Starting phenix.real_space_refine on Sat Jun 21 07:28:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7krz_23013/06_2025/7krz_23013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krz_23013/06_2025/7krz_23013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7krz_23013/06_2025/7krz_23013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krz_23013/06_2025/7krz_23013.map" model { file = "/net/cci-nas-00/data/ceres_data/7krz_23013/06_2025/7krz_23013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krz_23013/06_2025/7krz_23013.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 119 5.16 5 B 6 2.79 5 C 15667 2.51 5 N 4236 2.21 5 O 4697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24745 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4098 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "B" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4096 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4100 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4051 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4014 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 492} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 3976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3976 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 24, 'TRANS': 487} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'BO2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'BO2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'BO2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'BO2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ADP': 1, 'BO2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ADP': 1, 'BO2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.00, per 1000 atoms: 0.61 Number of scatterers: 24745 At special positions: 0 Unit cell: (135.7, 141.45, 131.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 119 16.00 P 16 15.00 Mg 4 11.99 O 4697 8.00 N 4236 7.00 C 15667 6.00 B 6 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 3.1 seconds 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5836 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 30 sheets defined 47.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 417 through 425 removed outlier: 3.716A pdb=" N LEU A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 4.689A pdb=" N VAL A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.797A pdb=" N ASN A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.887A pdb=" N ASP A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.878A pdb=" N ARG A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 540 removed outlier: 4.477A pdb=" N SER A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.819A pdb=" N GLU A 557 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.687A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 4.049A pdb=" N THR A 644 " --> pdb=" O VAL A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 938 through 947 removed outlier: 4.091A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.847A pdb=" N GLU B 427 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 removed outlier: 4.171A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.757A pdb=" N ASN B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'B' and resid 531 through 540 removed outlier: 3.912A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 570 through 581 removed outlier: 4.112A pdb=" N ILE B 574 " --> pdb=" O PRO B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.913A pdb=" N ILE B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 605 Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 614 through 618 removed outlier: 4.182A pdb=" N ALA B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 Processing helix chain 'B' and resid 662 through 683 removed outlier: 5.836A pdb=" N VAL B 675 " --> pdb=" O GLU B 671 " (cutoff:3.500A) Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 742 through 747 Processing helix chain 'B' and resid 807 through 829 Processing helix chain 'B' and resid 856 through 869 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 938 through 947 removed outlier: 4.050A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 4.234A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 removed outlier: 3.896A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'C' and resid 530 through 540 removed outlier: 4.282A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 592 through 595 removed outlier: 3.765A pdb=" N ILE C 595 " --> pdb=" O VAL C 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 592 through 595' Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.871A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 618 removed outlier: 4.119A pdb=" N ALA C 617 " --> pdb=" O GLU C 614 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN C 618 " --> pdb=" O GLN C 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 614 through 618' Processing helix chain 'C' and resid 646 through 651 Processing helix chain 'C' and resid 662 through 683 removed outlier: 5.625A pdb=" N VAL C 675 " --> pdb=" O GLU C 671 " (cutoff:3.500A) Proline residue: C 676 - end of helix Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 729 removed outlier: 3.612A pdb=" N GLN C 713 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 747 Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 938 through 947 removed outlier: 4.136A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 425 removed outlier: 3.852A pdb=" N LEU D 425 " --> pdb=" O PHE D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 452 through 467 removed outlier: 3.587A pdb=" N ASN D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 489 Processing helix chain 'D' and resid 494 through 512 Processing helix chain 'D' and resid 528 through 541 removed outlier: 3.672A pdb=" N ALA D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 570 through 581 removed outlier: 4.348A pdb=" N ILE D 574 " --> pdb=" O PRO D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 611 Processing helix chain 'D' and resid 612 through 617 removed outlier: 4.373A pdb=" N ALA D 617 " --> pdb=" O PRO D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 710 through 729 removed outlier: 3.624A pdb=" N LYS D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 747 Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 922 Processing helix chain 'D' and resid 938 through 947 removed outlier: 4.060A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 removed outlier: 3.563A pdb=" N LEU E 425 " --> pdb=" O ARG E 422 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS E 426 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 Processing helix chain 'E' and resid 452 through 468 Processing helix chain 'E' and resid 479 through 491 removed outlier: 3.623A pdb=" N GLU E 489 " --> pdb=" O ALA E 485 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS E 491 " --> pdb=" O LEU E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 512 removed outlier: 3.509A pdb=" N LYS E 498 " --> pdb=" O MET E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 540 removed outlier: 3.660A pdb=" N ARG E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 573 through 581 Processing helix chain 'E' and resid 603 through 611 Processing helix chain 'E' and resid 648 through 652 Processing helix chain 'E' and resid 662 through 683 removed outlier: 4.689A pdb=" N VAL E 675 " --> pdb=" O GLU E 671 " (cutoff:3.500A) Proline residue: E 676 - end of helix Processing helix chain 'E' and resid 692 through 702 Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 921 Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.981A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 426 Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.601A pdb=" N MET F 435 " --> pdb=" O PRO F 431 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 466 removed outlier: 3.861A pdb=" N THR F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 490 removed outlier: 4.180A pdb=" N ASP F 490 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 512 Processing helix chain 'F' and resid 530 through 540 Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.801A pdb=" N ILE F 595 " --> pdb=" O VAL F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 611 Processing helix chain 'F' and resid 646 through 652 removed outlier: 4.304A pdb=" N ARG F 650 " --> pdb=" O PRO F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 673 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.720A pdb=" N LYS F 714 " --> pdb=" O ARG F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 742 through 747 Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 856 through 869 Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 938 through 947 removed outlier: 4.072A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.743A pdb=" N PHE A 545 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP A 590 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 547 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE A 518 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE A 656 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 620 Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690 removed outlier: 3.536A pdb=" N LYS A 690 " --> pdb=" O VAL A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 765 through 769 removed outlier: 6.058A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.780A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA7, first strand: chain 'B' and resid 543 through 548 removed outlier: 6.796A pdb=" N GLU B 543 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 588 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP B 590 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE B 636 " --> pdb=" O PRO B 585 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR B 638 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE B 589 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 519 " --> pdb=" O CYS B 637 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA B 639 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE B 521 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=AA9, first strand: chain 'B' and resid 689 through 691 removed outlier: 3.788A pdb=" N VAL B 737 " --> pdb=" O LYS B 690 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 799 through 803 removed outlier: 5.929A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N MET B 766 " --> pdb=" O MET B 879 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AB3, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB4, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.482A pdb=" N ILE C 587 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N THR C 638 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE C 589 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 619 through 620 Processing sheet with id=AB6, first strand: chain 'C' and resid 689 through 690 removed outlier: 4.119A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 799 through 803 removed outlier: 6.094A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 765 " --> pdb=" O VAL C 780 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET C 766 " --> pdb=" O MET C 879 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C 910 " --> pdb=" O HIS C 934 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL C 936 " --> pdb=" O ILE C 910 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 912 " --> pdb=" O VAL C 936 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB9, first strand: chain 'D' and resid 544 through 548 removed outlier: 7.018A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D 587 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR D 638 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE D 589 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE D 518 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.931A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 765 through 771 removed outlier: 6.094A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 878 through 879 removed outlier: 6.916A pdb=" N ALA D 878 " --> pdb=" O VAL D 911 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC5, first strand: chain 'E' and resid 545 through 548 removed outlier: 6.358A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.783A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 799 through 803 removed outlier: 6.110A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N MET E 766 " --> pdb=" O MET E 879 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA E 878 " --> pdb=" O VAL E 911 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 882 through 883 Processing sheet with id=AC9, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.990A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU F 519 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA F 639 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE F 521 " --> pdb=" O ALA F 639 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 689 through 690 removed outlier: 3.667A pdb=" N LYS F 690 " --> pdb=" O VAL F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 799 through 803 removed outlier: 6.061A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET F 766 " --> pdb=" O MET F 879 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 882 through 883 1057 hydrogen bonds defined for protein. 3084 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: 8.53 Time building geometry restraints manager: 7.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4170 1.30 - 1.43: 6008 1.43 - 1.56: 14787 1.56 - 1.68: 32 1.68 - 1.81: 196 Bond restraints: 25193 Sorted by residual: bond pdb=" C4 ATP D1000 " pdb=" C5 ATP D1000 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.71e+01 bond pdb=" C4 ATP C1000 " pdb=" C5 ATP C1000 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.52e+01 bond pdb=" C4 ATP A1000 " pdb=" C5 ATP A1000 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C4 ATP B1000 " pdb=" C5 ATP B1000 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" C5 ATP A1000 " pdb=" C6 ATP A1000 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.42e+01 ... (remaining 25188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 33894 3.60 - 7.20: 188 7.20 - 10.80: 27 10.80 - 14.41: 9 14.41 - 18.01: 5 Bond angle restraints: 34123 Sorted by residual: angle pdb=" PB ATP D1000 " pdb=" O3B ATP D1000 " pdb=" PG ATP D1000 " ideal model delta sigma weight residual 139.87 121.86 18.01 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PA ATP C1000 " pdb=" O3A ATP C1000 " pdb=" PB ATP C1000 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP D1000 " pdb=" O3A ATP D1000 " pdb=" PB ATP D1000 " ideal model delta sigma weight residual 136.83 121.39 15.44 1.00e+00 1.00e+00 2.38e+02 angle pdb=" PB ATP A1000 " pdb=" O3B ATP A1000 " pdb=" PG ATP A1000 " ideal model delta sigma weight residual 139.87 124.54 15.33 1.00e+00 1.00e+00 2.35e+02 angle pdb=" PA ATP A1000 " pdb=" O3A ATP A1000 " pdb=" PB ATP A1000 " ideal model delta sigma weight residual 136.83 121.82 15.01 1.00e+00 1.00e+00 2.25e+02 ... (remaining 34118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13913 17.90 - 35.79: 1186 35.79 - 53.69: 235 53.69 - 71.59: 54 71.59 - 89.49: 40 Dihedral angle restraints: 15428 sinusoidal: 6373 harmonic: 9055 Sorted by residual: dihedral pdb=" CA PRO D 845 " pdb=" C PRO D 845 " pdb=" N GLU D 846 " pdb=" CA GLU D 846 " ideal model delta harmonic sigma weight residual 180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA PRO A 845 " pdb=" C PRO A 845 " pdb=" N GLU A 846 " pdb=" CA GLU A 846 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA THR A 752 " pdb=" C THR A 752 " pdb=" N VAL A 753 " pdb=" CA VAL A 753 " ideal model delta harmonic sigma weight residual 180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 15425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2255 0.035 - 0.070: 1159 0.070 - 0.105: 353 0.105 - 0.139: 123 0.139 - 0.174: 19 Chirality restraints: 3909 Sorted by residual: chirality pdb=" C21 BO2 B1002 " pdb=" B26 BO2 B1002 " pdb=" C22 BO2 B1002 " pdb=" N20 BO2 B1002 " both_signs ideal model delta sigma weight residual False 2.49 2.66 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" C1' ATP B1000 " pdb=" C2' ATP B1000 " pdb=" N9 ATP B1000 " pdb=" O4' ATP B1000 " both_signs ideal model delta sigma weight residual False 2.41 2.58 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C3' ADP E1001 " pdb=" C2' ADP E1001 " pdb=" C4' ADP E1001 " pdb=" O3' ADP E1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 3906 not shown) Planarity restraints: 4358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 761 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO E 762 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 762 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 762 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 569 " 0.038 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 570 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 761 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 762 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 762 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 762 " -0.027 5.00e-02 4.00e+02 ... (remaining 4355 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 139 2.50 - 3.10: 18109 3.10 - 3.70: 37323 3.70 - 4.30: 56144 4.30 - 4.90: 93616 Nonbonded interactions: 205331 Sorted by model distance: nonbonded pdb=" O1G ATP C1000 " pdb="MG MG C1001 " model vdw 1.906 2.170 nonbonded pdb=" O2B ATP A1000 " pdb="MG MG A1001 " model vdw 1.935 2.170 nonbonded pdb=" O3G ATP D1000 " pdb="MG MG D1001 " model vdw 1.984 2.170 nonbonded pdb=" OG1 THR C 530 " pdb="MG MG C1001 " model vdw 2.025 2.170 nonbonded pdb=" OG1 THR B 530 " pdb="MG MG B1001 " model vdw 2.038 2.170 ... (remaining 205326 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 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 550 or resid 5 \ 56 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 through 596 or resid 603 through 631 or (resid 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 through 649 or (resi \ d 650 and (name N or name CA or name C or name O or name CB )) or resid 651 or ( \ resid 652 and (name N or name CA or name C or name O or name CB )) or resid 653 \ through 685 or (resid 686 and (name N or name CA or name C or name O or name CB \ )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or na \ me O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'B' and (resid 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 550 or resid 5 \ 56 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 through 596 or resid 603 through 631 or (resid 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 through 649 or (resi \ d 650 and (name N or name CA or name C or name O or name CB )) or resid 651 or ( \ resid 652 and (name N or name CA or name C or name O or name CB )) or resid 653 \ through 685 or (resid 686 and (name N or name CA or name C or name O or name CB \ )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or na \ me O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'C' and (resid 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 550 or resid 5 \ 56 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 through 596 or resid 603 through 631 or (resid 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 through 649 or (resi \ d 650 and (name N or name CA or name C or name O or name CB )) or resid 651 or ( \ resid 652 and (name N or name CA or name C or name O or name CB )) or resid 653 \ through 685 or (resid 686 and (name N or name CA or name C or name O or name CB \ )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or na \ me O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'D' and (resid 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 550 or resid 5 \ 56 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 through 631 or (resid 632 and (name N or name CA or name C or \ name O or name CB )) or resid 633 through 649 or (resid 650 and (name N or name \ CA or name C or name O or name CB )) or resid 651 or (resid 652 and (name N or \ name CA or name C or name O or name CB )) or resid 653 through 685 or (resid 686 \ and (name N or name CA or name C or name O or name CB )) or resid 687 through 9 \ 47)) selection = (chain 'E' and (resid 421 through 461 or (resid 462 and (name N or name CA or na \ me C or name O or name CB )) or resid 463 through 550 or resid 556 through 596 o \ r resid 603 through 631 or (resid 632 and (name N or name CA or name C or name O \ or name CB )) or resid 633 through 651 or (resid 652 and (name N or name CA or \ name C or name O or name CB )) or resid 653 through 689 or (resid 690 and (name \ N or name CA or name C or name O or name CB )) or resid 691 through 788 or resid \ 796 through 947)) selection = (chain 'F' and (resid 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 562 or (resid 563 and (name N \ or name CA or name C or name O or name CB )) or resid 564 through 596 or resid 6 \ 03 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 788 or resid 796 through 947)) } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 54.030 Find NCS groups from input model: 1.400 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.009 0.494 25199 Z= 0.652 Angle : 0.799 18.008 34123 Z= 0.470 Chirality : 0.047 0.174 3909 Planarity : 0.005 0.060 4358 Dihedral : 14.695 89.486 9592 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.19 % Allowed : 6.68 % Favored : 93.13 % 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: -2.84 (0.13), residues: 3095 helix: -1.08 (0.12), residues: 1338 sheet: -1.65 (0.25), residues: 405 loop : -2.78 (0.14), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 770 HIS 0.005 0.001 HIS F 491 PHE 0.019 0.002 PHE C 820 TYR 0.016 0.002 TYR A 939 ARG 0.008 0.001 ARG C 710 Details of bonding type rmsd hydrogen bonds : bond 0.14552 ( 1057) hydrogen bonds : angle 6.50988 ( 3084) covalent geometry : bond 0.00737 (25193) covalent geometry : angle 0.79927 (34123) Misc. bond : bond 0.35567 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 382 time to evaluate : 3.022 Fit side-chains REVERT: A 562 ARG cc_start: 0.7431 (mpt180) cc_final: 0.7203 (mtt90) REVERT: A 569 MET cc_start: 0.8397 (mtm) cc_final: 0.8140 (mtp) REVERT: A 651 ASP cc_start: 0.7557 (m-30) cc_final: 0.7321 (m-30) REVERT: A 810 MET cc_start: 0.8064 (ttt) cc_final: 0.7820 (ttt) REVERT: A 915 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7199 (mp0) REVERT: A 922 ASP cc_start: 0.6613 (t0) cc_final: 0.6148 (t0) REVERT: B 579 LYS cc_start: 0.8037 (mttm) cc_final: 0.7832 (mtmm) REVERT: B 597 ARG cc_start: 0.7101 (ptp-110) cc_final: 0.6760 (ptp90) REVERT: B 776 SER cc_start: 0.8583 (t) cc_final: 0.8319 (m) REVERT: B 808 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6551 (tp30) REVERT: B 918 LYS cc_start: 0.7646 (mmtm) cc_final: 0.7318 (tptt) REVERT: C 423 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7129 (tm-30) REVERT: C 424 ARG cc_start: 0.8451 (mtt180) cc_final: 0.8098 (mtt180) REVERT: C 459 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7842 (ttp80) REVERT: C 655 MET cc_start: 0.8118 (mmm) cc_final: 0.7598 (mmm) REVERT: C 713 GLN cc_start: 0.7934 (tt0) cc_final: 0.7670 (mt0) REVERT: D 552 MET cc_start: 0.8592 (ttp) cc_final: 0.8286 (ttm) REVERT: D 569 MET cc_start: 0.8311 (mmm) cc_final: 0.8099 (mmm) REVERT: D 686 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7884 (tp30) REVERT: D 785 ARG cc_start: 0.7829 (mtp-110) cc_final: 0.7322 (mtp180) REVERT: D 915 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7179 (mp0) REVERT: E 432 LYS cc_start: 0.7920 (tmmt) cc_final: 0.7592 (ttpt) REVERT: E 475 ASN cc_start: 0.7522 (t0) cc_final: 0.7241 (t0) REVERT: E 552 MET cc_start: 0.5452 (ppp) cc_final: 0.5160 (ptm) REVERT: E 811 LYS cc_start: 0.7885 (mttt) cc_final: 0.7624 (mttp) REVERT: E 918 LYS cc_start: 0.7914 (pttp) cc_final: 0.7657 (ptpt) REVERT: F 459 ARG cc_start: 0.7163 (ttt180) cc_final: 0.6825 (ttt-90) REVERT: F 482 ARG cc_start: 0.8128 (tmt170) cc_final: 0.7861 (ttp80) REVERT: F 786 ARG cc_start: 0.7473 (mtp180) cc_final: 0.7249 (mtp180) outliers start: 5 outliers final: 4 residues processed: 387 average time/residue: 0.4902 time to fit residues: 277.1053 Evaluate side-chains 290 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 286 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 148 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 475 ASN A 515 GLN A 805 GLN A 832 ASN B 484 GLN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN C 615 GLN D 713 GLN E 743 GLN E 839 HIS F 575 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110217 restraints weight = 34769.240| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.19 r_work: 0.2990 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25199 Z= 0.139 Angle : 0.578 14.029 34123 Z= 0.291 Chirality : 0.043 0.154 3909 Planarity : 0.005 0.055 4358 Dihedral : 10.669 87.837 3670 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.06 % Allowed : 9.02 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3095 helix: 0.45 (0.14), residues: 1341 sheet: -0.89 (0.26), residues: 396 loop : -2.26 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS E 843 PHE 0.016 0.002 PHE F 751 TYR 0.017 0.002 TYR A 939 ARG 0.005 0.000 ARG E 562 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 1057) hydrogen bonds : angle 4.86949 ( 3084) covalent geometry : bond 0.00328 (25193) covalent geometry : angle 0.57757 (34123) Misc. bond : bond 0.00092 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 316 time to evaluate : 3.628 Fit side-chains revert: symmetry clash REVERT: A 609 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 810 MET cc_start: 0.8756 (ttt) cc_final: 0.8549 (ttt) REVERT: A 918 LYS cc_start: 0.8178 (mptt) cc_final: 0.7617 (ptpt) REVERT: A 922 ASP cc_start: 0.7838 (t0) cc_final: 0.7406 (t0) REVERT: B 484 GLN cc_start: 0.8542 (tt0) cc_final: 0.8281 (tt0) REVERT: B 597 ARG cc_start: 0.7033 (ptp-110) cc_final: 0.6695 (ptp90) REVERT: B 808 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7422 (tp30) REVERT: C 424 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8507 (mtt180) REVERT: D 785 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.7882 (mtp180) REVERT: F 459 ARG cc_start: 0.6706 (ttt180) cc_final: 0.6441 (ttt-90) REVERT: F 918 LYS cc_start: 0.8695 (tttt) cc_final: 0.8327 (tttp) outliers start: 28 outliers final: 20 residues processed: 337 average time/residue: 0.5774 time to fit residues: 285.7091 Evaluate side-chains 303 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 283 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 276 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 261 optimal weight: 0.0060 chunk 216 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 107 optimal weight: 0.0980 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 GLN F 433 HIS ** F 509 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 = 0.3591 r_free = 0.3591 target = 0.133602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108896 restraints weight = 34565.458| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.21 r_work: 0.2956 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25199 Z= 0.178 Angle : 0.588 11.720 34123 Z= 0.298 Chirality : 0.044 0.165 3909 Planarity : 0.005 0.054 4358 Dihedral : 10.733 89.670 3670 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.77 % Allowed : 11.25 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3095 helix: 0.91 (0.14), residues: 1339 sheet: -0.72 (0.25), residues: 422 loop : -2.00 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.005 0.001 HIS C 843 PHE 0.019 0.002 PHE B 820 TYR 0.021 0.002 TYR A 939 ARG 0.009 0.001 ARG B 482 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 1057) hydrogen bonds : angle 4.75541 ( 3084) covalent geometry : bond 0.00430 (25193) covalent geometry : angle 0.58788 (34123) Misc. bond : bond 0.00052 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 2.727 Fit side-chains revert: symmetry clash REVERT: A 609 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7798 (mt-10) REVERT: A 918 LYS cc_start: 0.8400 (mptt) cc_final: 0.7941 (ptpt) REVERT: A 922 ASP cc_start: 0.8343 (t0) cc_final: 0.7909 (t0) REVERT: B 484 GLN cc_start: 0.8561 (tt0) cc_final: 0.8294 (tt0) REVERT: B 597 ARG cc_start: 0.7224 (ptp-110) cc_final: 0.6825 (ptp90) REVERT: B 778 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8559 (pp) REVERT: B 808 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7854 (tp30) REVERT: C 424 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8435 (mtt180) REVERT: E 421 PHE cc_start: 0.5025 (OUTLIER) cc_final: 0.4451 (m-80) REVERT: E 460 ASN cc_start: 0.7919 (m-40) cc_final: 0.7570 (m-40) REVERT: F 918 LYS cc_start: 0.8684 (tttt) cc_final: 0.8391 (tttp) outliers start: 47 outliers final: 32 residues processed: 332 average time/residue: 0.4363 time to fit residues: 215.9006 Evaluate side-chains 311 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 292 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 105 optimal weight: 0.0980 chunk 260 optimal weight: 0.0570 chunk 206 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 291 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 290 optimal weight: 9.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN F 509 GLN F 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108685 restraints weight = 34714.863| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.24 r_work: 0.2969 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25199 Z= 0.128 Angle : 0.541 11.526 34123 Z= 0.273 Chirality : 0.042 0.153 3909 Planarity : 0.004 0.050 4358 Dihedral : 10.382 89.841 3670 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.62 % Allowed : 12.45 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3095 helix: 1.28 (0.14), residues: 1341 sheet: -0.53 (0.25), residues: 418 loop : -1.82 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS E 843 PHE 0.018 0.001 PHE A 926 TYR 0.016 0.001 TYR A 939 ARG 0.009 0.000 ARG D 422 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 1057) hydrogen bonds : angle 4.55729 ( 3084) covalent geometry : bond 0.00305 (25193) covalent geometry : angle 0.54071 (34123) Misc. bond : bond 0.00026 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 2.571 Fit side-chains revert: symmetry clash REVERT: A 609 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 918 LYS cc_start: 0.8338 (mptt) cc_final: 0.8048 (ptpt) REVERT: A 922 ASP cc_start: 0.8532 (t0) cc_final: 0.8147 (t0) REVERT: B 484 GLN cc_start: 0.8581 (tt0) cc_final: 0.8293 (tt0) REVERT: B 597 ARG cc_start: 0.6971 (ptp-110) cc_final: 0.6731 (mmm-85) REVERT: B 808 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7813 (tp30) REVERT: B 918 LYS cc_start: 0.8273 (tptt) cc_final: 0.7333 (mmmt) REVERT: C 424 ARG cc_start: 0.8895 (mtt180) cc_final: 0.8595 (mtt180) REVERT: C 651 ASP cc_start: 0.8374 (t0) cc_final: 0.8075 (t0) REVERT: C 918 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7843 (mmtt) REVERT: D 785 ARG cc_start: 0.8593 (mtp-110) cc_final: 0.8162 (mtp180) REVERT: E 421 PHE cc_start: 0.5424 (OUTLIER) cc_final: 0.4638 (m-80) REVERT: E 552 MET cc_start: 0.5713 (ppp) cc_final: 0.5270 (ptm) REVERT: E 778 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8451 (pp) REVERT: F 655 MET cc_start: 0.7618 (mmm) cc_final: 0.5701 (ptm) REVERT: F 918 LYS cc_start: 0.8643 (tttt) cc_final: 0.8376 (tttp) outliers start: 43 outliers final: 30 residues processed: 320 average time/residue: 0.4251 time to fit residues: 202.3270 Evaluate side-chains 310 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 213 optimal weight: 8.9990 chunk 289 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 222 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 268 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 chunk 288 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 HIS F 509 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109878 restraints weight = 34599.527| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.25 r_work: 0.2982 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25199 Z= 0.106 Angle : 0.516 11.164 34123 Z= 0.258 Chirality : 0.041 0.157 3909 Planarity : 0.004 0.049 4358 Dihedral : 10.041 88.856 3670 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 12.94 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3095 helix: 1.57 (0.14), residues: 1337 sheet: -0.42 (0.25), residues: 423 loop : -1.59 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.003 0.001 HIS E 843 PHE 0.014 0.001 PHE B 504 TYR 0.013 0.001 TYR A 939 ARG 0.012 0.000 ARG D 422 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 1057) hydrogen bonds : angle 4.42666 ( 3084) covalent geometry : bond 0.00246 (25193) covalent geometry : angle 0.51649 (34123) Misc. bond : bond 0.00026 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 291 time to evaluate : 3.577 Fit side-chains REVERT: A 609 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 922 ASP cc_start: 0.8408 (t0) cc_final: 0.8005 (t0) REVERT: B 484 GLN cc_start: 0.8537 (tt0) cc_final: 0.8236 (tt0) REVERT: B 597 ARG cc_start: 0.6996 (ptp-110) cc_final: 0.6696 (mmm-85) REVERT: B 778 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8511 (pp) REVERT: B 808 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7851 (tp30) REVERT: B 918 LYS cc_start: 0.8173 (tptt) cc_final: 0.7157 (mmmt) REVERT: C 424 ARG cc_start: 0.8702 (mtt180) cc_final: 0.8396 (mtt180) REVERT: C 651 ASP cc_start: 0.8299 (t0) cc_final: 0.7978 (t0) REVERT: C 918 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7755 (mmtt) REVERT: D 785 ARG cc_start: 0.8603 (mtp-110) cc_final: 0.8126 (mtp180) REVERT: E 421 PHE cc_start: 0.5169 (OUTLIER) cc_final: 0.4413 (m-80) REVERT: E 552 MET cc_start: 0.5362 (ppp) cc_final: 0.5027 (ptm) REVERT: E 778 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8363 (pp) REVERT: F 655 MET cc_start: 0.7465 (mmm) cc_final: 0.5242 (ptm) REVERT: F 918 LYS cc_start: 0.8613 (tttt) cc_final: 0.8353 (tttp) outliers start: 46 outliers final: 38 residues processed: 322 average time/residue: 0.4425 time to fit residues: 215.1647 Evaluate side-chains 315 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 183 optimal weight: 0.7980 chunk 204 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN C 805 GLN ** E 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106493 restraints weight = 34454.804| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.24 r_work: 0.2895 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 25199 Z= 0.326 Angle : 0.704 9.537 34123 Z= 0.356 Chirality : 0.050 0.224 3909 Planarity : 0.006 0.062 4358 Dihedral : 11.197 89.884 3670 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.26 % Allowed : 13.21 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3095 helix: 1.03 (0.14), residues: 1333 sheet: -0.40 (0.26), residues: 417 loop : -1.83 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 470 HIS 0.009 0.001 HIS E 843 PHE 0.028 0.003 PHE D 820 TYR 0.033 0.003 TYR F 939 ARG 0.008 0.001 ARG E 705 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 1057) hydrogen bonds : angle 4.83384 ( 3084) covalent geometry : bond 0.00798 (25193) covalent geometry : angle 0.70386 (34123) Misc. bond : bond 0.00144 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 285 time to evaluate : 3.307 Fit side-chains REVERT: A 918 LYS cc_start: 0.8444 (mptt) cc_final: 0.8080 (ptpt) REVERT: A 922 ASP cc_start: 0.8602 (t0) cc_final: 0.7922 (t0) REVERT: B 482 ARG cc_start: 0.8313 (tmm160) cc_final: 0.8039 (tmm160) REVERT: B 484 GLN cc_start: 0.8705 (tt0) cc_final: 0.8443 (tt0) REVERT: B 597 ARG cc_start: 0.7348 (ptp-110) cc_final: 0.6878 (mmm-85) REVERT: B 918 LYS cc_start: 0.8324 (tptt) cc_final: 0.7354 (mmmt) REVERT: C 424 ARG cc_start: 0.8860 (mtt180) cc_final: 0.8543 (mtt180) REVERT: C 811 LYS cc_start: 0.8640 (mttt) cc_final: 0.8357 (mttt) REVERT: C 918 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7832 (mmtt) REVERT: D 422 ARG cc_start: 0.8842 (mmm-85) cc_final: 0.8445 (mmt90) REVERT: D 770 TRP cc_start: 0.7793 (OUTLIER) cc_final: 0.6828 (p90) REVERT: E 684 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8579 (mp) REVERT: F 638 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8658 (p) REVERT: F 655 MET cc_start: 0.7435 (mmm) cc_final: 0.5274 (ptm) REVERT: F 918 LYS cc_start: 0.8661 (tttt) cc_final: 0.8445 (tttp) outliers start: 60 outliers final: 47 residues processed: 326 average time/residue: 0.4921 time to fit residues: 241.9669 Evaluate side-chains 330 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 chunk 222 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 832 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 640 ASN F 509 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109757 restraints weight = 34415.658| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.26 r_work: 0.2971 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25199 Z= 0.102 Angle : 0.528 10.877 34123 Z= 0.265 Chirality : 0.041 0.149 3909 Planarity : 0.004 0.052 4358 Dihedral : 10.196 88.583 3670 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.51 % Allowed : 14.04 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3095 helix: 1.60 (0.14), residues: 1335 sheet: -0.30 (0.26), residues: 423 loop : -1.51 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 470 HIS 0.002 0.001 HIS B 843 PHE 0.014 0.001 PHE B 504 TYR 0.014 0.001 TYR E 492 ARG 0.006 0.000 ARG E 562 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 1057) hydrogen bonds : angle 4.44392 ( 3084) covalent geometry : bond 0.00231 (25193) covalent geometry : angle 0.52840 (34123) Misc. bond : bond 0.00034 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7915 (pttt) REVERT: A 424 ARG cc_start: 0.8282 (ttm170) cc_final: 0.7851 (ttp-170) REVERT: A 456 ASN cc_start: 0.8118 (m-40) cc_final: 0.7902 (m-40) REVERT: A 569 MET cc_start: 0.8191 (mtm) cc_final: 0.7970 (mtm) REVERT: A 609 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 918 LYS cc_start: 0.8430 (mptt) cc_final: 0.8108 (ptpt) REVERT: A 922 ASP cc_start: 0.8538 (t0) cc_final: 0.7847 (t0) REVERT: B 482 ARG cc_start: 0.8217 (tmm160) cc_final: 0.7926 (tmm160) REVERT: B 484 GLN cc_start: 0.8617 (tt0) cc_final: 0.8321 (tt0) REVERT: B 597 ARG cc_start: 0.7029 (ptp-110) cc_final: 0.6681 (mmm-85) REVERT: C 424 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8331 (mtt180) REVERT: C 651 ASP cc_start: 0.8300 (t0) cc_final: 0.7974 (t0) REVERT: D 422 ARG cc_start: 0.8807 (mmm-85) cc_final: 0.8497 (mmt90) REVERT: D 626 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8707 (m) REVERT: D 770 TRP cc_start: 0.7763 (OUTLIER) cc_final: 0.6873 (p90) REVERT: D 785 ARG cc_start: 0.8597 (mtp-110) cc_final: 0.8109 (mtp180) REVERT: E 684 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8513 (mp) REVERT: F 655 MET cc_start: 0.7494 (mmm) cc_final: 0.5305 (ptm) REVERT: F 918 LYS cc_start: 0.8644 (tttt) cc_final: 0.8386 (tttp) outliers start: 40 outliers final: 33 residues processed: 313 average time/residue: 0.4388 time to fit residues: 205.0108 Evaluate side-chains 305 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 937 GLU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 149 optimal weight: 0.1980 chunk 220 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 119 optimal weight: 0.0870 chunk 147 optimal weight: 0.8980 chunk 290 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.3608 r_free = 0.3608 target = 0.134921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111246 restraints weight = 34358.501| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.27 r_work: 0.2975 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25199 Z= 0.103 Angle : 0.515 10.207 34123 Z= 0.257 Chirality : 0.040 0.149 3909 Planarity : 0.004 0.050 4358 Dihedral : 9.949 89.760 3670 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.66 % Allowed : 14.26 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3095 helix: 1.83 (0.14), residues: 1335 sheet: -0.21 (0.26), residues: 427 loop : -1.38 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 770 HIS 0.002 0.001 HIS D 433 PHE 0.017 0.001 PHE F 545 TYR 0.012 0.001 TYR A 939 ARG 0.006 0.000 ARG E 562 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 1057) hydrogen bonds : angle 4.33158 ( 3084) covalent geometry : bond 0.00237 (25193) covalent geometry : angle 0.51482 (34123) Misc. bond : bond 0.00028 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8140 (ttpt) cc_final: 0.7901 (pttt) REVERT: A 424 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7924 (ttp-170) REVERT: A 569 MET cc_start: 0.8115 (mtm) cc_final: 0.7897 (mtm) REVERT: A 609 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 918 LYS cc_start: 0.8404 (mptt) cc_final: 0.8098 (ptpt) REVERT: A 922 ASP cc_start: 0.8541 (t0) cc_final: 0.7895 (t0) REVERT: B 482 ARG cc_start: 0.8166 (tmm160) cc_final: 0.7913 (tmm160) REVERT: B 484 GLN cc_start: 0.8566 (tt0) cc_final: 0.8254 (tt0) REVERT: B 579 LYS cc_start: 0.8496 (mttp) cc_final: 0.8293 (mtmm) REVERT: B 597 ARG cc_start: 0.6977 (ptp-110) cc_final: 0.6674 (mmm-85) REVERT: C 424 ARG cc_start: 0.8585 (mtt180) cc_final: 0.8259 (mtt180) REVERT: C 651 ASP cc_start: 0.8279 (t0) cc_final: 0.8041 (t70) REVERT: D 626 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8727 (m) REVERT: D 651 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8427 (t0) REVERT: D 770 TRP cc_start: 0.7678 (OUTLIER) cc_final: 0.6816 (p90) REVERT: D 785 ARG cc_start: 0.8615 (mtp-110) cc_final: 0.8109 (mtp180) REVERT: F 655 MET cc_start: 0.7469 (mmm) cc_final: 0.5287 (ptm) REVERT: F 918 LYS cc_start: 0.8598 (tttt) cc_final: 0.8306 (tttm) outliers start: 44 outliers final: 36 residues processed: 310 average time/residue: 0.4602 time to fit residues: 217.4424 Evaluate side-chains 316 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 126 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 272 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 205 optimal weight: 0.0010 chunk 8 optimal weight: 0.8980 chunk 230 optimal weight: 0.0470 overall best weight: 0.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111352 restraints weight = 34536.541| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.23 r_work: 0.3002 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25199 Z= 0.096 Angle : 0.512 10.102 34123 Z= 0.254 Chirality : 0.040 0.150 3909 Planarity : 0.004 0.050 4358 Dihedral : 9.679 87.857 3670 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.66 % Allowed : 14.60 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3095 helix: 1.98 (0.14), residues: 1338 sheet: 0.03 (0.26), residues: 422 loop : -1.28 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 770 HIS 0.002 0.000 HIS C 433 PHE 0.022 0.001 PHE F 545 TYR 0.013 0.001 TYR E 492 ARG 0.011 0.000 ARG D 422 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 1057) hydrogen bonds : angle 4.24190 ( 3084) covalent geometry : bond 0.00218 (25193) covalent geometry : angle 0.51183 (34123) Misc. bond : bond 0.00030 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7929 (pttt) REVERT: A 424 ARG cc_start: 0.8384 (ttm170) cc_final: 0.7962 (ttp-170) REVERT: A 569 MET cc_start: 0.8081 (mtm) cc_final: 0.7859 (mtm) REVERT: A 609 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 918 LYS cc_start: 0.8407 (mptt) cc_final: 0.8105 (ptpt) REVERT: A 922 ASP cc_start: 0.8484 (t0) cc_final: 0.7845 (t0) REVERT: B 482 ARG cc_start: 0.8116 (tmm160) cc_final: 0.7895 (tmm160) REVERT: B 597 ARG cc_start: 0.7010 (ptp-110) cc_final: 0.6774 (mmm-85) REVERT: C 424 ARG cc_start: 0.8443 (mtt180) cc_final: 0.8126 (mtt180) REVERT: C 651 ASP cc_start: 0.8271 (t0) cc_final: 0.8039 (t70) REVERT: D 626 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8695 (m) REVERT: D 651 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8396 (t0) REVERT: D 770 TRP cc_start: 0.7688 (OUTLIER) cc_final: 0.6853 (p90) REVERT: D 785 ARG cc_start: 0.8555 (mtp-110) cc_final: 0.8052 (mtp180) REVERT: E 684 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8502 (mp) REVERT: E 778 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8446 (pp) REVERT: F 547 PHE cc_start: 0.7570 (p90) cc_final: 0.7229 (p90) REVERT: F 638 THR cc_start: 0.8769 (t) cc_final: 0.8557 (t) REVERT: F 655 MET cc_start: 0.7428 (mmm) cc_final: 0.5267 (ptm) REVERT: F 918 LYS cc_start: 0.8594 (tttt) cc_final: 0.8307 (tttm) outliers start: 44 outliers final: 34 residues processed: 313 average time/residue: 0.4788 time to fit residues: 224.5930 Evaluate side-chains 314 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 129 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 584 ASN C 713 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110736 restraints weight = 34439.144| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.27 r_work: 0.2964 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25199 Z= 0.137 Angle : 0.545 10.077 34123 Z= 0.271 Chirality : 0.042 0.149 3909 Planarity : 0.004 0.049 4358 Dihedral : 9.912 88.024 3670 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.51 % Allowed : 14.94 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3095 helix: 1.89 (0.14), residues: 1335 sheet: -0.07 (0.26), residues: 421 loop : -1.30 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 770 HIS 0.003 0.001 HIS E 843 PHE 0.025 0.002 PHE C 545 TYR 0.017 0.002 TYR A 939 ARG 0.013 0.000 ARG D 422 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1057) hydrogen bonds : angle 4.32706 ( 3084) covalent geometry : bond 0.00331 (25193) covalent geometry : angle 0.54521 (34123) Misc. bond : bond 0.00063 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 4.919 Fit side-chains revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7908 (pttt) REVERT: A 424 ARG cc_start: 0.8410 (ttm170) cc_final: 0.8007 (ttp-170) REVERT: A 918 LYS cc_start: 0.8440 (mptt) cc_final: 0.8109 (ptpt) REVERT: A 922 ASP cc_start: 0.8556 (t0) cc_final: 0.7946 (t0) REVERT: B 482 ARG cc_start: 0.8206 (tmm160) cc_final: 0.7908 (tmm160) REVERT: B 597 ARG cc_start: 0.7097 (ptp-110) cc_final: 0.6824 (mmm-85) REVERT: C 424 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8208 (mtt180) REVERT: C 651 ASP cc_start: 0.8315 (t0) cc_final: 0.8093 (t70) REVERT: D 626 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8815 (m) REVERT: D 651 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8482 (t0) REVERT: D 770 TRP cc_start: 0.7731 (OUTLIER) cc_final: 0.6907 (p90) REVERT: D 785 ARG cc_start: 0.8638 (mtp-110) cc_final: 0.8125 (mtp180) REVERT: E 684 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8510 (mp) REVERT: F 547 PHE cc_start: 0.7607 (p90) cc_final: 0.7291 (p90) REVERT: F 655 MET cc_start: 0.7532 (mmm) cc_final: 0.5363 (ptm) REVERT: F 918 LYS cc_start: 0.8620 (tttt) cc_final: 0.8359 (tttm) outliers start: 40 outliers final: 34 residues processed: 308 average time/residue: 0.5400 time to fit residues: 253.4999 Evaluate side-chains 315 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 159 optimal weight: 0.0770 chunk 142 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110540 restraints weight = 34377.984| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.20 r_work: 0.2986 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25199 Z= 0.113 Angle : 0.531 10.158 34123 Z= 0.264 Chirality : 0.041 0.149 3909 Planarity : 0.004 0.051 4358 Dihedral : 9.762 87.465 3670 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.55 % Allowed : 15.02 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3095 helix: 1.95 (0.14), residues: 1336 sheet: 0.00 (0.26), residues: 425 loop : -1.28 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 770 HIS 0.003 0.001 HIS E 843 PHE 0.026 0.001 PHE C 545 TYR 0.014 0.001 TYR A 939 ARG 0.013 0.000 ARG D 422 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 1057) hydrogen bonds : angle 4.28009 ( 3084) covalent geometry : bond 0.00268 (25193) covalent geometry : angle 0.53057 (34123) Misc. bond : bond 0.00046 ( 6) =============================================================================== Job complete usr+sys time: 13091.97 seconds wall clock time: 229 minutes 40.28 seconds (13780.28 seconds total)