Starting phenix.real_space_refine on Wed Jan 22 01:29:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y69_38982/01_2025/8y69_38982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y69_38982/01_2025/8y69_38982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y69_38982/01_2025/8y69_38982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y69_38982/01_2025/8y69_38982.map" model { file = "/net/cci-nas-00/data/ceres_data/8y69_38982/01_2025/8y69_38982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y69_38982/01_2025/8y69_38982.cif" } resolution = 3.38 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= 0.006 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 116 5.16 5 C 11320 2.51 5 N 2934 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17577 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5697 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 36, 'TRANS': 693} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1409 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5733 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 698} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1362 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.28, per 1000 atoms: 0.76 Number of scatterers: 17577 At special positions: 0 Unit cell: (148.869, 126.378, 159.579, 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 116 16.00 O 3207 8.00 N 2934 7.00 C 11320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.03 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS E 447 " - pdb=" SG CYS E 520 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 52 " distance=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 78 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 110 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 124 " distance=2.03 Simple disulfide: pdb=" SG CYS G 128 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 43 " distance=2.03 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 364 " distance=2.03 Simple disulfide: pdb=" SG CYS D 618 " - pdb=" SG CYS D 693 " distance=2.03 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 136 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 52 " distance=2.04 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 78 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 110 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 124 " distance=2.03 Simple disulfide: pdb=" SG CYS J 128 " - pdb=" SG CYS J 141 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 2.3 seconds 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4226 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 25 sheets defined 28.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.571A pdb=" N ILE A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 126' Processing helix chain 'A' and resid 169 through 175 removed outlier: 3.743A pdb=" N ASN A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.743A pdb=" N ILE A 244 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.783A pdb=" N THR A 384 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 386 " --> pdb=" O GLY A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 466 through 473 removed outlier: 4.428A pdb=" N CYS A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 555 removed outlier: 3.565A pdb=" N ARG A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.625A pdb=" N LEU A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.753A pdb=" N PHE A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 removed outlier: 4.077A pdb=" N PHE A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 649 removed outlier: 3.756A pdb=" N GLY A 622 " --> pdb=" O CYS A 618 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 641 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 683 removed outlier: 3.594A pdb=" N ALA A 665 " --> pdb=" O GLN A 661 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N THR A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 680 - end of helix removed outlier: 3.847A pdb=" N HIS A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 732 removed outlier: 3.878A pdb=" N VAL A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 718 " --> pdb=" O ASN A 714 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS A 730 " --> pdb=" O THR A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 742 through 760 removed outlier: 3.815A pdb=" N ILE A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS A 757 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 758 " --> pdb=" O PHE A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 768 removed outlier: 3.762A pdb=" N ALA A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE A 765 " --> pdb=" O CYS A 761 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE A 766 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 767 " --> pdb=" O VAL A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.708A pdb=" N MET A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 783 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 784 " --> pdb=" O GLU A 780 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 805 removed outlier: 3.542A pdb=" N VAL A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 818 removed outlier: 3.984A pdb=" N LYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 815 " --> pdb=" O ASP A 811 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 816 " --> pdb=" O TRP A 812 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 817 " --> pdb=" O LYS A 813 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.501A pdb=" N LYS C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 Processing helix chain 'C' and resid 186 through 198 removed outlier: 3.937A pdb=" N LYS C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.807A pdb=" N PHE C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU C 223 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 229 " --> pdb=" O PHE C 225 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N CYS C 233 " --> pdb=" O VAL C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 243 removed outlier: 3.804A pdb=" N LEU C 237 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 533 through 537 removed outlier: 4.022A pdb=" N ILE E 536 " --> pdb=" O ASN E 533 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE E 537 " --> pdb=" O TRP E 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 533 through 537' Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 241 through 247 removed outlier: 4.180A pdb=" N ILE D 244 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 471 removed outlier: 3.907A pdb=" N CYS D 470 " --> pdb=" O TYR D 466 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 466 through 471' Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 538 through 552 removed outlier: 3.959A pdb=" N LEU D 543 " --> pdb=" O TRP D 539 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR D 544 " --> pdb=" O MET D 540 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 545 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 564 removed outlier: 3.804A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU D 558 " --> pdb=" O PHE D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 601 removed outlier: 3.914A pdb=" N PHE D 576 " --> pdb=" O SER D 572 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE D 577 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 581 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 582 " --> pdb=" O GLY D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 615 removed outlier: 3.870A pdb=" N ILE D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 614 " --> pdb=" O ILE D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 648 removed outlier: 3.630A pdb=" N GLY D 622 " --> pdb=" O CYS D 618 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 623 " --> pdb=" O LYS D 619 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 641 " --> pdb=" O MET D 637 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 683 removed outlier: 3.734A pdb=" N LEU D 668 " --> pdb=" O VAL D 664 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) Proline residue: D 680 - end of helix removed outlier: 4.456A pdb=" N HIS D 683 " --> pdb=" O PHE D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 727 removed outlier: 3.709A pdb=" N VAL D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR D 709 " --> pdb=" O GLY D 705 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 714 " --> pdb=" O LEU D 710 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA D 717 " --> pdb=" O LEU D 713 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 718 " --> pdb=" O ASN D 714 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 719 " --> pdb=" O SER D 715 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 724 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR D 725 " --> pdb=" O MET D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 732 removed outlier: 4.121A pdb=" N ASN D 731 " --> pdb=" O LYS D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 766 removed outlier: 4.188A pdb=" N LYS D 747 " --> pdb=" O SER D 743 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS D 748 " --> pdb=" O SER D 744 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 760 " --> pdb=" O ASN D 756 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS D 761 " --> pdb=" O CYS D 757 " (cutoff:3.500A) Proline residue: D 762 - end of helix removed outlier: 3.832A pdb=" N PHE D 766 " --> pdb=" O PRO D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 790 removed outlier: 3.570A pdb=" N MET D 782 " --> pdb=" O SER D 778 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 783 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 784 " --> pdb=" O GLU D 780 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 804 removed outlier: 4.593A pdb=" N VAL D 799 " --> pdb=" O CYS D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 820 removed outlier: 3.712A pdb=" N ASP D 811 " --> pdb=" O LYS D 807 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 813 " --> pdb=" O LYS D 809 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D 814 " --> pdb=" O GLU D 810 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 816 " --> pdb=" O TRP D 812 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 819 " --> pdb=" O LEU D 815 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 106 removed outlier: 3.566A pdb=" N LEU H 106 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 150 Processing helix chain 'H' and resid 163 through 171 removed outlier: 3.905A pdb=" N GLY H 171 " --> pdb=" O GLN H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 198 removed outlier: 3.645A pdb=" N LYS H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS H 197 " --> pdb=" O ASN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 243 removed outlier: 4.395A pdb=" N ILE H 221 " --> pdb=" O PHE H 217 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE H 222 " --> pdb=" O ASP H 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE H 226 " --> pdb=" O PHE H 222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 227 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS H 233 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS H 243 " --> pdb=" O LYS H 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 7.003A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 86 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N HIS A 157 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N LEU A 184 " --> pdb=" O HIS A 157 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N TRP A 159 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N LEU A 186 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASP A 161 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.876A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254 removed outlier: 7.157A pdb=" N LEU A 253 " --> pdb=" O HIS A 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 303 removed outlier: 6.317A pdb=" N LEU A 324 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A 348 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 395 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 394 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.652A pdb=" N ILE A 380 " --> pdb=" O GLU A 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 65 removed outlier: 7.691A pdb=" N ILE C 155 " --> pdb=" O TRP C 120 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY C 122 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP C 157 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 124 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.502A pdb=" N VAL E 24 " --> pdb=" O ALA E 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E 497 " --> pdb=" O THR E 502 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN E 506 " --> pdb=" O THR E 493 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 482 through 484 removed outlier: 5.637A pdb=" N GLY E 472 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG E 463 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA E 474 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS E 458 " --> pdb=" O ARG E 523 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG E 523 " --> pdb=" O CYS E 458 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 482 through 484 removed outlier: 5.637A pdb=" N GLY E 472 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG E 463 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA E 474 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS E 458 " --> pdb=" O ARG E 523 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG E 523 " --> pdb=" O CYS E 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 70 through 75 removed outlier: 3.595A pdb=" N GLU G 73 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE G 62 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE G 61 " --> pdb=" O CYS G 93 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ARG G 95 " --> pdb=" O PHE G 61 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N LEU G 63 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 101 through 104 Processing sheet with id=AB4, first strand: chain 'D' and resid 34 through 35 removed outlier: 6.647A pdb=" N LEU D 62 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU D 86 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'D' and resid 191 through 192 removed outlier: 4.448A pdb=" N ILE D 192 " --> pdb=" O SER D 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 252 through 254 removed outlier: 7.190A pdb=" N LEU D 253 " --> pdb=" O HIS D 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 301 through 303 removed outlier: 6.281A pdb=" N LEU D 301 " --> pdb=" O THR D 325 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU D 324 " --> pdb=" O ASP D 349 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE D 370 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU D 394 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 440 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 439 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 58 through 65 removed outlier: 3.741A pdb=" N TYR H 77 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP H 120 " --> pdb=" O ALA H 153 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE H 155 " --> pdb=" O TRP H 120 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY H 122 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP H 157 " --> pdb=" O GLY H 122 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL H 124 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 23 through 26 removed outlier: 3.704A pdb=" N VAL I 24 " --> pdb=" O ALA I 448 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER I 446 " --> pdb=" O SER I 26 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU I 443 " --> pdb=" O MET I 507 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP I 497 " --> pdb=" O THR I 502 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 482 through 484 removed outlier: 6.086A pdb=" N GLY I 472 " --> pdb=" O ARG I 463 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG I 463 " --> pdb=" O GLY I 472 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA I 474 " --> pdb=" O TRP I 461 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N CYS I 458 " --> pdb=" O ARG I 523 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG I 523 " --> pdb=" O CYS I 458 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 482 through 484 removed outlier: 6.086A pdb=" N GLY I 472 " --> pdb=" O ARG I 463 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG I 463 " --> pdb=" O GLY I 472 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA I 474 " --> pdb=" O TRP I 461 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N CYS I 458 " --> pdb=" O ARG I 523 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG I 523 " --> pdb=" O CYS I 458 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 60 through 65 Processing sheet with id=AC6, first strand: chain 'J' and resid 82 through 85 Processing sheet with id=AC7, first strand: chain 'J' and resid 101 through 106 removed outlier: 6.209A pdb=" N CYS J 101 " --> pdb=" O CYS J 113 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N CYS J 113 " --> pdb=" O CYS J 101 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER J 103 " --> pdb=" O THR J 111 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE J 109 " --> pdb=" O PHE J 105 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1383 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: 6.22 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5631 1.34 - 1.46: 4230 1.46 - 1.59: 7960 1.59 - 1.71: 0 1.71 - 1.83: 151 Bond restraints: 17972 Sorted by residual: bond pdb=" C THR A 701 " pdb=" N PRO A 702 " ideal model delta sigma weight residual 1.335 1.354 -0.019 8.70e-03 1.32e+04 4.73e+00 bond pdb=" CA GLY A 537 " pdb=" C GLY A 537 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.53e+00 bond pdb=" N GLY A 537 " pdb=" CA GLY A 537 " ideal model delta sigma weight residual 1.464 1.449 0.016 1.12e-02 7.97e+03 1.94e+00 bond pdb=" CA CYS J 43 " pdb=" CB CYS J 43 " ideal model delta sigma weight residual 1.539 1.520 0.019 1.36e-02 5.41e+03 1.87e+00 bond pdb=" C PHE A 268 " pdb=" N ASP A 269 " ideal model delta sigma weight residual 1.332 1.316 0.015 1.29e-02 6.01e+03 1.42e+00 ... (remaining 17967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 23553 1.61 - 3.22: 735 3.22 - 4.83: 94 4.83 - 6.44: 13 6.44 - 8.05: 1 Bond angle restraints: 24396 Sorted by residual: angle pdb=" N LYS D 46 " pdb=" CA LYS D 46 " pdb=" C LYS D 46 " ideal model delta sigma weight residual 112.72 107.50 5.22 1.28e+00 6.10e-01 1.66e+01 angle pdb=" N ILE A 788 " pdb=" CA ILE A 788 " pdb=" C ILE A 788 " ideal model delta sigma weight residual 113.53 110.02 3.51 9.80e-01 1.04e+00 1.28e+01 angle pdb=" N ILE A 758 " pdb=" CA ILE A 758 " pdb=" C ILE A 758 " ideal model delta sigma weight residual 112.35 107.61 4.74 1.41e+00 5.03e-01 1.13e+01 angle pdb=" N LYS A 46 " pdb=" CA LYS A 46 " pdb=" C LYS A 46 " ideal model delta sigma weight residual 114.04 110.24 3.80 1.24e+00 6.50e-01 9.38e+00 angle pdb=" N THR A 416 " pdb=" CA THR A 416 " pdb=" C THR A 416 " ideal model delta sigma weight residual 113.12 109.34 3.78 1.25e+00 6.40e-01 9.17e+00 ... (remaining 24391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.44: 9868 12.44 - 24.87: 732 24.87 - 37.31: 184 37.31 - 49.75: 46 49.75 - 62.18: 16 Dihedral angle restraints: 10846 sinusoidal: 4329 harmonic: 6517 Sorted by residual: dihedral pdb=" CB CYS G 78 " pdb=" SG CYS G 78 " pdb=" SG CYS G 93 " pdb=" CB CYS G 93 " ideal model delta sinusoidal sigma weight residual 93.00 142.98 -49.98 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS J 78 " pdb=" SG CYS J 78 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual 93.00 142.33 -49.33 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CA LEU D 208 " pdb=" C LEU D 208 " pdb=" N HIS D 209 " pdb=" CA HIS D 209 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 10843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1696 0.032 - 0.064: 820 0.064 - 0.096: 180 0.096 - 0.128: 106 0.128 - 0.160: 10 Chirality restraints: 2812 Sorted by residual: chirality pdb=" CA ASN D 210 " pdb=" N ASN D 210 " pdb=" C ASN D 210 " pdb=" CB ASN D 210 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CG LEU D 441 " pdb=" CB LEU D 441 " pdb=" CD1 LEU D 441 " pdb=" CD2 LEU D 441 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE A 263 " pdb=" N ILE A 263 " pdb=" C ILE A 263 " pdb=" CB ILE A 263 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 2809 not shown) Planarity restraints: 3097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 209 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO C 210 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 210 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 210 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 373 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C GLN A 373 " -0.021 2.00e-02 2.50e+03 pdb=" O GLN A 373 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 374 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 351 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C SER D 351 " 0.021 2.00e-02 2.50e+03 pdb=" O SER D 351 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR D 352 " -0.007 2.00e-02 2.50e+03 ... (remaining 3094 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1207 2.73 - 3.28: 18029 3.28 - 3.82: 28388 3.82 - 4.36: 33352 4.36 - 4.90: 57001 Nonbonded interactions: 137977 Sorted by model distance: nonbonded pdb=" OG1 THR A 526 " pdb=" O LYS A 530 " model vdw 2.194 3.040 nonbonded pdb=" N ASP D 161 " pdb=" OD1 ASP D 161 " model vdw 2.212 3.120 nonbonded pdb=" NE2 GLN D 113 " pdb=" O HIS J 76 " model vdw 2.218 3.120 nonbonded pdb=" OH TYR A 468 " pdb=" OE2 GLU A 613 " model vdw 2.233 3.040 nonbonded pdb=" O ILE D 541 " pdb=" OG1 THR D 544 " model vdw 2.245 3.040 ... (remaining 137972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 744 or (resid 745 and (name N or name CA or nam \ e C or name O or name CB )) or resid 746 through 820)) selection = (chain 'D' and (resid 33 through 564 or resid 570 through 724 or (resid 725 and \ (name N or name CA or name C or name O or name CB )) or resid 726 through 727 or \ (resid 728 and (name N or name CA or name C or name O or name CB )) or resid 72 \ 9 through 820)) } ncs_group { reference = (chain 'C' and (resid 56 through 86 or (resid 87 through 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 207 or (resid 208 and ( \ name N or name CA or name C or name O or name CB )) or resid 209 through 210 or \ (resid 211 through 212 and (name N or name CA or name C or name O or name CB )) \ or (resid 215 through 216 and (name N or name CA or name C or name O or name CB \ )) or resid 217 through 243)) selection = (chain 'H' and resid 56 through 243) } ncs_group { reference = chain 'E' selection = (chain 'I' and (resid 21 through 499 or (resid 500 and (name N or name CA or nam \ e C or name O or name CB )) or resid 501 through 549)) } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.000 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.250 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17972 Z= 0.223 Angle : 0.662 8.045 24396 Z= 0.395 Chirality : 0.041 0.160 2812 Planarity : 0.003 0.039 3097 Dihedral : 9.883 62.183 6554 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 3.56 % Allowed : 8.31 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.18), residues: 2215 helix: -0.10 (0.24), residues: 521 sheet: -2.15 (0.26), residues: 368 loop : -1.82 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 159 HIS 0.005 0.001 HIS A 209 PHE 0.014 0.001 PHE D 696 TYR 0.010 0.001 TYR J 83 ARG 0.002 0.000 ARG I 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.7671 (ptp) cc_final: 0.7380 (ptp) REVERT: A 638 LEU cc_start: 0.8863 (mm) cc_final: 0.8657 (mt) REVERT: A 782 MET cc_start: 0.8096 (ttm) cc_final: 0.7753 (ttt) REVERT: C 221 ILE cc_start: 0.8333 (mt) cc_final: 0.7686 (mm) REVERT: E 22 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7653 (tm-30) REVERT: E 24 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8228 (m) REVERT: E 459 MET cc_start: 0.8431 (mmm) cc_final: 0.7849 (mmt) REVERT: E 475 THR cc_start: 0.8641 (m) cc_final: 0.8369 (p) REVERT: E 484 TYR cc_start: 0.8709 (m-80) cc_final: 0.7925 (m-80) REVERT: E 504 TYR cc_start: 0.8551 (m-80) cc_final: 0.8286 (m-80) REVERT: E 510 LEU cc_start: 0.7359 (mp) cc_final: 0.6834 (pp) REVERT: E 519 TYR cc_start: 0.8427 (m-80) cc_final: 0.8196 (m-80) REVERT: E 532 LEU cc_start: 0.8233 (mt) cc_final: 0.8016 (mp) REVERT: G 139 MET cc_start: 0.7471 (tpp) cc_final: 0.6802 (tpp) REVERT: D 80 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7371 (p90) REVERT: D 211 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8060 (p0) REVERT: D 546 TRP cc_start: 0.7473 (m100) cc_final: 0.7099 (m100) REVERT: D 549 PHE cc_start: 0.8841 (t80) cc_final: 0.8569 (t80) REVERT: H 108 ASN cc_start: 0.8371 (t0) cc_final: 0.8118 (t0) REVERT: I 464 GLN cc_start: 0.7563 (tt0) cc_final: 0.7299 (tt0) REVERT: I 475 THR cc_start: 0.7571 (m) cc_final: 0.7308 (p) REVERT: I 486 ASP cc_start: 0.8033 (p0) cc_final: 0.7780 (p0) REVERT: I 517 MET cc_start: 0.8271 (tpp) cc_final: 0.8028 (tpt) REVERT: I 519 TYR cc_start: 0.8344 (m-80) cc_final: 0.8127 (m-80) REVERT: J 64 ARG cc_start: 0.8061 (tpp80) cc_final: 0.7843 (ttm-80) REVERT: J 71 TYR cc_start: 0.8479 (p90) cc_final: 0.8092 (p90) REVERT: J 112 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8641 (ttpp) outliers start: 69 outliers final: 33 residues processed: 357 average time/residue: 0.3285 time to fit residues: 175.8268 Evaluate side-chains 225 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 114 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 202 optimal weight: 0.0770 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 140 HIS A 157 HIS A 187 ASN A 199 ASN A 282 ASN A 293 HIS A 354 ASN ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN C 169 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN D 67 ASN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN D 402 HIS D 444 ASN H 100 GLN I 506 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.098574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.068374 restraints weight = 53464.251| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.50 r_work: 0.3143 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17972 Z= 0.216 Angle : 0.640 11.418 24396 Z= 0.316 Chirality : 0.043 0.186 2812 Planarity : 0.004 0.044 3097 Dihedral : 6.202 59.751 2575 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.13 % Favored : 92.73 % Rotamer: Outliers : 3.36 % Allowed : 12.44 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.18), residues: 2215 helix: 0.14 (0.23), residues: 549 sheet: -1.77 (0.27), residues: 363 loop : -1.87 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 474 HIS 0.005 0.001 HIS A 209 PHE 0.027 0.001 PHE A 547 TYR 0.014 0.001 TYR H 182 ARG 0.008 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8518 (pt) REVERT: A 308 MET cc_start: 0.8647 (tmm) cc_final: 0.8313 (tmm) REVERT: A 344 MET cc_start: 0.8319 (ptp) cc_final: 0.7739 (ptp) REVERT: A 540 MET cc_start: 0.8748 (mtm) cc_final: 0.8408 (mtm) REVERT: A 638 LEU cc_start: 0.8858 (mm) cc_final: 0.8573 (mt) REVERT: A 782 MET cc_start: 0.8525 (ttm) cc_final: 0.8161 (ttt) REVERT: A 788 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8111 (mt) REVERT: A 801 TYR cc_start: 0.7836 (t80) cc_final: 0.7554 (t80) REVERT: C 128 GLN cc_start: 0.8408 (mp10) cc_final: 0.8166 (mp10) REVERT: C 190 LYS cc_start: 0.8940 (ttmt) cc_final: 0.8722 (ptmt) REVERT: C 221 ILE cc_start: 0.8081 (mt) cc_final: 0.7850 (mm) REVERT: E 22 GLN cc_start: 0.8364 (tm-30) cc_final: 0.7992 (tm-30) REVERT: E 459 MET cc_start: 0.8992 (mmm) cc_final: 0.8398 (mmt) REVERT: E 477 ASP cc_start: 0.7563 (t0) cc_final: 0.7295 (t70) REVERT: E 484 TYR cc_start: 0.8881 (m-80) cc_final: 0.8607 (m-80) REVERT: E 491 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.6110 (ttt-90) REVERT: E 492 PHE cc_start: 0.6700 (m-10) cc_final: 0.6245 (m-10) REVERT: E 504 TYR cc_start: 0.8813 (m-80) cc_final: 0.8589 (m-80) REVERT: E 510 LEU cc_start: 0.7669 (mp) cc_final: 0.7422 (pp) REVERT: E 519 TYR cc_start: 0.8103 (m-80) cc_final: 0.7851 (m-80) REVERT: E 532 LEU cc_start: 0.7868 (mt) cc_final: 0.7623 (mp) REVERT: G 66 GLU cc_start: 0.8800 (pm20) cc_final: 0.8491 (pm20) REVERT: G 68 MET cc_start: 0.8597 (mtm) cc_final: 0.8367 (mtp) REVERT: G 114 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8665 (mmtm) REVERT: G 139 MET cc_start: 0.7196 (tpp) cc_final: 0.6943 (tpp) REVERT: D 80 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7622 (p90) REVERT: D 137 ASP cc_start: 0.8475 (m-30) cc_final: 0.8013 (m-30) REVERT: D 308 MET cc_start: 0.9060 (ttt) cc_final: 0.8739 (tmm) REVERT: D 549 PHE cc_start: 0.8860 (t80) cc_final: 0.8439 (t80) REVERT: D 754 PHE cc_start: 0.9092 (m-80) cc_final: 0.8624 (m-80) REVERT: I 486 ASP cc_start: 0.8853 (p0) cc_final: 0.8583 (p0) REVERT: I 497 ASP cc_start: 0.8349 (t0) cc_final: 0.8049 (t0) REVERT: I 517 MET cc_start: 0.8363 (tpp) cc_final: 0.8160 (tpt) REVERT: I 519 TYR cc_start: 0.8448 (m-80) cc_final: 0.8066 (m-80) REVERT: I 539 TYR cc_start: 0.8457 (m-80) cc_final: 0.8096 (m-80) REVERT: J 64 ARG cc_start: 0.8460 (tpp80) cc_final: 0.8022 (ttm-80) REVERT: J 66 GLU cc_start: 0.8588 (pm20) cc_final: 0.8121 (pm20) REVERT: J 71 TYR cc_start: 0.8369 (p90) cc_final: 0.8083 (p90) REVERT: J 99 GLU cc_start: 0.8797 (pp20) cc_final: 0.8499 (pp20) REVERT: J 102 ASP cc_start: 0.8685 (m-30) cc_final: 0.8372 (m-30) outliers start: 65 outliers final: 34 residues processed: 282 average time/residue: 0.3077 time to fit residues: 132.9390 Evaluate side-chains 225 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN A 756 ASN J 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.097565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.067240 restraints weight = 53705.466| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.43 r_work: 0.3123 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17972 Z= 0.261 Angle : 0.629 8.733 24396 Z= 0.311 Chirality : 0.043 0.153 2812 Planarity : 0.004 0.048 3097 Dihedral : 5.717 53.500 2553 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.40 % Favored : 92.51 % Rotamer: Outliers : 3.77 % Allowed : 12.55 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.18), residues: 2215 helix: 0.48 (0.24), residues: 539 sheet: -1.49 (0.29), residues: 340 loop : -1.86 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 474 HIS 0.006 0.001 HIS A 209 PHE 0.022 0.001 PHE A 547 TYR 0.013 0.001 TYR J 83 ARG 0.007 0.000 ARG I 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8651 (p) REVERT: A 308 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8364 (tmm) REVERT: A 344 MET cc_start: 0.8315 (ptp) cc_final: 0.7752 (ptp) REVERT: A 597 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8154 (tp) REVERT: A 623 PHE cc_start: 0.8363 (t80) cc_final: 0.8071 (t80) REVERT: A 638 LEU cc_start: 0.8792 (mm) cc_final: 0.8474 (mt) REVERT: A 782 MET cc_start: 0.8530 (ttm) cc_final: 0.8207 (ttt) REVERT: A 801 TYR cc_start: 0.7839 (t80) cc_final: 0.7498 (t80) REVERT: C 128 GLN cc_start: 0.8527 (mp10) cc_final: 0.8297 (mp10) REVERT: C 190 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8708 (ttmt) REVERT: C 197 LYS cc_start: 0.9537 (mmmt) cc_final: 0.8956 (mppt) REVERT: E 459 MET cc_start: 0.8910 (mmm) cc_final: 0.8170 (mmp) REVERT: E 463 ARG cc_start: 0.8134 (ptt90) cc_final: 0.7928 (ptt90) REVERT: E 464 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 477 ASP cc_start: 0.7575 (t0) cc_final: 0.7231 (t70) REVERT: E 484 TYR cc_start: 0.8872 (m-80) cc_final: 0.8662 (m-80) REVERT: E 504 TYR cc_start: 0.8583 (m-80) cc_final: 0.8371 (m-80) REVERT: G 66 GLU cc_start: 0.8804 (pm20) cc_final: 0.8456 (pm20) REVERT: G 68 MET cc_start: 0.8721 (mtm) cc_final: 0.8394 (mtp) REVERT: G 114 LYS cc_start: 0.9136 (ttpp) cc_final: 0.8817 (mmtm) REVERT: D 80 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7760 (p90) REVERT: D 137 ASP cc_start: 0.8383 (m-30) cc_final: 0.7843 (m-30) REVERT: D 308 MET cc_start: 0.9103 (ttt) cc_final: 0.8779 (tmm) REVERT: D 721 MET cc_start: 0.8253 (tmm) cc_final: 0.7849 (tmm) REVERT: D 754 PHE cc_start: 0.9094 (m-80) cc_final: 0.8617 (m-80) REVERT: H 100 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.6252 (tm-30) REVERT: H 134 LYS cc_start: 0.9230 (tptp) cc_final: 0.8990 (tptp) REVERT: H 144 LYS cc_start: 0.9249 (tmmt) cc_final: 0.8996 (tptt) REVERT: H 239 LYS cc_start: 0.9072 (tptt) cc_final: 0.8764 (tttt) REVERT: I 22 GLN cc_start: 0.6937 (tm-30) cc_final: 0.6669 (tm-30) REVERT: I 497 ASP cc_start: 0.8414 (t0) cc_final: 0.7960 (t0) REVERT: I 517 MET cc_start: 0.8340 (tpp) cc_final: 0.8102 (tpt) REVERT: I 519 TYR cc_start: 0.8399 (m-80) cc_final: 0.8012 (m-80) REVERT: I 539 TYR cc_start: 0.8426 (m-80) cc_final: 0.8101 (m-80) REVERT: J 64 ARG cc_start: 0.8441 (tpp80) cc_final: 0.8018 (ttm-80) REVERT: J 66 GLU cc_start: 0.8564 (pm20) cc_final: 0.8044 (pm20) REVERT: J 71 TYR cc_start: 0.8353 (p90) cc_final: 0.8023 (p90) REVERT: J 99 GLU cc_start: 0.8878 (pp20) cc_final: 0.8631 (pp20) REVERT: J 102 ASP cc_start: 0.8721 (m-30) cc_final: 0.8499 (m-30) outliers start: 73 outliers final: 39 residues processed: 271 average time/residue: 0.2951 time to fit residues: 122.3905 Evaluate side-chains 223 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 209 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN A 282 ASN ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 209 HIS D 556 ASN ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 ASN D 748 HIS H 110 ASN I 464 GLN ** I 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.093889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063138 restraints weight = 54384.548| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.38 r_work: 0.3023 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 17972 Z= 0.517 Angle : 0.777 9.330 24396 Z= 0.392 Chirality : 0.047 0.208 2812 Planarity : 0.005 0.050 3097 Dihedral : 6.370 57.375 2549 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.74 % Favored : 89.16 % Rotamer: Outliers : 5.01 % Allowed : 13.84 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.18), residues: 2215 helix: 0.55 (0.24), residues: 535 sheet: -1.68 (0.29), residues: 316 loop : -2.05 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 474 HIS 0.011 0.001 HIS H 207 PHE 0.039 0.002 PHE D 634 TYR 0.030 0.002 TYR J 83 ARG 0.006 0.001 ARG E 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 184 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8676 (p) REVERT: A 308 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8428 (tmm) REVERT: A 344 MET cc_start: 0.8594 (ptp) cc_final: 0.8042 (ptp) REVERT: A 634 PHE cc_start: 0.7841 (m-10) cc_final: 0.7621 (m-80) REVERT: A 638 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8510 (mt) REVERT: A 782 MET cc_start: 0.8679 (ttm) cc_final: 0.8390 (ttt) REVERT: C 128 GLN cc_start: 0.8583 (mp10) cc_final: 0.8275 (mp10) REVERT: C 190 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8780 (ttmt) REVERT: E 539 TYR cc_start: 0.8340 (m-80) cc_final: 0.7755 (m-80) REVERT: G 66 GLU cc_start: 0.8745 (pm20) cc_final: 0.8403 (pm20) REVERT: G 68 MET cc_start: 0.8953 (mtm) cc_final: 0.8554 (mtp) REVERT: G 114 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8806 (mmtm) REVERT: D 80 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8074 (p90) REVERT: D 308 MET cc_start: 0.9176 (ttt) cc_final: 0.8875 (tmm) REVERT: D 392 ARG cc_start: 0.8101 (ptm-80) cc_final: 0.7631 (ttm-80) REVERT: D 754 PHE cc_start: 0.9092 (m-80) cc_final: 0.8615 (m-80) REVERT: H 100 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: I 479 ASP cc_start: 0.9639 (m-30) cc_final: 0.9376 (p0) REVERT: I 497 ASP cc_start: 0.8291 (t0) cc_final: 0.7833 (t0) REVERT: I 519 TYR cc_start: 0.8357 (m-80) cc_final: 0.7962 (m-80) REVERT: I 539 TYR cc_start: 0.8539 (m-80) cc_final: 0.8076 (m-80) REVERT: J 64 ARG cc_start: 0.8381 (tpp80) cc_final: 0.7994 (ttm-80) REVERT: J 99 GLU cc_start: 0.8994 (pp20) cc_final: 0.8634 (pp20) REVERT: J 102 ASP cc_start: 0.8478 (m-30) cc_final: 0.8191 (m-30) REVERT: J 107 LYS cc_start: 0.9543 (ttmm) cc_final: 0.9249 (ttmm) outliers start: 97 outliers final: 58 residues processed: 260 average time/residue: 0.2776 time to fit residues: 113.8018 Evaluate side-chains 226 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 761 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 219 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 477 ASP Chi-restraints excluded: chain I residue 493 THR Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 189 optimal weight: 0.0470 chunk 76 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN A 379 GLN ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.097372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.067036 restraints weight = 53807.607| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 4.44 r_work: 0.3106 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17972 Z= 0.188 Angle : 0.633 19.411 24396 Z= 0.311 Chirality : 0.043 0.253 2812 Planarity : 0.003 0.039 3097 Dihedral : 5.701 53.226 2549 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.00 % Favored : 93.91 % Rotamer: Outliers : 3.30 % Allowed : 16.47 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2215 helix: 0.71 (0.24), residues: 534 sheet: -1.33 (0.31), residues: 306 loop : -1.95 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 474 HIS 0.006 0.000 HIS A 209 PHE 0.025 0.001 PHE A 547 TYR 0.014 0.001 TYR C 118 ARG 0.004 0.000 ARG I 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8235 (mp0) cc_final: 0.7922 (mp0) REVERT: A 111 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8727 (p) REVERT: A 308 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8377 (tmm) REVERT: A 344 MET cc_start: 0.8533 (ptp) cc_final: 0.8020 (ptp) REVERT: A 623 PHE cc_start: 0.8416 (t80) cc_final: 0.8101 (t80) REVERT: A 634 PHE cc_start: 0.7709 (m-10) cc_final: 0.7482 (m-80) REVERT: A 638 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8474 (mt) REVERT: A 782 MET cc_start: 0.8648 (ttm) cc_final: 0.8336 (ttt) REVERT: C 128 GLN cc_start: 0.8464 (mp10) cc_final: 0.8151 (mp10) REVERT: E 464 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7218 (tm-30) REVERT: E 514 ASP cc_start: 0.8827 (t0) cc_final: 0.8084 (m-30) REVERT: E 539 TYR cc_start: 0.8361 (m-80) cc_final: 0.7756 (m-80) REVERT: G 66 GLU cc_start: 0.8869 (pm20) cc_final: 0.8597 (pm20) REVERT: G 68 MET cc_start: 0.8722 (mtm) cc_final: 0.8482 (mtp) REVERT: G 114 LYS cc_start: 0.9171 (ttpp) cc_final: 0.8740 (mmtm) REVERT: G 139 MET cc_start: 0.6849 (tpp) cc_final: 0.6177 (tpp) REVERT: D 80 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8017 (p90) REVERT: D 137 ASP cc_start: 0.8359 (m-30) cc_final: 0.7904 (m-30) REVERT: D 308 MET cc_start: 0.9142 (ttt) cc_final: 0.8795 (tmm) REVERT: D 637 MET cc_start: 0.5310 (tpt) cc_final: 0.5038 (tpp) REVERT: D 721 MET cc_start: 0.8101 (tmm) cc_final: 0.7802 (tmm) REVERT: D 754 PHE cc_start: 0.9086 (m-80) cc_final: 0.8616 (m-80) REVERT: H 100 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.5931 (tm-30) REVERT: H 134 LYS cc_start: 0.9187 (tptp) cc_final: 0.8961 (tptp) REVERT: H 144 LYS cc_start: 0.9273 (tmmt) cc_final: 0.9013 (tptp) REVERT: I 475 THR cc_start: 0.8004 (m) cc_final: 0.7594 (p) REVERT: I 479 ASP cc_start: 0.9624 (m-30) cc_final: 0.9401 (p0) REVERT: I 497 ASP cc_start: 0.8232 (t0) cc_final: 0.7667 (t0) REVERT: I 517 MET cc_start: 0.7828 (tpp) cc_final: 0.7478 (tpt) REVERT: I 539 TYR cc_start: 0.8501 (m-80) cc_final: 0.8053 (m-80) REVERT: J 64 ARG cc_start: 0.8388 (tpp80) cc_final: 0.8078 (ttm-80) REVERT: J 99 GLU cc_start: 0.9066 (pp20) cc_final: 0.8494 (pp20) REVERT: J 100 ASN cc_start: 0.9608 (m-40) cc_final: 0.9251 (m-40) REVERT: J 102 ASP cc_start: 0.8552 (m-30) cc_final: 0.8261 (m-30) REVERT: J 107 LYS cc_start: 0.9564 (ttmm) cc_final: 0.9295 (ttmm) outliers start: 64 outliers final: 43 residues processed: 243 average time/residue: 0.2875 time to fit residues: 108.4818 Evaluate side-chains 223 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 477 ASP Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 17 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN ** I 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.096206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065666 restraints weight = 54070.000| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.44 r_work: 0.3074 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17972 Z= 0.275 Angle : 0.650 12.405 24396 Z= 0.319 Chirality : 0.043 0.193 2812 Planarity : 0.004 0.037 3097 Dihedral : 5.591 54.651 2543 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 3.72 % Allowed : 16.73 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.67 (0.18), residues: 2215 helix: 0.71 (0.24), residues: 532 sheet: -1.28 (0.31), residues: 311 loop : -1.91 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 474 HIS 0.008 0.001 HIS A 209 PHE 0.025 0.001 PHE D 547 TYR 0.020 0.002 TYR E 484 ARG 0.003 0.000 ARG I 470 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 174 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7912 (p90) REVERT: A 85 GLU cc_start: 0.8222 (mp0) cc_final: 0.7890 (mp0) REVERT: A 111 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8688 (p) REVERT: A 308 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8321 (tmm) REVERT: A 344 MET cc_start: 0.8533 (ptp) cc_final: 0.8015 (ptp) REVERT: A 587 MET cc_start: 0.8103 (tpp) cc_final: 0.7865 (mmt) REVERT: A 623 PHE cc_start: 0.8433 (t80) cc_final: 0.8113 (t80) REVERT: A 634 PHE cc_start: 0.7781 (m-10) cc_final: 0.7546 (m-80) REVERT: A 638 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8565 (mt) REVERT: A 782 MET cc_start: 0.8643 (ttm) cc_final: 0.8316 (ttt) REVERT: C 128 GLN cc_start: 0.8502 (mp10) cc_final: 0.8193 (mp10) REVERT: E 484 TYR cc_start: 0.8798 (m-80) cc_final: 0.7549 (m-80) REVERT: E 486 ASP cc_start: 0.9202 (p0) cc_final: 0.8943 (p0) REVERT: E 514 ASP cc_start: 0.8889 (t0) cc_final: 0.8140 (m-30) REVERT: E 539 TYR cc_start: 0.8374 (m-80) cc_final: 0.7723 (m-80) REVERT: G 66 GLU cc_start: 0.8830 (pm20) cc_final: 0.8522 (pm20) REVERT: G 68 MET cc_start: 0.8854 (mtm) cc_final: 0.8491 (mtp) REVERT: G 114 LYS cc_start: 0.9190 (ttpp) cc_final: 0.8843 (mmtm) REVERT: G 139 MET cc_start: 0.6987 (tpp) cc_final: 0.6736 (tpp) REVERT: D 80 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8069 (p90) REVERT: D 137 ASP cc_start: 0.8480 (m-30) cc_final: 0.8138 (m-30) REVERT: D 308 MET cc_start: 0.9152 (ttt) cc_final: 0.8909 (ttt) REVERT: D 587 MET cc_start: 0.8198 (tpp) cc_final: 0.7874 (mmt) REVERT: D 721 MET cc_start: 0.8072 (tmm) cc_final: 0.7827 (tmm) REVERT: D 754 PHE cc_start: 0.9079 (m-80) cc_final: 0.8607 (m-80) REVERT: H 100 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.6169 (tm-30) REVERT: I 475 THR cc_start: 0.8053 (m) cc_final: 0.7621 (p) REVERT: I 479 ASP cc_start: 0.9617 (m-30) cc_final: 0.9379 (p0) REVERT: I 497 ASP cc_start: 0.8231 (t0) cc_final: 0.7884 (t0) REVERT: I 517 MET cc_start: 0.7836 (tpp) cc_final: 0.7398 (tpt) REVERT: I 539 TYR cc_start: 0.8513 (m-80) cc_final: 0.8046 (m-80) REVERT: J 64 ARG cc_start: 0.8391 (tpp80) cc_final: 0.8051 (ttm-80) REVERT: J 99 GLU cc_start: 0.9114 (pp20) cc_final: 0.8545 (pp20) REVERT: J 100 ASN cc_start: 0.9587 (m-40) cc_final: 0.9196 (m-40) REVERT: J 102 ASP cc_start: 0.8533 (m-30) cc_final: 0.8219 (m-30) REVERT: J 107 LYS cc_start: 0.9586 (ttmm) cc_final: 0.9313 (ttmm) outliers start: 72 outliers final: 52 residues processed: 229 average time/residue: 0.2539 time to fit residues: 93.8793 Evaluate side-chains 225 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 477 ASP Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 87 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 191 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN A 379 GLN A 756 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.097770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.067479 restraints weight = 53118.919| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 4.42 r_work: 0.3125 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17972 Z= 0.182 Angle : 0.614 12.120 24396 Z= 0.299 Chirality : 0.042 0.160 2812 Planarity : 0.003 0.038 3097 Dihedral : 5.350 57.226 2543 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.14 % Favored : 93.77 % Rotamer: Outliers : 3.30 % Allowed : 17.50 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.52 (0.18), residues: 2215 helix: 0.77 (0.24), residues: 533 sheet: -1.15 (0.31), residues: 320 loop : -1.80 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 751 HIS 0.005 0.000 HIS A 209 PHE 0.027 0.001 PHE A 547 TYR 0.020 0.001 TYR E 484 ARG 0.003 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 188 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7895 (p90) REVERT: A 85 GLU cc_start: 0.8247 (mp0) cc_final: 0.7908 (mp0) REVERT: A 111 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8666 (p) REVERT: A 308 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8348 (tmm) REVERT: A 344 MET cc_start: 0.8423 (ptp) cc_final: 0.7906 (ptp) REVERT: A 354 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8395 (p0) REVERT: A 587 MET cc_start: 0.8048 (tpp) cc_final: 0.7809 (mmt) REVERT: A 623 PHE cc_start: 0.8458 (t80) cc_final: 0.8108 (t80) REVERT: A 634 PHE cc_start: 0.7740 (m-10) cc_final: 0.7530 (m-80) REVERT: A 638 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 782 MET cc_start: 0.8628 (ttm) cc_final: 0.8270 (ttt) REVERT: C 128 GLN cc_start: 0.8463 (mp10) cc_final: 0.8145 (mp10) REVERT: E 459 MET cc_start: 0.8912 (mtp) cc_final: 0.8590 (ttm) REVERT: E 464 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7346 (tm-30) REVERT: E 484 TYR cc_start: 0.8757 (m-80) cc_final: 0.7512 (m-80) REVERT: E 486 ASP cc_start: 0.9192 (p0) cc_final: 0.8944 (p0) REVERT: E 514 ASP cc_start: 0.8817 (t0) cc_final: 0.8164 (m-30) REVERT: E 539 TYR cc_start: 0.8418 (m-80) cc_final: 0.7746 (m-80) REVERT: G 64 ARG cc_start: 0.8021 (ptp-110) cc_final: 0.7362 (ptp-110) REVERT: G 66 GLU cc_start: 0.8889 (pm20) cc_final: 0.8571 (pm20) REVERT: G 114 LYS cc_start: 0.9199 (ttpp) cc_final: 0.8869 (mmtm) REVERT: G 139 MET cc_start: 0.6915 (tpp) cc_final: 0.6669 (tpp) REVERT: D 80 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8055 (p90) REVERT: D 85 GLU cc_start: 0.7872 (mp0) cc_final: 0.7479 (mp0) REVERT: D 137 ASP cc_start: 0.8302 (m-30) cc_final: 0.7882 (m-30) REVERT: D 308 MET cc_start: 0.9158 (ttt) cc_final: 0.8909 (ttt) REVERT: D 587 MET cc_start: 0.8222 (tpp) cc_final: 0.7877 (mmt) REVERT: D 623 PHE cc_start: 0.8298 (t80) cc_final: 0.8068 (t80) REVERT: D 637 MET cc_start: 0.5330 (tpt) cc_final: 0.5066 (tpp) REVERT: D 721 MET cc_start: 0.8071 (tmm) cc_final: 0.7710 (tmm) REVERT: D 754 PHE cc_start: 0.9046 (m-80) cc_final: 0.8559 (m-80) REVERT: I 475 THR cc_start: 0.7921 (m) cc_final: 0.7190 (p) REVERT: I 479 ASP cc_start: 0.9620 (m-30) cc_final: 0.9405 (p0) REVERT: I 497 ASP cc_start: 0.8121 (t0) cc_final: 0.7791 (t0) REVERT: I 517 MET cc_start: 0.7960 (tpp) cc_final: 0.7695 (tpt) REVERT: I 539 TYR cc_start: 0.8475 (m-80) cc_final: 0.8042 (m-80) REVERT: J 64 ARG cc_start: 0.8413 (tpp80) cc_final: 0.8185 (tpp80) REVERT: J 102 ASP cc_start: 0.8604 (m-30) cc_final: 0.8311 (m-30) REVERT: J 107 LYS cc_start: 0.9584 (ttmm) cc_final: 0.9298 (ttmm) outliers start: 64 outliers final: 46 residues processed: 237 average time/residue: 0.2790 time to fit residues: 106.0618 Evaluate side-chains 224 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 477 ASP Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 155 optimal weight: 0.0000 chunk 106 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** 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 = 0.3927 r_free = 0.3927 target = 0.096856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.066363 restraints weight = 53673.236| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.43 r_work: 0.3091 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17972 Z= 0.245 Angle : 0.651 12.131 24396 Z= 0.318 Chirality : 0.043 0.201 2812 Planarity : 0.004 0.036 3097 Dihedral : 5.400 58.505 2541 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.81 % Favored : 92.10 % Rotamer: Outliers : 3.46 % Allowed : 17.40 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2215 helix: 0.83 (0.24), residues: 527 sheet: -1.09 (0.31), residues: 320 loop : -1.80 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 751 HIS 0.007 0.001 HIS A 209 PHE 0.027 0.001 PHE D 547 TYR 0.017 0.001 TYR E 484 ARG 0.004 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 178 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7911 (p90) REVERT: A 85 GLU cc_start: 0.8242 (mp0) cc_final: 0.7895 (mp0) REVERT: A 111 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8646 (p) REVERT: A 308 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8376 (tmm) REVERT: A 344 MET cc_start: 0.8417 (ptp) cc_final: 0.7891 (ptp) REVERT: A 354 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8403 (p0) REVERT: A 587 MET cc_start: 0.8160 (tpp) cc_final: 0.7919 (mmt) REVERT: A 623 PHE cc_start: 0.8476 (t80) cc_final: 0.8147 (t80) REVERT: A 634 PHE cc_start: 0.7718 (m-10) cc_final: 0.7508 (m-80) REVERT: A 638 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 721 MET cc_start: 0.7034 (ptp) cc_final: 0.6596 (ttp) REVERT: A 782 MET cc_start: 0.8674 (ttm) cc_final: 0.8340 (ttt) REVERT: C 128 GLN cc_start: 0.8502 (mp10) cc_final: 0.8184 (mp10) REVERT: E 464 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7362 (tm-30) REVERT: E 484 TYR cc_start: 0.8789 (m-80) cc_final: 0.7571 (m-80) REVERT: E 486 ASP cc_start: 0.9184 (p0) cc_final: 0.8956 (p0) REVERT: E 514 ASP cc_start: 0.9014 (t0) cc_final: 0.8252 (m-30) REVERT: E 539 TYR cc_start: 0.8409 (m-80) cc_final: 0.7741 (m-80) REVERT: G 64 ARG cc_start: 0.8028 (ptp-110) cc_final: 0.6919 (ptp-110) REVERT: G 66 GLU cc_start: 0.8844 (pm20) cc_final: 0.8530 (pm20) REVERT: G 114 LYS cc_start: 0.9204 (ttpp) cc_final: 0.8865 (mmtm) REVERT: G 139 MET cc_start: 0.6926 (tpp) cc_final: 0.6689 (tpp) REVERT: D 80 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8083 (p90) REVERT: D 137 ASP cc_start: 0.8407 (m-30) cc_final: 0.8086 (m-30) REVERT: D 308 MET cc_start: 0.9150 (ttt) cc_final: 0.8892 (ttt) REVERT: D 623 PHE cc_start: 0.8318 (t80) cc_final: 0.8079 (t80) REVERT: D 637 MET cc_start: 0.5379 (tpt) cc_final: 0.5077 (tpp) REVERT: D 721 MET cc_start: 0.8032 (tmm) cc_final: 0.7664 (tmm) REVERT: D 754 PHE cc_start: 0.9054 (m-80) cc_final: 0.8582 (m-80) REVERT: H 100 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.5851 (tm-30) REVERT: I 479 ASP cc_start: 0.9620 (m-30) cc_final: 0.9399 (p0) REVERT: I 497 ASP cc_start: 0.7941 (t0) cc_final: 0.7698 (t0) REVERT: I 504 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8930 (m-80) REVERT: I 517 MET cc_start: 0.7929 (tpp) cc_final: 0.7665 (tpt) REVERT: I 539 TYR cc_start: 0.8401 (m-80) cc_final: 0.7962 (m-80) REVERT: J 107 LYS cc_start: 0.9595 (ttmm) cc_final: 0.9315 (ttmm) outliers start: 67 outliers final: 52 residues processed: 231 average time/residue: 0.2700 time to fit residues: 99.8363 Evaluate side-chains 228 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 520 CYS Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 504 TYR Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 142 optimal weight: 0.0050 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 chunk 65 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 222 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 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 = 0.3958 r_free = 0.3958 target = 0.098505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068291 restraints weight = 53798.918| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 4.46 r_work: 0.3137 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17972 Z= 0.172 Angle : 0.632 14.687 24396 Z= 0.305 Chirality : 0.042 0.176 2812 Planarity : 0.003 0.060 3097 Dihedral : 5.217 59.801 2541 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 2.79 % Allowed : 18.17 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.38 (0.18), residues: 2215 helix: 0.73 (0.24), residues: 549 sheet: -0.96 (0.32), residues: 320 loop : -1.68 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 751 HIS 0.005 0.000 HIS A 209 PHE 0.028 0.001 PHE D 547 TYR 0.019 0.001 TYR E 484 ARG 0.005 0.000 ARG J 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.7870 (p90) REVERT: A 85 GLU cc_start: 0.8280 (mp0) cc_final: 0.7942 (mp0) REVERT: A 111 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8724 (p) REVERT: A 308 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8341 (tmm) REVERT: A 344 MET cc_start: 0.8390 (ptp) cc_final: 0.7867 (ptp) REVERT: A 354 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8385 (p0) REVERT: A 587 MET cc_start: 0.8058 (tpp) cc_final: 0.7835 (mmt) REVERT: A 623 PHE cc_start: 0.8502 (t80) cc_final: 0.8136 (t80) REVERT: A 638 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8492 (mt) REVERT: A 721 MET cc_start: 0.7171 (ptp) cc_final: 0.6663 (ttp) REVERT: A 782 MET cc_start: 0.8595 (ttm) cc_final: 0.8227 (ttt) REVERT: C 97 GLU cc_start: 0.8580 (pm20) cc_final: 0.8327 (pm20) REVERT: C 128 GLN cc_start: 0.8454 (mp10) cc_final: 0.8130 (mp10) REVERT: E 484 TYR cc_start: 0.8793 (m-80) cc_final: 0.8391 (m-80) REVERT: E 486 ASP cc_start: 0.9183 (p0) cc_final: 0.8960 (p0) REVERT: E 514 ASP cc_start: 0.8991 (t0) cc_final: 0.8246 (m-30) REVERT: E 539 TYR cc_start: 0.8454 (m-80) cc_final: 0.7782 (m-80) REVERT: G 64 ARG cc_start: 0.8097 (ptp-110) cc_final: 0.7459 (ptp-110) REVERT: G 66 GLU cc_start: 0.8881 (pm20) cc_final: 0.8595 (pm20) REVERT: G 114 LYS cc_start: 0.9206 (ttpp) cc_final: 0.8839 (mmtm) REVERT: G 139 MET cc_start: 0.7014 (tpp) cc_final: 0.6717 (tpt) REVERT: D 85 GLU cc_start: 0.7868 (mp0) cc_final: 0.7459 (mp0) REVERT: D 137 ASP cc_start: 0.8258 (m-30) cc_final: 0.7871 (m-30) REVERT: D 308 MET cc_start: 0.9197 (ttt) cc_final: 0.8942 (ttt) REVERT: D 344 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8164 (ptt) REVERT: D 419 ASP cc_start: 0.8432 (t0) cc_final: 0.8192 (t0) REVERT: D 623 PHE cc_start: 0.8250 (t80) cc_final: 0.7988 (t80) REVERT: D 637 MET cc_start: 0.5322 (tpt) cc_final: 0.5037 (tpp) REVERT: D 721 MET cc_start: 0.8043 (tmm) cc_final: 0.7669 (tmm) REVERT: D 754 PHE cc_start: 0.9055 (m-80) cc_final: 0.8564 (m-80) REVERT: I 475 THR cc_start: 0.7884 (m) cc_final: 0.7452 (p) REVERT: I 486 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8749 (p0) REVERT: I 517 MET cc_start: 0.8039 (tpp) cc_final: 0.7839 (tpt) REVERT: I 522 SER cc_start: 0.8581 (t) cc_final: 0.8033 (t) REVERT: I 539 TYR cc_start: 0.8387 (m-80) cc_final: 0.7948 (m-80) REVERT: J 64 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: J 66 GLU cc_start: 0.8511 (pm20) cc_final: 0.8094 (pm20) REVERT: J 99 GLU cc_start: 0.9040 (pp20) cc_final: 0.8833 (pp20) REVERT: J 107 LYS cc_start: 0.9579 (ttmm) cc_final: 0.9297 (ttmm) REVERT: J 118 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: J 126 ASP cc_start: 0.8199 (p0) cc_final: 0.7267 (p0) outliers start: 54 outliers final: 42 residues processed: 226 average time/residue: 0.2701 time to fit residues: 97.9212 Evaluate side-chains 222 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 84 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 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 = 0.3938 r_free = 0.3938 target = 0.097502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067041 restraints weight = 53809.896| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.46 r_work: 0.3107 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17972 Z= 0.227 Angle : 0.644 11.744 24396 Z= 0.315 Chirality : 0.043 0.199 2812 Planarity : 0.003 0.057 3097 Dihedral : 5.159 59.137 2537 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.40 % Favored : 92.51 % Rotamer: Outliers : 2.94 % Allowed : 18.38 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.40 (0.18), residues: 2215 helix: 0.77 (0.24), residues: 546 sheet: -0.95 (0.32), residues: 320 loop : -1.73 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 751 HIS 0.007 0.001 HIS A 209 PHE 0.027 0.001 PHE D 547 TYR 0.018 0.001 TYR E 484 ARG 0.005 0.000 ARG J 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8538 (m-30) cc_final: 0.8245 (t0) REVERT: A 80 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7879 (p90) REVERT: A 85 GLU cc_start: 0.8273 (mp0) cc_final: 0.8063 (mp0) REVERT: A 87 GLN cc_start: 0.8824 (mp10) cc_final: 0.8429 (mp10) REVERT: A 111 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8636 (p) REVERT: A 308 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8374 (tmm) REVERT: A 344 MET cc_start: 0.8337 (ptp) cc_final: 0.7820 (ptp) REVERT: A 354 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8429 (p0) REVERT: A 587 MET cc_start: 0.8098 (tpp) cc_final: 0.7864 (mmt) REVERT: A 623 PHE cc_start: 0.8564 (t80) cc_final: 0.8199 (t80) REVERT: A 638 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 718 PHE cc_start: 0.8585 (m-80) cc_final: 0.8231 (m-80) REVERT: A 721 MET cc_start: 0.7125 (ptp) cc_final: 0.6584 (ttp) REVERT: A 782 MET cc_start: 0.8593 (ttm) cc_final: 0.8233 (ttt) REVERT: C 97 GLU cc_start: 0.8612 (pm20) cc_final: 0.8349 (pm20) REVERT: C 128 GLN cc_start: 0.8502 (mp10) cc_final: 0.8166 (mp10) REVERT: C 226 PHE cc_start: 0.5996 (m-10) cc_final: 0.5762 (m-10) REVERT: E 484 TYR cc_start: 0.8828 (m-80) cc_final: 0.8430 (m-80) REVERT: E 486 ASP cc_start: 0.9189 (p0) cc_final: 0.8987 (p0) REVERT: E 514 ASP cc_start: 0.9045 (t0) cc_final: 0.8303 (m-30) REVERT: E 539 TYR cc_start: 0.8426 (m-80) cc_final: 0.7736 (m-80) REVERT: G 64 ARG cc_start: 0.8074 (ptp-110) cc_final: 0.7078 (ptp-110) REVERT: G 66 GLU cc_start: 0.8852 (pm20) cc_final: 0.8556 (pm20) REVERT: G 114 LYS cc_start: 0.9215 (ttpp) cc_final: 0.8845 (mmtm) REVERT: G 139 MET cc_start: 0.6999 (tpp) cc_final: 0.6714 (tpt) REVERT: D 85 GLU cc_start: 0.7864 (mp0) cc_final: 0.7412 (mp0) REVERT: D 308 MET cc_start: 0.9166 (ttt) cc_final: 0.8909 (ttt) REVERT: D 344 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8116 (ptp) REVERT: D 623 PHE cc_start: 0.8256 (t80) cc_final: 0.7995 (t80) REVERT: D 637 MET cc_start: 0.5440 (tpt) cc_final: 0.5134 (tpp) REVERT: D 721 MET cc_start: 0.8029 (tmm) cc_final: 0.7671 (tmm) REVERT: D 754 PHE cc_start: 0.9057 (m-80) cc_final: 0.8585 (m-80) REVERT: I 475 THR cc_start: 0.7962 (m) cc_final: 0.7479 (p) REVERT: I 486 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8707 (p0) REVERT: I 522 SER cc_start: 0.8528 (t) cc_final: 0.7919 (t) REVERT: I 539 TYR cc_start: 0.8394 (m-80) cc_final: 0.7947 (m-80) REVERT: J 64 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.8069 (ttm-80) REVERT: J 66 GLU cc_start: 0.8365 (pm20) cc_final: 0.7942 (pm20) REVERT: J 107 LYS cc_start: 0.9581 (ttmm) cc_final: 0.9288 (ttmm) outliers start: 57 outliers final: 47 residues processed: 223 average time/residue: 0.2630 time to fit residues: 94.3085 Evaluate side-chains 226 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 520 CYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 104 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 181 optimal weight: 0.0170 chunk 162 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 183 optimal weight: 0.1980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN C 206 GLN ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.098983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068825 restraints weight = 53632.480| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.46 r_work: 0.3151 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17972 Z= 0.167 Angle : 0.674 25.075 24396 Z= 0.325 Chirality : 0.043 0.245 2812 Planarity : 0.003 0.055 3097 Dihedral : 5.050 58.315 2537 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 2.84 % Allowed : 18.43 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.32 (0.18), residues: 2215 helix: 0.81 (0.24), residues: 543 sheet: -0.80 (0.32), residues: 316 loop : -1.69 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 751 HIS 0.005 0.000 HIS A 209 PHE 0.030 0.001 PHE A 759 TYR 0.018 0.001 TYR E 484 ARG 0.005 0.000 ARG J 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11625.71 seconds wall clock time: 206 minutes 42.44 seconds (12402.44 seconds total)