: 374 average time/residue: 0.2872 time to fit residues: 152.8271 Evaluate side-chains 243 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 HIS I 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13900 Z= 0.198 Angle : 0.512 7.257 18972 Z= 0.277 Chirality : 0.040 0.145 2246 Planarity : 0.004 0.039 2414 Dihedral : 9.200 70.961 2300 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 1.60 % Allowed : 12.36 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 2.09 (0.19), residues: 1942 helix: 2.77 (0.15), residues: 1122 sheet: -0.49 (0.39), residues: 174 loop : -0.62 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 766 HIS 0.006 0.002 HIS J 198 PHE 0.014 0.001 PHE A 527 TYR 0.019 0.002 TYR D 768 ARG 0.002 0.000 ARG I 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 273 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 THR cc_start: 0.3595 (t) cc_final: 0.3380 (m) REVERT: A 415 ASP cc_start: 0.7294 (m-30) cc_final: 0.7091 (t0) REVERT: A 646 LEU cc_start: 0.7884 (tp) cc_final: 0.7462 (mt) REVERT: A 663 PHE cc_start: 0.8772 (m-80) cc_final: 0.8507 (m-80) REVERT: A 678 PHE cc_start: 0.7901 (m-80) cc_final: 0.7598 (m-80) REVERT: B 661 ARG cc_start: 0.8600 (ptt180) cc_final: 0.8357 (ppt90) REVERT: B 694 ARG cc_start: 0.8271 (mtt90) cc_final: 0.7969 (mtt90) REVERT: B 813 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6821 (mm-30) REVERT: C 416 ARG cc_start: 0.6760 (ttp-170) cc_final: 0.5869 (tpt90) REVERT: C 646 LEU cc_start: 0.7917 (tp) cc_final: 0.7493 (mt) REVERT: C 663 PHE cc_start: 0.8765 (m-80) cc_final: 0.8481 (m-80) REVERT: C 678 PHE cc_start: 0.7859 (m-80) cc_final: 0.7554 (m-80) REVERT: D 460 TRP cc_start: 0.7407 (m-90) cc_final: 0.7145 (m-90) REVERT: D 661 ARG cc_start: 0.8650 (ptt180) cc_final: 0.8416 (ptt90) REVERT: D 694 ARG cc_start: 0.8295 (mtt90) cc_final: 0.8016 (ttm110) REVERT: D 813 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6821 (mm-30) REVERT: J 231 ARG cc_start: 0.6906 (tpm170) cc_final: 0.6478 (tpp-160) REVERT: I 231 ARG cc_start: 0.6859 (tpm170) cc_final: 0.6488 (tpp-160) outliers start: 17 outliers final: 7 residues processed: 284 average time/residue: 0.2480 time to fit residues: 103.5207 Evaluate side-chains 254 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 247 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13900 Z= 0.250 Angle : 0.495 7.699 18972 Z= 0.261 Chirality : 0.040 0.148 2246 Planarity : 0.004 0.042 2414 Dihedral : 8.090 58.919 2300 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.36 % Allowed : 14.34 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 2.24 (0.19), residues: 1942 helix: 2.95 (0.15), residues: 1128 sheet: -1.12 (0.35), residues: 204 loop : -0.44 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 766 HIS 0.002 0.001 HIS I 105 PHE 0.019 0.002 PHE I 165 TYR 0.018 0.002 TYR B 816 ARG 0.002 0.000 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 1.423 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 646 LEU cc_start: 0.7854 (tp) cc_final: 0.7473 (mt) REVERT: A 678 PHE cc_start: 0.7924 (m-80) cc_final: 0.7604 (m-80) REVERT: B 408 MET cc_start: 0.6039 (mmt) cc_final: 0.5789 (mmp) REVERT: B 661 ARG cc_start: 0.8436 (ptt180) cc_final: 0.8217 (ptt90) REVERT: B 767 TRP cc_start: 0.7340 (m-90) cc_final: 0.6988 (m-90) REVERT: B 813 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6939 (mm-30) REVERT: C 416 ARG cc_start: 0.6603 (ttp-170) cc_final: 0.5756 (tpt90) REVERT: C 646 LEU cc_start: 0.7894 (tp) cc_final: 0.7511 (mt) REVERT: C 678 PHE cc_start: 0.7899 (m-80) cc_final: 0.7555 (m-80) REVERT: D 460 TRP cc_start: 0.7494 (m-90) cc_final: 0.7251 (m-90) REVERT: D 661 ARG cc_start: 0.8495 (ptt180) cc_final: 0.8253 (ptt90) REVERT: D 694 ARG cc_start: 0.8284 (mtt90) cc_final: 0.8023 (ttm110) REVERT: D 767 TRP cc_start: 0.7415 (m-90) cc_final: 0.7176 (m-90) REVERT: D 813 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6990 (mm-30) REVERT: J 231 ARG cc_start: 0.6585 (tpm170) cc_final: 0.6270 (tpp-160) REVERT: I 231 ARG cc_start: 0.6580 (tpm170) cc_final: 0.6262 (tpp-160) outliers start: 25 outliers final: 23 residues processed: 279 average time/residue: 0.2473 time to fit residues: 101.7552 Evaluate side-chains 264 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 164 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 85 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13900 Z= 0.267 Angle : 0.499 7.721 18972 Z= 0.262 Chirality : 0.040 0.148 2246 Planarity : 0.004 0.044 2414 Dihedral : 7.824 58.518 2300 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.40 % Allowed : 14.91 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 2.03 (0.19), residues: 1942 helix: 2.77 (0.15), residues: 1136 sheet: -1.30 (0.36), residues: 192 loop : -0.53 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 762 HIS 0.003 0.001 HIS J 83 PHE 0.026 0.002 PHE J 165 TYR 0.028 0.001 TYR I 226 ARG 0.001 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LEU cc_start: 0.7913 (tp) cc_final: 0.7482 (mt) REVERT: A 663 PHE cc_start: 0.8777 (m-80) cc_final: 0.8531 (m-80) REVERT: A 678 PHE cc_start: 0.7937 (m-80) cc_final: 0.7637 (m-80) REVERT: A 808 ILE cc_start: 0.8316 (mm) cc_final: 0.8023 (mt) REVERT: B 408 MET cc_start: 0.6076 (mmt) cc_final: 0.5781 (mmp) REVERT: B 661 ARG cc_start: 0.8331 (ptt180) cc_final: 0.8123 (ptt90) REVERT: B 813 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6995 (mm-30) REVERT: C 416 ARG cc_start: 0.6641 (ttp-170) cc_final: 0.5786 (tpt90) REVERT: C 646 LEU cc_start: 0.7879 (tp) cc_final: 0.7526 (mt) REVERT: C 663 PHE cc_start: 0.8752 (m-80) cc_final: 0.8497 (m-80) REVERT: C 678 PHE cc_start: 0.7892 (m-80) cc_final: 0.7603 (m-80) REVERT: C 808 ILE cc_start: 0.8378 (mm) cc_final: 0.8111 (mt) REVERT: D 460 TRP cc_start: 0.7584 (m-90) cc_final: 0.7311 (m-90) REVERT: D 661 ARG cc_start: 0.8328 (ptt180) cc_final: 0.8037 (pmt170) REVERT: D 813 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7041 (mm-30) outliers start: 36 outliers final: 21 residues processed: 272 average time/residue: 0.2337 time to fit residues: 95.5389 Evaluate side-chains 257 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 164 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.2980 chunk 107 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 141 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 96 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13900 Z= 0.295 Angle : 0.517 9.258 18972 Z= 0.268 Chirality : 0.040 0.149 2246 Planarity : 0.003 0.046 2414 Dihedral : 7.757 58.520 2300 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.77 % Allowed : 15.75 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.89 (0.19), residues: 1942 helix: 2.62 (0.15), residues: 1142 sheet: -1.54 (0.36), residues: 182 loop : -0.48 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 763 HIS 0.004 0.001 HIS I 83 PHE 0.018 0.002 PHE I 165 TYR 0.031 0.001 TYR J 226 ARG 0.002 0.000 ARG I 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8490 (m) cc_final: 0.8160 (t) REVERT: A 646 LEU cc_start: 0.7925 (tp) cc_final: 0.7512 (mt) REVERT: A 663 PHE cc_start: 0.8736 (m-80) cc_final: 0.8479 (m-80) REVERT: A 678 PHE cc_start: 0.7932 (m-80) cc_final: 0.7671 (m-80) REVERT: A 762 TRP cc_start: 0.7562 (m100) cc_final: 0.7010 (m-10) REVERT: A 808 ILE cc_start: 0.8345 (mm) cc_final: 0.8057 (mt) REVERT: B 460 TRP cc_start: 0.7810 (m-90) cc_final: 0.7403 (m-90) REVERT: B 813 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7051 (mm-30) REVERT: C 415 ASP cc_start: 0.7853 (m-30) cc_final: 0.7511 (p0) REVERT: C 416 ARG cc_start: 0.6747 (ttp-170) cc_final: 0.5956 (tpt90) REVERT: C 572 SER cc_start: 0.8481 (m) cc_final: 0.8156 (t) REVERT: C 646 LEU cc_start: 0.7943 (tp) cc_final: 0.7560 (mt) REVERT: C 663 PHE cc_start: 0.8720 (m-80) cc_final: 0.8456 (m-80) REVERT: C 678 PHE cc_start: 0.7964 (m-80) cc_final: 0.7654 (m-80) REVERT: C 762 TRP cc_start: 0.7808 (m100) cc_final: 0.7504 (m100) REVERT: D 408 MET cc_start: 0.6348 (mmt) cc_final: 0.6090 (mmp) REVERT: D 661 ARG cc_start: 0.8267 (ptt180) cc_final: 0.8063 (pmt170) REVERT: D 813 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7046 (mm-30) outliers start: 40 outliers final: 28 residues processed: 275 average time/residue: 0.2365 time to fit residues: 98.3311 Evaluate side-chains 274 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 46 optimal weight: 0.0370 chunk 189 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13900 Z= 0.192 Angle : 0.500 7.675 18972 Z= 0.254 Chirality : 0.039 0.129 2246 Planarity : 0.003 0.048 2414 Dihedral : 7.134 56.231 2300 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.17 % Allowed : 18.30 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 2.07 (0.19), residues: 1942 helix: 2.78 (0.15), residues: 1134 sheet: -1.56 (0.36), residues: 182 loop : -0.37 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 766 HIS 0.002 0.001 HIS I 83 PHE 0.013 0.001 PHE I 165 TYR 0.029 0.001 TYR J 226 ARG 0.005 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 1.525 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 646 LEU cc_start: 0.7873 (tp) cc_final: 0.7485 (mt) REVERT: A 663 PHE cc_start: 0.8780 (m-80) cc_final: 0.8547 (m-80) REVERT: A 678 PHE cc_start: 0.7952 (m-80) cc_final: 0.7695 (m-80) REVERT: A 762 TRP cc_start: 0.7599 (m100) cc_final: 0.7036 (m-10) REVERT: A 808 ILE cc_start: 0.8380 (mm) cc_final: 0.8102 (mt) REVERT: B 408 MET cc_start: 0.6498 (mmt) cc_final: 0.6200 (mmp) REVERT: B 460 TRP cc_start: 0.7688 (m-90) cc_final: 0.7251 (m-90) REVERT: B 813 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6966 (mm-30) REVERT: C 415 ASP cc_start: 0.7828 (m-30) cc_final: 0.7486 (p0) REVERT: C 416 ARG cc_start: 0.6774 (ttp-170) cc_final: 0.5999 (tpt90) REVERT: C 646 LEU cc_start: 0.7881 (tp) cc_final: 0.7544 (mt) REVERT: C 663 PHE cc_start: 0.8754 (m-80) cc_final: 0.8526 (m-80) REVERT: C 678 PHE cc_start: 0.7959 (m-80) cc_final: 0.7674 (m-80) REVERT: C 762 TRP cc_start: 0.7764 (m100) cc_final: 0.7483 (m100) REVERT: C 808 ILE cc_start: 0.8430 (mm) cc_final: 0.8174 (mt) REVERT: D 460 TRP cc_start: 0.7792 (m-90) cc_final: 0.7478 (m-90) REVERT: D 661 ARG cc_start: 0.8254 (ptt180) cc_final: 0.8053 (pmt170) REVERT: D 813 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7023 (mm-30) outliers start: 23 outliers final: 21 residues processed: 261 average time/residue: 0.2389 time to fit residues: 94.9097 Evaluate side-chains 260 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.0070 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 0.0870 chunk 188 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13900 Z= 0.227 Angle : 0.511 7.743 18972 Z= 0.258 Chirality : 0.039 0.189 2246 Planarity : 0.003 0.047 2414 Dihedral : 6.800 55.700 2300 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.21 % Allowed : 18.40 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.19), residues: 1942 helix: 2.73 (0.15), residues: 1134 sheet: -1.27 (0.39), residues: 164 loop : -0.47 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 766 HIS 0.002 0.001 HIS I 83 PHE 0.017 0.001 PHE I 165 TYR 0.033 0.001 TYR J 226 ARG 0.005 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.7943 (m-30) cc_final: 0.7555 (p0) REVERT: A 572 SER cc_start: 0.8453 (m) cc_final: 0.8141 (t) REVERT: A 646 LEU cc_start: 0.7902 (tp) cc_final: 0.7514 (mt) REVERT: A 663 PHE cc_start: 0.8728 (m-80) cc_final: 0.8488 (m-80) REVERT: A 678 PHE cc_start: 0.7985 (m-80) cc_final: 0.7685 (m-80) REVERT: A 762 TRP cc_start: 0.7661 (m100) cc_final: 0.7054 (m-10) REVERT: A 808 ILE cc_start: 0.8383 (mm) cc_final: 0.8112 (mt) REVERT: B 408 MET cc_start: 0.6414 (mmt) cc_final: 0.6209 (mmp) REVERT: B 422 GLU cc_start: 0.6968 (pm20) cc_final: 0.6724 (pm20) REVERT: B 767 TRP cc_start: 0.7155 (m-90) cc_final: 0.6710 (t-100) REVERT: B 813 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7022 (mm-30) REVERT: C 415 ASP cc_start: 0.7855 (m-30) cc_final: 0.7480 (p0) REVERT: C 416 ARG cc_start: 0.6729 (ttp-170) cc_final: 0.5938 (tpt90) REVERT: C 572 SER cc_start: 0.8431 (m) cc_final: 0.8144 (t) REVERT: C 646 LEU cc_start: 0.7905 (tp) cc_final: 0.7566 (mt) REVERT: C 663 PHE cc_start: 0.8719 (m-80) cc_final: 0.8487 (m-80) REVERT: C 678 PHE cc_start: 0.7999 (m-80) cc_final: 0.7713 (m-80) REVERT: C 762 TRP cc_start: 0.7746 (m100) cc_final: 0.7472 (m100) REVERT: C 808 ILE cc_start: 0.8447 (mm) cc_final: 0.8187 (mt) REVERT: D 460 TRP cc_start: 0.7764 (m-90) cc_final: 0.7431 (m-90) REVERT: D 767 TRP cc_start: 0.7172 (m-90) cc_final: 0.6835 (t-100) REVERT: D 813 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7027 (mm-30) outliers start: 34 outliers final: 26 residues processed: 271 average time/residue: 0.2421 time to fit residues: 99.8257 Evaluate side-chains 268 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 40.0000 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 120 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 93 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 148 optimal weight: 10.0000 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13900 Z= 0.165 Angle : 0.509 8.624 18972 Z= 0.257 Chirality : 0.039 0.182 2246 Planarity : 0.003 0.048 2414 Dihedral : 6.392 53.361 2300 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.92 % Allowed : 18.68 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 2.12 (0.19), residues: 1942 helix: 2.80 (0.15), residues: 1136 sheet: -1.29 (0.38), residues: 164 loop : -0.44 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 766 HIS 0.002 0.001 HIS J 105 PHE 0.013 0.001 PHE J 130 TYR 0.029 0.001 TYR I 226 ARG 0.008 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.7951 (m-30) cc_final: 0.7531 (p0) REVERT: A 646 LEU cc_start: 0.7860 (tp) cc_final: 0.7490 (mt) REVERT: A 663 PHE cc_start: 0.8728 (m-80) cc_final: 0.8485 (m-80) REVERT: A 678 PHE cc_start: 0.8006 (m-80) cc_final: 0.7739 (m-80) REVERT: A 762 TRP cc_start: 0.7638 (m100) cc_final: 0.7076 (m-10) REVERT: A 808 ILE cc_start: 0.8367 (mm) cc_final: 0.8100 (mt) REVERT: B 460 TRP cc_start: 0.7751 (m-90) cc_final: 0.7339 (m-90) REVERT: B 813 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6985 (mm-30) REVERT: C 415 ASP cc_start: 0.7790 (m-30) cc_final: 0.7458 (p0) REVERT: C 416 ARG cc_start: 0.6729 (ttp-170) cc_final: 0.5980 (tpt90) REVERT: C 646 LEU cc_start: 0.7869 (tp) cc_final: 0.7564 (mt) REVERT: C 663 PHE cc_start: 0.8719 (m-80) cc_final: 0.8476 (m-80) REVERT: C 678 PHE cc_start: 0.7992 (m-80) cc_final: 0.7722 (m-80) REVERT: C 762 TRP cc_start: 0.7726 (m100) cc_final: 0.7510 (m100) REVERT: C 808 ILE cc_start: 0.8384 (mm) cc_final: 0.8128 (mt) REVERT: D 460 TRP cc_start: 0.7761 (m-90) cc_final: 0.7493 (m-90) REVERT: D 767 TRP cc_start: 0.7170 (m-90) cc_final: 0.6799 (t-100) REVERT: D 813 GLU cc_start: 0.7266 (mm-30) cc_final: 0.7003 (mm-30) outliers start: 31 outliers final: 25 residues processed: 272 average time/residue: 0.2345 time to fit residues: 96.9615 Evaluate side-chains 263 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13900 Z= 0.218 Angle : 0.547 10.592 18972 Z= 0.269 Chirality : 0.040 0.204 2246 Planarity : 0.004 0.048 2414 Dihedral : 6.490 55.163 2300 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.45 % Allowed : 19.25 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 2.05 (0.19), residues: 1942 helix: 2.73 (0.15), residues: 1136 sheet: -1.32 (0.38), residues: 164 loop : -0.44 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 766 HIS 0.002 0.001 HIS I 105 PHE 0.045 0.001 PHE I 165 TYR 0.029 0.001 TYR J 226 ARG 0.007 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.7950 (m-30) cc_final: 0.7498 (p0) REVERT: A 646 LEU cc_start: 0.7894 (tp) cc_final: 0.7509 (mt) REVERT: A 663 PHE cc_start: 0.8726 (m-80) cc_final: 0.8505 (m-80) REVERT: A 678 PHE cc_start: 0.8011 (m-80) cc_final: 0.7723 (m-80) REVERT: A 762 TRP cc_start: 0.7657 (m100) cc_final: 0.7084 (m-10) REVERT: A 808 ILE cc_start: 0.8364 (mm) cc_final: 0.8101 (mt) REVERT: B 460 TRP cc_start: 0.7710 (m-90) cc_final: 0.7354 (m-90) REVERT: B 767 TRP cc_start: 0.7083 (m-90) cc_final: 0.6569 (t-100) REVERT: B 813 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7011 (mm-30) REVERT: C 415 ASP cc_start: 0.7808 (m-30) cc_final: 0.7459 (p0) REVERT: C 416 ARG cc_start: 0.6800 (ttp-170) cc_final: 0.6033 (tpt90) REVERT: C 646 LEU cc_start: 0.7908 (tp) cc_final: 0.7581 (mt) REVERT: C 663 PHE cc_start: 0.8714 (m-80) cc_final: 0.8499 (m-80) REVERT: C 678 PHE cc_start: 0.8014 (m-80) cc_final: 0.7742 (m-80) REVERT: C 762 TRP cc_start: 0.7732 (m100) cc_final: 0.7514 (m100) REVERT: C 808 ILE cc_start: 0.8439 (mm) cc_final: 0.8190 (mt) REVERT: D 460 TRP cc_start: 0.7780 (m-90) cc_final: 0.7511 (m-90) REVERT: D 767 TRP cc_start: 0.7044 (m-90) cc_final: 0.6684 (t-100) REVERT: D 813 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7027 (mm-30) outliers start: 26 outliers final: 23 residues processed: 265 average time/residue: 0.2332 time to fit residues: 94.3151 Evaluate side-chains 265 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 95 optimal weight: 0.4980 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13900 Z= 0.434 Angle : 0.647 10.924 18972 Z= 0.319 Chirality : 0.043 0.186 2246 Planarity : 0.004 0.048 2414 Dihedral : 7.501 58.050 2300 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.02 % Allowed : 19.34 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.71 (0.19), residues: 1942 helix: 2.42 (0.15), residues: 1130 sheet: -1.11 (0.39), residues: 168 loop : -0.58 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 766 HIS 0.005 0.002 HIS I 83 PHE 0.047 0.002 PHE J 165 TYR 0.032 0.002 TYR J 226 ARG 0.012 0.001 ARG D 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.7948 (m-30) cc_final: 0.7490 (p0) REVERT: A 646 LEU cc_start: 0.7983 (tp) cc_final: 0.7538 (mt) REVERT: A 663 PHE cc_start: 0.8727 (m-80) cc_final: 0.8481 (m-80) REVERT: A 678 PHE cc_start: 0.7889 (m-80) cc_final: 0.7620 (m-80) REVERT: B 460 TRP cc_start: 0.7707 (m-90) cc_final: 0.7400 (m-90) REVERT: B 767 TRP cc_start: 0.7204 (m-90) cc_final: 0.6786 (t-100) REVERT: B 813 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7067 (mm-30) REVERT: C 415 ASP cc_start: 0.7830 (m-30) cc_final: 0.7461 (p0) REVERT: C 416 ARG cc_start: 0.6872 (ttp-170) cc_final: 0.6031 (tpt90) REVERT: C 646 LEU cc_start: 0.8050 (tp) cc_final: 0.7623 (mt) REVERT: C 663 PHE cc_start: 0.8728 (m-80) cc_final: 0.8494 (m-80) REVERT: C 678 PHE cc_start: 0.7931 (m-80) cc_final: 0.7665 (m-80) REVERT: C 762 TRP cc_start: 0.7755 (m100) cc_final: 0.7525 (m100) REVERT: D 460 TRP cc_start: 0.7746 (m-90) cc_final: 0.7532 (m-90) REVERT: D 767 TRP cc_start: 0.7203 (m-90) cc_final: 0.6871 (t-100) outliers start: 32 outliers final: 29 residues processed: 266 average time/residue: 0.2386 time to fit residues: 95.4593 Evaluate side-chains 265 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 143 optimal weight: 0.0030 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN ** C 705 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 = 0.4473 r_free = 0.4473 target = 0.202037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156602 restraints weight = 20224.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145534 restraints weight = 25872.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.146302 restraints weight = 23786.053| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13900 Z= 0.278 Angle : 0.601 10.879 18972 Z= 0.295 Chirality : 0.041 0.193 2246 Planarity : 0.004 0.047 2414 Dihedral : 7.069 56.721 2300 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.55 % Allowed : 20.38 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.75 (0.19), residues: 1942 helix: 2.45 (0.15), residues: 1134 sheet: -1.31 (0.39), residues: 160 loop : -0.52 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 766 HIS 0.002 0.001 HIS J 105 PHE 0.050 0.002 PHE J 165 TYR 0.052 0.002 TYR J 179 ARG 0.004 0.000 ARG B 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2728.69 seconds wall clock time: 50 minutes 39.09 seconds (3039.09 seconds total)