Starting phenix.real_space_refine on Thu Jun 12 13:07:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qhh_13972/06_2025/7qhh_13972.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qhh_13972/06_2025/7qhh_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_13972/06_2025/7qhh_13972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qhh_13972/06_2025/7qhh_13972.map" model { file = "/net/cci-nas-00/data/ceres_data/7qhh_13972/06_2025/7qhh_13972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qhh_13972/06_2025/7qhh_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.28, per 1000 atoms: 0.75 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: 4.12 Conformation dependent library (CDL) restraints added in 2.0 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: 1.73 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: 5.24 Time building geometry restraints manager: 4.53 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 38.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.040 ------------------------------------------------------------------------------- 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 13908 Z= 1.066 Angle : 1.829 6.433 18988 Z= 1.428 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 Details of bonding type rmsd hydrogen bonds : bond 0.18419 ( 920) hydrogen bonds : angle 7.05859 ( 2766) SS BOND : bond 0.01315 ( 8) SS BOND : angle 1.95171 ( 16) covalent geometry : bond 0.01402 (13900) covalent geometry : angle 1.82936 (18972) *********************** 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 : 1.545 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: 0.2604 time to fit residues: 139.2544 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 : 1.516 ------------------------------------------------------------------------------- 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: 4.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.205658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.168262 restraints weight = 20271.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156609 restraints weight = 25120.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154669 restraints weight = 25425.274| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 13908 Z= 0.135 Angle : 0.513 7.257 18988 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 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 920) hydrogen bonds : angle 4.23945 ( 2766) SS BOND : bond 0.00359 ( 8) SS BOND : angle 1.30335 ( 16) covalent geometry : bond 0.00293 (13900) covalent geometry : angle 0.51157 (18972) *********************** 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 : 1.384 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: 0.7486 (tp) cc_final: 0.7258 (mt) REVERT: B 813 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7455 (mm-30) REVERT: C 646 LEU cc_start: 0.7519 (tp) cc_final: 0.7290 (mt) REVERT: D 813 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7439 (mm-30) outliers start: 17 outliers final: 7 residues processed: 284 average time/residue: 0.2416 time to fit residues: 101.3292 Evaluate side-chains 249 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 242 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 118 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 140 optimal weight: 0.7980 chunk 120 optimal weight: 30.0000 chunk 169 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.200645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.161658 restraints weight = 20378.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154496 restraints weight = 26079.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150947 restraints weight = 27654.536| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13908 Z= 0.296 Angle : 0.604 8.057 18988 Z= 0.318 Chirality : 0.043 0.192 2246 Planarity : 0.004 0.042 2414 Dihedral : 9.159 57.679 2300 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.77 % Allowed : 14.06 % Favored : 82.17 % 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: 1.71 (0.19), residues: 1942 helix: 2.44 (0.15), residues: 1138 sheet: -1.16 (0.35), residues: 196 loop : -0.60 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 766 HIS 0.004 0.002 HIS J 83 PHE 0.026 0.002 PHE C 527 TYR 0.018 0.002 TYR I 201 ARG 0.004 0.001 ARG I 125 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 920) hydrogen bonds : angle 4.34211 ( 2766) SS BOND : bond 0.00421 ( 8) SS BOND : angle 1.18129 ( 16) covalent geometry : bond 0.00711 (13900) covalent geometry : angle 0.60378 (18972) *********************** 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 303 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8910 (m) cc_final: 0.8615 (t) REVERT: B 767 TRP cc_start: 0.6263 (m-90) cc_final: 0.5488 (m-90) REVERT: B 813 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7624 (mm-30) REVERT: C 572 SER cc_start: 0.8842 (m) cc_final: 0.8574 (t) REVERT: D 721 MET cc_start: 0.7432 (ptt) cc_final: 0.7210 (ptt) REVERT: D 813 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7657 (mm-30) outliers start: 40 outliers final: 29 residues processed: 288 average time/residue: 0.2164 time to fit residues: 96.0161 Evaluate side-chains 270 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 476 THR 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 24 THR 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 143 VAL Chi-restraints excluded: chain J residue 164 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 82 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 143 VAL 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 31 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 88 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 overall best weight: 4.6586 ------------------------------------------------------------------------------- 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** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 HIS ** 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 = 0.4422 r_free = 0.4422 target = 0.197156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.153931 restraints weight = 20276.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140869 restraints weight = 26081.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139949 restraints weight = 25535.712| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.090 13908 Z= 0.447 Angle : 0.728 8.695 18988 Z= 0.380 Chirality : 0.047 0.222 2246 Planarity : 0.004 0.044 2414 Dihedral : 9.779 58.687 2300 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.81 % Allowed : 16.79 % 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: 0.82 (0.19), residues: 1942 helix: 1.64 (0.15), residues: 1140 sheet: -1.66 (0.38), residues: 170 loop : -0.78 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP B 766 HIS 0.009 0.003 HIS J 83 PHE 0.025 0.003 PHE I 165 TYR 0.031 0.003 TYR J 226 ARG 0.005 0.001 ARG D 661 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 920) hydrogen bonds : angle 4.81865 ( 2766) SS BOND : bond 0.00578 ( 8) SS BOND : angle 1.29892 ( 16) covalent geometry : bond 0.01077 (13900) covalent geometry : angle 0.72691 (18972) *********************** 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 291 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7954 (tp) REVERT: B 408 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6479 (mmp) REVERT: C 646 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8003 (tp) REVERT: C 700 LEU cc_start: 0.8081 (pp) cc_final: 0.7838 (pt) REVERT: D 721 MET cc_start: 0.7897 (ptt) cc_final: 0.7626 (ptp) REVERT: D 767 TRP cc_start: 0.6658 (m-90) cc_final: 0.5684 (t-100) outliers start: 51 outliers final: 43 residues processed: 262 average time/residue: 0.2062 time to fit residues: 83.6478 Evaluate side-chains 280 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 GLU 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 646 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 708 MET 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 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 143 VAL 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 82 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 143 VAL 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 66 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 157 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 147 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 overall best weight: 3.6584 ------------------------------------------------------------------------------- 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 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.197459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.154175 restraints weight = 20339.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.148557 restraints weight = 27695.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146673 restraints weight = 23624.634| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 13908 Z= 0.356 Angle : 0.646 8.007 18988 Z= 0.338 Chirality : 0.044 0.219 2246 Planarity : 0.004 0.057 2414 Dihedral : 9.066 59.691 2300 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 5.57 % Allowed : 16.23 % Favored : 78.21 % 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: 0.89 (0.19), residues: 1942 helix: 1.75 (0.15), residues: 1138 sheet: -1.49 (0.41), residues: 148 loop : -0.96 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP B 766 HIS 0.004 0.002 HIS I 83 PHE 0.020 0.002 PHE A 580 TYR 0.033 0.002 TYR I 226 ARG 0.007 0.001 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 920) hydrogen bonds : angle 4.58484 ( 2766) SS BOND : bond 0.00434 ( 8) SS BOND : angle 1.10770 ( 16) covalent geometry : bond 0.00858 (13900) covalent geometry : angle 0.64560 (18972) *********************** 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 297 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8895 (m) cc_final: 0.8686 (t) REVERT: B 408 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5471 (mmp) REVERT: B 627 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7756 (pm20) REVERT: D 627 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: D 721 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7583 (ptt) REVERT: D 767 TRP cc_start: 0.6441 (m-90) cc_final: 0.5465 (t-100) outliers start: 59 outliers final: 43 residues processed: 265 average time/residue: 0.2307 time to fit residues: 94.4807 Evaluate side-chains 274 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 587 ILE 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 684 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 476 THR 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 684 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 721 MET 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 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 164 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 82 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 164 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.4980 chunk 47 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 192 optimal weight: 0.0040 chunk 53 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.203015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3879 r_free = 0.3879 target = 0.149163 restraints weight = 20340.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.147266 restraints weight = 21302.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.149146 restraints weight = 19148.634| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13908 Z= 0.116 Angle : 0.515 7.344 18988 Z= 0.264 Chirality : 0.039 0.153 2246 Planarity : 0.004 0.048 2414 Dihedral : 8.182 59.837 2300 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.21 % Allowed : 18.96 % Favored : 77.83 % 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: 1.54 (0.19), residues: 1942 helix: 2.44 (0.15), residues: 1126 sheet: -1.36 (0.44), residues: 138 loop : -0.94 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 766 HIS 0.002 0.001 HIS J 105 PHE 0.014 0.001 PHE I 130 TYR 0.032 0.001 TYR I 226 ARG 0.003 0.000 ARG C 416 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 920) hydrogen bonds : angle 4.08477 ( 2766) SS BOND : bond 0.00185 ( 8) SS BOND : angle 1.32607 ( 16) covalent geometry : bond 0.00259 (13900) covalent geometry : angle 0.51393 (18972) *********************** 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 284 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 ILE cc_start: 0.8772 (mm) cc_final: 0.8537 (mt) REVERT: B 408 MET cc_start: 0.6180 (mmp) cc_final: 0.5603 (mmp) REVERT: B 627 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: D 627 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: D 721 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7597 (ptt) outliers start: 34 outliers final: 19 residues processed: 271 average time/residue: 0.2532 time to fit residues: 107.4086 Evaluate side-chains 250 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 627 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 627 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.201305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.156152 restraints weight = 20175.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.145912 restraints weight = 26137.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141048 restraints weight = 24542.976| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13908 Z= 0.138 Angle : 0.522 8.170 18988 Z= 0.267 Chirality : 0.040 0.157 2246 Planarity : 0.003 0.048 2414 Dihedral : 7.407 57.360 2300 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.74 % Allowed : 19.72 % Favored : 77.55 % 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: 1.62 (0.19), residues: 1942 helix: 2.50 (0.15), residues: 1126 sheet: -1.45 (0.44), residues: 142 loop : -0.86 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 762 HIS 0.002 0.001 HIS J 105 PHE 0.031 0.001 PHE I 165 TYR 0.033 0.002 TYR I 226 ARG 0.002 0.000 ARG B 694 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 920) hydrogen bonds : angle 4.05808 ( 2766) SS BOND : bond 0.00239 ( 8) SS BOND : angle 1.16296 ( 16) covalent geometry : bond 0.00322 (13900) covalent geometry : angle 0.52131 (18972) *********************** 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 269 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8763 (m) cc_final: 0.8482 (t) REVERT: A 808 ILE cc_start: 0.8780 (mm) cc_final: 0.8558 (mt) REVERT: B 408 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.5742 (mmp) REVERT: B 627 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: C 808 ILE cc_start: 0.8778 (mm) cc_final: 0.8556 (mt) REVERT: D 627 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: D 721 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7678 (ptt) REVERT: D 767 TRP cc_start: 0.6352 (m-90) cc_final: 0.5395 (t-100) outliers start: 29 outliers final: 22 residues processed: 255 average time/residue: 0.2881 time to fit residues: 116.1035 Evaluate side-chains 256 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 645 THR 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 627 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET 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 164 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 191 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.199454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151929 restraints weight = 20402.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.134837 restraints weight = 25522.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135259 restraints weight = 24335.738| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13908 Z= 0.225 Angle : 0.553 8.629 18988 Z= 0.285 Chirality : 0.041 0.202 2246 Planarity : 0.004 0.048 2414 Dihedral : 7.618 56.211 2300 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.87 % Allowed : 19.15 % Favored : 76.98 % 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: 1.47 (0.19), residues: 1942 helix: 2.31 (0.15), residues: 1138 sheet: -1.41 (0.47), residues: 122 loop : -0.91 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 762 HIS 0.003 0.001 HIS J 105 PHE 0.037 0.002 PHE I 165 TYR 0.033 0.002 TYR J 226 ARG 0.002 0.000 ARG J 231 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 920) hydrogen bonds : angle 4.18370 ( 2766) SS BOND : bond 0.00354 ( 8) SS BOND : angle 1.15227 ( 16) covalent geometry : bond 0.00538 (13900) covalent geometry : angle 0.55252 (18972) *********************** 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 278 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8848 (m) cc_final: 0.8608 (t) REVERT: A 808 ILE cc_start: 0.8751 (mm) cc_final: 0.8514 (mt) REVERT: B 408 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5723 (mmp) REVERT: B 627 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: C 808 ILE cc_start: 0.8727 (mm) cc_final: 0.8509 (mt) REVERT: D 627 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: D 721 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7765 (ptt) REVERT: D 767 TRP cc_start: 0.6698 (m-90) cc_final: 0.5742 (t-100) outliers start: 41 outliers final: 33 residues processed: 258 average time/residue: 0.2711 time to fit residues: 109.6304 Evaluate side-chains 266 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 645 THR 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 B residue 408 MET Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 476 THR 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 D residue 431 GLU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET 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 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 164 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 82 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 41 optimal weight: 20.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.200761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162096 restraints weight = 19899.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.150691 restraints weight = 26835.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149691 restraints weight = 30379.898| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13908 Z= 0.238 Angle : 0.575 9.014 18988 Z= 0.296 Chirality : 0.041 0.184 2246 Planarity : 0.004 0.048 2414 Dihedral : 7.699 59.824 2300 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.68 % Allowed : 19.43 % Favored : 76.89 % 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: 1.37 (0.19), residues: 1942 helix: 2.21 (0.15), residues: 1138 sheet: -1.46 (0.46), residues: 122 loop : -0.90 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 762 HIS 0.003 0.001 HIS J 105 PHE 0.039 0.002 PHE I 165 TYR 0.034 0.002 TYR I 226 ARG 0.002 0.000 ARG J 125 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 920) hydrogen bonds : angle 4.27943 ( 2766) SS BOND : bond 0.00349 ( 8) SS BOND : angle 1.19395 ( 16) covalent geometry : bond 0.00573 (13900) covalent geometry : angle 0.57461 (18972) *********************** 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 271 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8833 (m) cc_final: 0.8612 (t) REVERT: B 408 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5380 (mmp) REVERT: B 627 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: D 627 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: D 721 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7460 (ptt) outliers start: 39 outliers final: 32 residues processed: 250 average time/residue: 0.3012 time to fit residues: 119.4823 Evaluate side-chains 262 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 645 THR 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 B residue 408 MET Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 476 THR 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 D residue 591 ILE Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET 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 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 164 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 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 83 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 571 ASN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** 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 = 0.4464 r_free = 0.4464 target = 0.201874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.160038 restraints weight = 19965.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.148379 restraints weight = 25658.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147419 restraints weight = 25323.062| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13908 Z= 0.151 Angle : 0.530 8.746 18988 Z= 0.271 Chirality : 0.040 0.201 2246 Planarity : 0.003 0.048 2414 Dihedral : 7.126 58.505 2300 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.40 % Allowed : 19.43 % Favored : 77.17 % 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: 1.55 (0.20), residues: 1942 helix: 2.42 (0.15), residues: 1126 sheet: -1.45 (0.46), residues: 122 loop : -0.87 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 762 HIS 0.003 0.001 HIS I 105 PHE 0.042 0.002 PHE J 165 TYR 0.035 0.001 TYR I 226 ARG 0.002 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 920) hydrogen bonds : angle 4.10551 ( 2766) SS BOND : bond 0.00263 ( 8) SS BOND : angle 1.10234 ( 16) covalent geometry : bond 0.00356 (13900) covalent geometry : angle 0.52932 (18972) ********************** 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 268 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8787 (m) cc_final: 0.8539 (t) REVERT: B 408 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5533 (mmp) REVERT: B 627 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: B 813 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7656 (mm-30) REVERT: C 808 ILE cc_start: 0.8790 (mm) cc_final: 0.8560 (mt) REVERT: D 627 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: D 721 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7610 (ptt) outliers start: 36 outliers final: 30 residues processed: 251 average time/residue: 0.2110 time to fit residues: 82.2746 Evaluate side-chains 263 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE 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 679 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 476 THR 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 D residue 589 CYS Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET 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 137 LEU 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 82 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 10 optimal weight: 40.0000 chunk 135 optimal weight: 6.9990 chunk 189 optimal weight: 0.3980 chunk 86 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.200971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.158044 restraints weight = 20233.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148751 restraints weight = 27410.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145672 restraints weight = 25733.135| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13908 Z= 0.194 Angle : 0.560 8.550 18988 Z= 0.286 Chirality : 0.041 0.189 2246 Planarity : 0.004 0.049 2414 Dihedral : 7.337 59.880 2300 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.49 % Allowed : 19.62 % Favored : 76.89 % 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: 1.50 (0.19), residues: 1942 helix: 2.37 (0.15), residues: 1122 sheet: -1.17 (0.45), residues: 126 loop : -0.92 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 762 HIS 0.003 0.001 HIS I 105 PHE 0.049 0.002 PHE J 165 TYR 0.035 0.002 TYR J 226 ARG 0.007 0.000 ARG D 661 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 920) hydrogen bonds : angle 4.19830 ( 2766) SS BOND : bond 0.00322 ( 8) SS BOND : angle 1.09740 ( 16) covalent geometry : bond 0.00464 (13900) covalent geometry : angle 0.55920 (18972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4808.25 seconds wall clock time: 87 minutes 8.10 seconds (5228.10 seconds total)