Starting phenix.real_space_refine on Mon Sep 30 06:18:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/09_2024/7krz_23013.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/09_2024/7krz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/09_2024/7krz_23013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/09_2024/7krz_23013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/09_2024/7krz_23013.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/09_2024/7krz_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 15.76, per 1000 atoms: 0.64 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: 6.35 Conformation dependent library (CDL) restraints added in 3.2 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: 2.72 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: 9.50 Time building geometry restraints manager: 7.19 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 56.490 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.050 ------------------------------------------------------------------------------- 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 : 0.007 0.108 25193 Z= 0.488 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 382 time to evaluate : 2.872 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: 0.4590 time to fit residues: 257.5802 Evaluate side-chains 290 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 286 time to evaluate : 2.896 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 25193 Z= 0.216 Angle : 0.578 14.029 34123 Z= 0.291 Chirality : 0.043 0.154 3909 Planarity : 0.005 0.055 4358 Dihedral : 10.669 87.836 3670 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.33 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 *********************** 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 fitting. rotamer outliers: 28 poor density : 316 time to evaluate : 2.805 Fit side-chains revert: symmetry clash REVERT: A 422 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7807 (mtt-85) REVERT: A 456 ASN cc_start: 0.8105 (m-40) cc_final: 0.7904 (m-40) REVERT: A 562 ARG cc_start: 0.7358 (mpt180) cc_final: 0.7155 (mtt90) REVERT: A 609 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7077 (mt-10) REVERT: A 651 ASP cc_start: 0.7537 (m-30) cc_final: 0.7318 (m-30) REVERT: A 810 MET cc_start: 0.8320 (ttt) cc_final: 0.8020 (ttt) REVERT: A 918 LYS cc_start: 0.7801 (mptt) cc_final: 0.6921 (ptpt) REVERT: A 922 ASP cc_start: 0.7117 (t0) cc_final: 0.6640 (t0) REVERT: B 482 ARG cc_start: 0.7572 (tmm160) cc_final: 0.7237 (tmm160) REVERT: B 484 GLN cc_start: 0.8050 (tt0) cc_final: 0.7727 (tt0) REVERT: B 597 ARG cc_start: 0.6984 (ptp-110) cc_final: 0.6632 (ptp90) REVERT: B 625 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7817 (t0) REVERT: B 808 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6708 (tp30) REVERT: B 918 LYS cc_start: 0.7472 (mmtm) cc_final: 0.7162 (tptt) REVERT: C 423 GLU cc_start: 0.7282 (tm-30) cc_final: 0.7012 (tm-30) REVERT: C 424 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8178 (mtt180) REVERT: C 459 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7814 (ttp80) REVERT: C 597 ARG cc_start: 0.7481 (tpt-90) cc_final: 0.7269 (tpt-90) REVERT: D 489 GLU cc_start: 0.7539 (pp20) cc_final: 0.7301 (pp20) REVERT: D 785 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7427 (mtp180) REVERT: D 915 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7321 (mp0) REVERT: E 460 ASN cc_start: 0.7636 (m-40) cc_final: 0.7413 (m-40) REVERT: E 475 ASN cc_start: 0.7399 (t0) cc_final: 0.7128 (t0) REVERT: E 811 LYS cc_start: 0.8011 (mttt) cc_final: 0.7784 (mttp) REVERT: E 918 LYS cc_start: 0.7950 (pttp) cc_final: 0.7606 (tmtt) REVERT: F 459 ARG cc_start: 0.7101 (ttt180) cc_final: 0.6827 (ttt-90) REVERT: F 786 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7361 (mtp180) REVERT: F 918 LYS cc_start: 0.8141 (tttt) cc_final: 0.7712 (tttp) outliers start: 28 outliers final: 20 residues processed: 337 average time/residue: 0.4502 time to fit residues: 223.8775 Evaluate side-chains 308 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 287 time to evaluate : 3.277 ------------------------------------------------------------------------------- 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 625 ASP 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 156 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 280 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25193 Z= 0.222 Angle : 0.552 11.761 34123 Z= 0.279 Chirality : 0.042 0.165 3909 Planarity : 0.004 0.052 4358 Dihedral : 10.463 89.676 3670 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.58 % Allowed : 11.13 % Favored : 87.28 % 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: -0.65 (0.15), residues: 3095 helix: 1.05 (0.14), residues: 1341 sheet: -0.68 (0.25), residues: 421 loop : -1.94 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.004 0.001 HIS E 843 PHE 0.016 0.001 PHE C 820 TYR 0.017 0.002 TYR A 939 ARG 0.006 0.000 ARG E 562 *********************** 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 352 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 310 time to evaluate : 2.701 Fit side-chains REVERT: A 456 ASN cc_start: 0.8055 (m-40) cc_final: 0.7780 (m-40) REVERT: A 609 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 778 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8426 (pp) REVERT: A 918 LYS cc_start: 0.7886 (mptt) cc_final: 0.7112 (ptpt) REVERT: A 922 ASP cc_start: 0.7512 (t0) cc_final: 0.7017 (t0) REVERT: B 482 ARG cc_start: 0.7605 (tmm160) cc_final: 0.7261 (tmm160) REVERT: B 484 GLN cc_start: 0.8064 (tt0) cc_final: 0.7710 (tt0) REVERT: B 579 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7883 (mtmm) REVERT: B 597 ARG cc_start: 0.6978 (ptp-110) cc_final: 0.6544 (mmm-85) REVERT: B 625 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7837 (t0) REVERT: B 778 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8216 (pp) REVERT: B 808 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6920 (tp30) REVERT: B 811 LYS cc_start: 0.8228 (mttm) cc_final: 0.7938 (mttp) REVERT: B 918 LYS cc_start: 0.7540 (mmtm) cc_final: 0.7060 (mmmt) REVERT: C 423 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6958 (tm-30) REVERT: C 424 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8159 (mtt180) REVERT: C 785 ARG cc_start: 0.7289 (mtp-110) cc_final: 0.7075 (mtp-110) REVERT: D 440 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7368 (mt-10) REVERT: D 785 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7411 (mtp180) REVERT: D 915 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7369 (mp0) REVERT: E 421 PHE cc_start: 0.4381 (OUTLIER) cc_final: 0.4089 (m-80) REVERT: E 460 ASN cc_start: 0.7659 (m-40) cc_final: 0.7396 (m-40) REVERT: E 475 ASN cc_start: 0.7275 (t0) cc_final: 0.7059 (t0) REVERT: E 778 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8122 (pp) REVERT: E 811 LYS cc_start: 0.7985 (mttt) cc_final: 0.7749 (mttp) REVERT: E 918 LYS cc_start: 0.7981 (pttp) cc_final: 0.7680 (tmtt) REVERT: F 918 LYS cc_start: 0.8037 (tttt) cc_final: 0.7698 (tttp) outliers start: 42 outliers final: 25 residues processed: 339 average time/residue: 0.4312 time to fit residues: 215.7288 Evaluate side-chains 312 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 282 time to evaluate : 2.854 ------------------------------------------------------------------------------- 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 778 LEU 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 625 ASP 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 146 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 chunk 300 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 269 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** F 509 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25193 Z= 0.147 Angle : 0.509 11.730 34123 Z= 0.256 Chirality : 0.041 0.155 3909 Planarity : 0.004 0.047 4358 Dihedral : 10.027 89.038 3670 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.55 % Allowed : 11.96 % Favored : 86.49 % 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: -0.16 (0.15), residues: 3095 helix: 1.48 (0.14), residues: 1339 sheet: -0.48 (0.25), residues: 422 loop : -1.69 (0.16), residues: 1334 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 0.016 0.001 PHE A 926 TYR 0.012 0.001 TYR B 939 ARG 0.007 0.000 ARG D 422 *********************** 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 343 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 302 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8228 (ttpt) cc_final: 0.8005 (pttt) REVERT: A 456 ASN cc_start: 0.7953 (m-40) cc_final: 0.7692 (m-40) REVERT: A 609 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7088 (mt-10) REVERT: A 918 LYS cc_start: 0.7920 (mptt) cc_final: 0.7212 (ptpt) REVERT: A 922 ASP cc_start: 0.7509 (t0) cc_final: 0.7019 (t0) REVERT: B 484 GLN cc_start: 0.8009 (tt0) cc_final: 0.7651 (tt0) REVERT: B 597 ARG cc_start: 0.6965 (ptp-110) cc_final: 0.6636 (mmm-85) REVERT: B 625 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7851 (t0) REVERT: B 808 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6909 (tp30) REVERT: B 811 LYS cc_start: 0.8264 (mttm) cc_final: 0.8005 (mttp) REVERT: B 918 LYS cc_start: 0.7529 (mmtm) cc_final: 0.6987 (mmmt) REVERT: C 423 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6926 (tm-30) REVERT: C 424 ARG cc_start: 0.8413 (mtt180) cc_final: 0.8068 (mtt180) REVERT: C 651 ASP cc_start: 0.8079 (t0) cc_final: 0.7822 (t70) REVERT: C 786 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7499 (mmm-85) REVERT: C 827 GLN cc_start: 0.7835 (pp30) cc_final: 0.7610 (pp30) REVERT: D 419 GLU cc_start: 0.7195 (mp0) cc_final: 0.6934 (mp0) REVERT: D 440 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7337 (mt-10) REVERT: D 785 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7443 (mtp180) REVERT: D 915 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7346 (mp0) REVERT: E 421 PHE cc_start: 0.4340 (OUTLIER) cc_final: 0.3858 (m-80) REVERT: E 475 ASN cc_start: 0.7280 (t0) cc_final: 0.7062 (t0) REVERT: E 552 MET cc_start: 0.5399 (ppp) cc_final: 0.4983 (ptm) REVERT: E 778 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8018 (pp) REVERT: E 811 LYS cc_start: 0.7959 (mttt) cc_final: 0.7727 (mttp) REVERT: E 918 LYS cc_start: 0.7966 (pttp) cc_final: 0.7681 (tmtt) REVERT: F 459 ARG cc_start: 0.7156 (ttt180) cc_final: 0.6815 (ttt-90) REVERT: F 635 PHE cc_start: 0.8498 (m-80) cc_final: 0.8295 (m-10) REVERT: F 655 MET cc_start: 0.7164 (mmm) cc_final: 0.4948 (ptm) REVERT: F 918 LYS cc_start: 0.7995 (tttt) cc_final: 0.7746 (tttp) outliers start: 41 outliers final: 24 residues processed: 331 average time/residue: 0.4315 time to fit residues: 212.6814 Evaluate side-chains 311 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 284 time to evaluate : 2.870 ------------------------------------------------------------------------------- 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 764 VAL Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 641 VAL 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 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 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 E residue 849 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 256 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN B 743 GLN C 805 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25193 Z= 0.171 Angle : 0.514 11.126 34123 Z= 0.257 Chirality : 0.041 0.156 3909 Planarity : 0.004 0.047 4358 Dihedral : 9.964 89.546 3670 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.77 % Allowed : 12.45 % Favored : 85.77 % 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: 1.63 (0.14), residues: 1338 sheet: -0.37 (0.25), residues: 424 loop : -1.58 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 470 HIS 0.003 0.001 HIS E 843 PHE 0.015 0.001 PHE C 820 TYR 0.015 0.001 TYR B 939 ARG 0.006 0.000 ARG E 562 *********************** 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 347 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 300 time to evaluate : 2.882 Fit side-chains revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8242 (ttpt) cc_final: 0.8017 (pttt) REVERT: A 609 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7016 (mt-10) REVERT: A 918 LYS cc_start: 0.7971 (mptt) cc_final: 0.7296 (ptpt) REVERT: A 922 ASP cc_start: 0.7523 (t0) cc_final: 0.7036 (t0) REVERT: B 482 ARG cc_start: 0.7313 (tmm160) cc_final: 0.7015 (tmm160) REVERT: B 484 GLN cc_start: 0.8027 (tt0) cc_final: 0.7678 (tt0) REVERT: B 597 ARG cc_start: 0.6923 (ptp-110) cc_final: 0.6604 (mmm-85) REVERT: B 625 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7873 (t0) REVERT: B 778 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8275 (pp) REVERT: B 808 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6876 (tp30) REVERT: B 811 LYS cc_start: 0.8272 (mttm) cc_final: 0.8007 (mttp) REVERT: B 918 LYS cc_start: 0.7579 (mmtm) cc_final: 0.7036 (mmmt) REVERT: C 423 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6928 (tm-30) REVERT: C 424 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8049 (mtt180) REVERT: C 651 ASP cc_start: 0.8100 (t0) cc_final: 0.7839 (t70) REVERT: D 785 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7406 (mtp180) REVERT: D 915 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7382 (mp0) REVERT: E 421 PHE cc_start: 0.4425 (OUTLIER) cc_final: 0.3927 (m-80) REVERT: E 552 MET cc_start: 0.5149 (ppp) cc_final: 0.4912 (ptm) REVERT: E 778 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7961 (pp) REVERT: E 811 LYS cc_start: 0.7960 (mttt) cc_final: 0.7734 (mttp) REVERT: E 918 LYS cc_start: 0.7983 (pttp) cc_final: 0.7695 (tmtt) REVERT: F 635 PHE cc_start: 0.8497 (m-80) cc_final: 0.8294 (m-10) REVERT: F 655 MET cc_start: 0.7199 (mmm) cc_final: 0.5025 (ptm) REVERT: F 918 LYS cc_start: 0.8041 (tttt) cc_final: 0.7744 (tttp) outliers start: 47 outliers final: 35 residues processed: 333 average time/residue: 0.4209 time to fit residues: 209.3568 Evaluate side-chains 327 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 288 time to evaluate : 3.053 ------------------------------------------------------------------------------- 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 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 625 ASP 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 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 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 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR 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 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 101 optimal weight: 0.3980 chunk 270 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 249 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** E 575 GLN F 433 HIS F 509 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25193 Z= 0.271 Angle : 0.566 10.479 34123 Z= 0.285 Chirality : 0.043 0.152 3909 Planarity : 0.004 0.048 4358 Dihedral : 10.306 88.703 3670 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.85 % Allowed : 13.21 % Favored : 84.94 % 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: 1.54 (0.14), residues: 1334 sheet: -0.29 (0.26), residues: 419 loop : -1.59 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 470 HIS 0.004 0.001 HIS E 843 PHE 0.021 0.002 PHE B 820 TYR 0.022 0.002 TYR A 939 ARG 0.011 0.000 ARG D 422 *********************** 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 335 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 286 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7997 (pttt) REVERT: A 609 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7094 (mt-10) REVERT: A 922 ASP cc_start: 0.7645 (t0) cc_final: 0.7157 (t0) REVERT: B 484 GLN cc_start: 0.8041 (tt0) cc_final: 0.7677 (tt0) REVERT: B 597 ARG cc_start: 0.7002 (ptp-110) cc_final: 0.6672 (mmm-85) REVERT: B 625 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7887 (t0) REVERT: B 778 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8299 (pp) REVERT: B 808 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6906 (tp30) REVERT: B 811 LYS cc_start: 0.8208 (mttm) cc_final: 0.7957 (mttp) REVERT: B 918 LYS cc_start: 0.7702 (mmtm) cc_final: 0.7485 (mmtt) REVERT: C 423 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6965 (tm-30) REVERT: C 424 ARG cc_start: 0.8418 (mtt180) cc_final: 0.8065 (mtt180) REVERT: D 915 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7396 (mp0) REVERT: E 552 MET cc_start: 0.5094 (ppp) cc_final: 0.4675 (ptm) REVERT: E 778 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8113 (pp) REVERT: E 811 LYS cc_start: 0.7948 (mttt) cc_final: 0.7735 (mttp) REVERT: E 918 LYS cc_start: 0.7975 (pttp) cc_final: 0.7640 (tmtt) REVERT: F 655 MET cc_start: 0.7244 (mmm) cc_final: 0.5077 (ptm) REVERT: F 918 LYS cc_start: 0.8103 (tttt) cc_final: 0.7763 (tttp) outliers start: 49 outliers final: 43 residues processed: 319 average time/residue: 0.4154 time to fit residues: 198.0092 Evaluate side-chains 321 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 275 time to evaluate : 3.087 ------------------------------------------------------------------------------- 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 754 GLU 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 576 CYS Chi-restraints excluded: chain B residue 625 ASP 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 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 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 E residue 879 MET 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 Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 299 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 743 GLN C 477 ASN F 433 HIS F 509 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25193 Z= 0.216 Angle : 0.540 10.494 34123 Z= 0.271 Chirality : 0.042 0.153 3909 Planarity : 0.004 0.049 4358 Dihedral : 10.098 88.752 3670 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.92 % Allowed : 13.40 % Favored : 84.68 % 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: 0.12 (0.15), residues: 3095 helix: 1.64 (0.14), residues: 1336 sheet: -0.25 (0.26), residues: 423 loop : -1.48 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 770 HIS 0.003 0.001 HIS E 843 PHE 0.017 0.001 PHE C 820 TYR 0.017 0.002 TYR A 939 ARG 0.007 0.000 ARG E 562 *********************** 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 339 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 288 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7999 (pttt) REVERT: A 424 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7667 (ttp-170) REVERT: A 607 LEU cc_start: 0.8397 (mm) cc_final: 0.8178 (mm) REVERT: A 609 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 849 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8419 (t) REVERT: A 922 ASP cc_start: 0.7679 (t0) cc_final: 0.7158 (t0) REVERT: B 484 GLN cc_start: 0.8025 (tt0) cc_final: 0.7663 (tt0) REVERT: B 597 ARG cc_start: 0.6985 (ptp-110) cc_final: 0.6660 (mmm-85) REVERT: B 625 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7905 (t0) REVERT: B 778 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8258 (pp) REVERT: B 811 LYS cc_start: 0.8189 (mttm) cc_final: 0.7924 (mttp) REVERT: C 423 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6946 (tm-30) REVERT: C 424 ARG cc_start: 0.8418 (mtt180) cc_final: 0.8059 (mtt180) REVERT: C 651 ASP cc_start: 0.8092 (t0) cc_final: 0.7826 (t70) REVERT: D 422 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8250 (mmt90) REVERT: D 770 TRP cc_start: 0.7353 (OUTLIER) cc_final: 0.6305 (p90) REVERT: D 785 ARG cc_start: 0.8170 (mtp-110) cc_final: 0.7491 (mtp180) REVERT: D 915 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7383 (mp0) REVERT: E 778 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8039 (pp) REVERT: E 811 LYS cc_start: 0.7952 (mttt) cc_final: 0.7744 (mttp) REVERT: E 918 LYS cc_start: 0.7965 (pttp) cc_final: 0.7629 (tmtt) REVERT: F 655 MET cc_start: 0.7237 (mmm) cc_final: 0.5053 (ptm) REVERT: F 918 LYS cc_start: 0.8053 (tttt) cc_final: 0.7760 (tttp) outliers start: 51 outliers final: 41 residues processed: 324 average time/residue: 0.4500 time to fit residues: 216.7699 Evaluate side-chains 323 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 277 time to evaluate : 3.093 ------------------------------------------------------------------------------- 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 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 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 625 ASP 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 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 553 THR 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 770 TRP Chi-restraints excluded: chain D residue 783 SER 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 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 752 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 6.9990 chunk 119 optimal weight: 0.0170 chunk 179 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 272 optimal weight: 20.0000 overall best weight: 0.7422 ------------------------------------------------------------------------------- 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** F 433 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25193 Z= 0.160 Angle : 0.515 10.549 34123 Z= 0.256 Chirality : 0.040 0.147 3909 Planarity : 0.004 0.048 4358 Dihedral : 9.763 89.316 3670 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.89 % Allowed : 13.74 % Favored : 84.38 % 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: 0.34 (0.15), residues: 3095 helix: 1.83 (0.14), residues: 1338 sheet: -0.15 (0.26), residues: 426 loop : -1.36 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 770 HIS 0.003 0.001 HIS E 843 PHE 0.018 0.001 PHE F 545 TYR 0.013 0.001 TYR A 939 ARG 0.006 0.000 ARG E 562 *********************** 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 332 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 282 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7989 (pttt) REVERT: A 424 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7693 (ttp-170) REVERT: A 609 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 922 ASP cc_start: 0.7678 (t0) cc_final: 0.7145 (t0) REVERT: B 579 LYS cc_start: 0.8180 (mttp) cc_final: 0.7917 (mtmm) REVERT: B 597 ARG cc_start: 0.6802 (ptp-110) cc_final: 0.6511 (mmm-85) REVERT: B 625 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7907 (t0) REVERT: B 778 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8305 (pp) REVERT: B 811 LYS cc_start: 0.8250 (mttm) cc_final: 0.8003 (mttp) REVERT: C 423 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6918 (tm-30) REVERT: C 424 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7939 (mtt180) REVERT: C 651 ASP cc_start: 0.8055 (t0) cc_final: 0.7785 (t70) REVERT: D 422 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8314 (mmt90) REVERT: D 626 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8598 (m) REVERT: D 770 TRP cc_start: 0.7331 (OUTLIER) cc_final: 0.6365 (p90) REVERT: D 785 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7478 (mtp180) REVERT: D 915 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7381 (mp0) REVERT: E 684 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8466 (mp) REVERT: E 778 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8075 (pp) REVERT: E 811 LYS cc_start: 0.7935 (mttt) cc_final: 0.7729 (mttp) REVERT: E 918 LYS cc_start: 0.7944 (pttp) cc_final: 0.7608 (tmtt) REVERT: F 655 MET cc_start: 0.7209 (mmm) cc_final: 0.5031 (ptm) REVERT: F 918 LYS cc_start: 0.8009 (tttt) cc_final: 0.7725 (tttp) outliers start: 50 outliers final: 39 residues processed: 316 average time/residue: 0.4231 time to fit residues: 198.7418 Evaluate side-chains 323 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 278 time to evaluate : 2.826 ------------------------------------------------------------------------------- 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 468 ILE 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 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 625 ASP 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 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 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 E residue 849 THR 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 Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 252 optimal weight: 0.0670 chunk 264 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 183 optimal weight: 0.0970 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 HIS F 839 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25193 Z= 0.185 Angle : 0.524 10.527 34123 Z= 0.261 Chirality : 0.041 0.155 3909 Planarity : 0.004 0.047 4358 Dihedral : 9.789 88.537 3670 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.77 % Allowed : 13.89 % Favored : 84.34 % 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: 1.84 (0.14), residues: 1338 sheet: -0.08 (0.26), residues: 426 loop : -1.32 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 770 HIS 0.003 0.001 HIS E 843 PHE 0.022 0.001 PHE F 545 TYR 0.016 0.001 TYR A 939 ARG 0.004 0.000 ARG E 562 *********************** 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 324 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 277 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8296 (ttpt) cc_final: 0.8009 (pttt) REVERT: A 424 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7720 (ttp-170) REVERT: A 609 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 922 ASP cc_start: 0.7699 (t0) cc_final: 0.6947 (t0) REVERT: B 597 ARG cc_start: 0.6798 (ptp-110) cc_final: 0.6497 (mmm-85) REVERT: B 625 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7903 (t0) REVERT: B 778 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8265 (pp) REVERT: B 811 LYS cc_start: 0.8251 (mttm) cc_final: 0.8007 (mttp) REVERT: C 423 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6932 (tm-30) REVERT: C 424 ARG cc_start: 0.8312 (mtt180) cc_final: 0.7950 (mtt180) REVERT: C 651 ASP cc_start: 0.8064 (t0) cc_final: 0.7797 (t70) REVERT: D 422 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8360 (mmt90) REVERT: D 770 TRP cc_start: 0.7357 (OUTLIER) cc_final: 0.6370 (p90) REVERT: D 785 ARG cc_start: 0.8180 (mtp-110) cc_final: 0.7498 (mtp180) REVERT: D 915 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7348 (mp0) REVERT: E 684 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8473 (mp) REVERT: E 778 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8020 (pp) REVERT: E 811 LYS cc_start: 0.7943 (mttt) cc_final: 0.7739 (mttp) REVERT: E 918 LYS cc_start: 0.7944 (pttp) cc_final: 0.7610 (tmtt) REVERT: F 655 MET cc_start: 0.7210 (mmm) cc_final: 0.5046 (ptm) REVERT: F 918 LYS cc_start: 0.8007 (tttt) cc_final: 0.7721 (tttp) outliers start: 47 outliers final: 40 residues processed: 312 average time/residue: 0.4152 time to fit residues: 193.5914 Evaluate side-chains 316 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 271 time to evaluate : 2.832 ------------------------------------------------------------------------------- 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 468 ILE 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 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 625 ASP 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 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 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 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 E residue 849 THR 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 Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 309 optimal weight: 2.9990 chunk 285 optimal weight: 0.0980 chunk 246 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 151 optimal weight: 0.0050 chunk 195 optimal weight: 7.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 GLN D 433 HIS D 615 GLN F 433 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25193 Z= 0.139 Angle : 0.507 10.618 34123 Z= 0.252 Chirality : 0.040 0.155 3909 Planarity : 0.004 0.049 4358 Dihedral : 9.461 86.908 3670 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.58 % Allowed : 14.11 % Favored : 84.30 % 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: 0.58 (0.15), residues: 3095 helix: 2.01 (0.14), residues: 1338 sheet: -0.11 (0.26), residues: 438 loop : -1.20 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 770 HIS 0.003 0.000 HIS E 839 PHE 0.022 0.001 PHE F 545 TYR 0.012 0.001 TYR E 492 ARG 0.004 0.000 ARG B 482 ********************** 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 327 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 285 time to evaluate : 3.096 Fit side-chains revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7993 (pttt) REVERT: A 424 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7715 (ttp-170) REVERT: A 609 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 922 ASP cc_start: 0.7715 (t0) cc_final: 0.6974 (t0) REVERT: B 579 LYS cc_start: 0.8125 (mttp) cc_final: 0.7766 (mtmm) REVERT: B 597 ARG cc_start: 0.6775 (ptp-110) cc_final: 0.6502 (mmm-85) REVERT: B 625 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7901 (t0) REVERT: B 778 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8292 (pp) REVERT: B 811 LYS cc_start: 0.8275 (mttm) cc_final: 0.8032 (mttp) REVERT: C 423 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6888 (tm-30) REVERT: C 424 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7831 (mtt180) REVERT: C 651 ASP cc_start: 0.8036 (t0) cc_final: 0.7774 (t70) REVERT: D 770 TRP cc_start: 0.7307 (OUTLIER) cc_final: 0.6363 (p90) REVERT: D 785 ARG cc_start: 0.8156 (mtp-110) cc_final: 0.7466 (mtp180) REVERT: D 915 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7280 (mp0) REVERT: E 684 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8470 (mp) REVERT: E 778 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8054 (pp) REVERT: E 811 LYS cc_start: 0.7929 (mttt) cc_final: 0.7723 (mttp) REVERT: E 918 LYS cc_start: 0.7912 (pttp) cc_final: 0.7569 (tmtt) REVERT: F 638 THR cc_start: 0.8690 (t) cc_final: 0.8470 (t) REVERT: F 655 MET cc_start: 0.7186 (mmm) cc_final: 0.5033 (ptm) REVERT: F 918 LYS cc_start: 0.7989 (tttt) cc_final: 0.7703 (tttp) outliers start: 42 outliers final: 33 residues processed: 315 average time/residue: 0.4469 time to fit residues: 209.5076 Evaluate side-chains 314 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 276 time to evaluate : 2.850 ------------------------------------------------------------------------------- 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 468 ILE 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 B residue 425 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 625 ASP 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 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 764 VAL Chi-restraints excluded: chain D residue 770 TRP 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 E residue 849 THR Chi-restraints excluded: chain F residue 752 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 247 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 216 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 GLN F 433 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110578 restraints weight = 34298.352| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.28 r_work: 0.3061 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25193 Z= 0.165 Angle : 0.519 10.337 34123 Z= 0.258 Chirality : 0.041 0.158 3909 Planarity : 0.004 0.049 4358 Dihedral : 9.500 86.626 3670 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.74 % Allowed : 13.92 % Favored : 84.34 % 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: 0.60 (0.15), residues: 3095 helix: 2.00 (0.14), residues: 1341 sheet: 0.06 (0.26), residues: 423 loop : -1.22 (0.17), residues: 1331 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 0.062 0.001 PHE C 545 TYR 0.013 0.001 TYR A 939 ARG 0.010 0.000 ARG D 422 =============================================================================== Job complete usr+sys time: 5244.49 seconds wall clock time: 94 minutes 39.81 seconds (5679.81 seconds total)