Starting phenix.real_space_refine on Thu Mar 5 18:45:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7krz_23013/03_2026/7krz_23013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krz_23013/03_2026/7krz_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 { model { file = "/net/cci-nas-00/data/ceres_data/7krz_23013/03_2026/7krz_23013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krz_23013/03_2026/7krz_23013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7krz_23013/03_2026/7krz_23013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krz_23013/03_2026/7krz_23013.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.51, per 1000 atoms: 0.22 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: 2.18 Conformation dependent library (CDL) restraints added in 1.0 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: 0.79 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: 4.28 Time building geometry restraints manager: 2.65 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.620 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.494 25199 Z= 0.652 Angle : 0.799 18.008 34123 Z= 0.470 Chirality : 0.047 0.174 3909 Planarity : 0.005 0.060 4358 Dihedral : 14.695 89.486 9592 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.19 % Allowed : 6.68 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG C 710 TYR 0.016 0.002 TYR A 939 PHE 0.019 0.002 PHE C 820 TRP 0.013 0.002 TRP F 770 HIS 0.005 0.001 HIS F 491 Details of bonding type rmsd covalent geometry : bond 0.00737 (25193) covalent geometry : angle 0.79927 (34123) hydrogen bonds : bond 0.14552 ( 1057) hydrogen bonds : angle 6.50988 ( 3084) Misc. bond : bond 0.35567 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 382 time to evaluate : 0.969 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: 0.7180 (mp0) REVERT: E 432 LYS cc_start: 0.7920 (tmmt) cc_final: 0.7591 (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: 0.5161 (ptm) REVERT: E 811 LYS cc_start: 0.7884 (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: 0.7860 (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: 0.2101 time to fit residues: 118.4226 Evaluate side-chains 291 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 287 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0870 overall best weight: 0.5360 ------------------------------------------------------------------------------- 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 702 GLN A 805 GLN A 832 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 713 GLN E 743 GLN E 839 HIS F 575 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112852 restraints weight = 35148.456| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.25 r_work: 0.3025 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25199 Z= 0.113 Angle : 0.554 14.512 34123 Z= 0.278 Chirality : 0.041 0.154 3909 Planarity : 0.004 0.052 4358 Dihedral : 10.433 89.177 3670 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.09 % Allowed : 8.75 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.14), residues: 3095 helix: 0.57 (0.14), residues: 1339 sheet: -1.05 (0.25), residues: 408 loop : -2.19 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 562 TYR 0.013 0.001 TYR B 939 PHE 0.015 0.001 PHE B 504 TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS B 843 Details of bonding type rmsd covalent geometry : bond 0.00248 (25193) covalent geometry : angle 0.55424 (34123) hydrogen bonds : bond 0.03619 ( 1057) hydrogen bonds : angle 4.81277 ( 3084) Misc. bond : bond 0.00139 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 320 time to evaluate : 0.923 Fit side-chains REVERT: A 609 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 922 ASP cc_start: 0.7626 (t0) cc_final: 0.7149 (t0) REVERT: B 484 GLN cc_start: 0.8559 (tt0) cc_final: 0.8300 (tt0) REVERT: B 597 ARG cc_start: 0.7033 (ptp-110) cc_final: 0.6701 (ptp90) REVERT: B 777 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 808 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7408 (tp30) REVERT: C 423 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7198 (tm-30) REVERT: C 424 ARG cc_start: 0.8857 (mtt180) cc_final: 0.8530 (mtt180) REVERT: D 569 MET cc_start: 0.8668 (mmm) cc_final: 0.8462 (mmm) REVERT: D 785 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7764 (mtp180) REVERT: D 915 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7846 (mp0) REVERT: E 552 MET cc_start: 0.5625 (ppp) cc_final: 0.5344 (ptm) REVERT: F 459 ARG cc_start: 0.6733 (ttt180) cc_final: 0.6479 (ttt-90) outliers start: 29 outliers final: 19 residues processed: 342 average time/residue: 0.2032 time to fit residues: 102.9315 Evaluate side-chains 297 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 277 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 777 THR 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 764 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 131 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN A 832 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN C 615 GLN C 805 GLN F 433 HIS ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110436 restraints weight = 34718.292| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.25 r_work: 0.2955 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25199 Z= 0.180 Angle : 0.591 12.270 34123 Z= 0.299 Chirality : 0.044 0.161 3909 Planarity : 0.005 0.052 4358 Dihedral : 10.683 89.794 3670 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.66 % Allowed : 10.60 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 3095 helix: 0.89 (0.14), residues: 1337 sheet: -0.74 (0.26), residues: 418 loop : -1.98 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 482 TYR 0.023 0.002 TYR A 939 PHE 0.019 0.002 PHE B 820 TRP 0.007 0.001 TRP C 470 HIS 0.005 0.001 HIS C 843 Details of bonding type rmsd covalent geometry : bond 0.00435 (25193) covalent geometry : angle 0.59110 (34123) hydrogen bonds : bond 0.04102 ( 1057) hydrogen bonds : angle 4.75535 ( 3084) Misc. bond : bond 0.00070 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 0.981 Fit side-chains REVERT: A 609 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7765 (mt-10) REVERT: A 918 LYS cc_start: 0.8357 (mptt) cc_final: 0.7838 (ptpt) REVERT: A 922 ASP cc_start: 0.8345 (t0) cc_final: 0.7924 (t0) REVERT: A 926 PHE cc_start: 0.7704 (p90) cc_final: 0.7461 (p90) REVERT: B 484 GLN cc_start: 0.8587 (tt0) cc_final: 0.8290 (tt0) REVERT: B 597 ARG cc_start: 0.7166 (ptp-110) cc_final: 0.6760 (ptp90) REVERT: B 778 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8514 (pp) REVERT: B 918 LYS cc_start: 0.7992 (mmtm) cc_final: 0.7678 (mmmt) REVERT: C 423 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7338 (tm-30) REVERT: C 424 ARG cc_start: 0.8819 (mtt180) cc_final: 0.8424 (mtt180) REVERT: C 918 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7879 (mmtt) REVERT: D 785 ARG cc_start: 0.8665 (mtp-110) cc_final: 0.8233 (mtp180) REVERT: D 915 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8146 (mp0) REVERT: E 421 PHE cc_start: 0.4963 (OUTLIER) cc_final: 0.4358 (m-80) REVERT: E 552 MET cc_start: 0.5486 (ppp) cc_final: 0.5164 (ptm) REVERT: E 778 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8432 (pp) REVERT: F 918 LYS cc_start: 0.8783 (tttt) cc_final: 0.8421 (tttp) outliers start: 44 outliers final: 30 residues processed: 326 average time/residue: 0.1969 time to fit residues: 95.4042 Evaluate side-chains 308 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 177 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 309 optimal weight: 0.6980 chunk 211 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** E 575 GLN F 433 HIS F 509 GLN F 839 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108039 restraints weight = 34462.596| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.22 r_work: 0.2932 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25199 Z= 0.194 Angle : 0.594 11.106 34123 Z= 0.300 Chirality : 0.044 0.159 3909 Planarity : 0.005 0.053 4358 Dihedral : 10.773 88.455 3670 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.96 % Allowed : 11.62 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 3095 helix: 1.07 (0.14), residues: 1338 sheet: -0.50 (0.26), residues: 409 loop : -1.87 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 422 TYR 0.022 0.002 TYR A 939 PHE 0.020 0.002 PHE B 820 TRP 0.009 0.001 TRP C 470 HIS 0.005 0.001 HIS E 843 Details of bonding type rmsd covalent geometry : bond 0.00471 (25193) covalent geometry : angle 0.59376 (34123) hydrogen bonds : bond 0.03994 ( 1057) hydrogen bonds : angle 4.69199 ( 3084) Misc. bond : bond 0.00060 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 281 time to evaluate : 1.002 Fit side-chains REVERT: A 922 ASP cc_start: 0.8490 (t0) cc_final: 0.8109 (t0) REVERT: B 484 GLN cc_start: 0.8696 (tt0) cc_final: 0.8415 (tt0) REVERT: B 597 ARG cc_start: 0.7235 (ptp-110) cc_final: 0.6784 (mmm-85) REVERT: B 918 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7714 (mmmt) REVERT: C 423 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7433 (tm-30) REVERT: C 424 ARG cc_start: 0.8789 (mtt180) cc_final: 0.8464 (mtt180) REVERT: C 918 LYS cc_start: 0.8360 (mmtt) cc_final: 0.7765 (mmtt) REVERT: D 915 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8288 (mp0) REVERT: D 922 ASP cc_start: 0.8614 (t70) cc_final: 0.8134 (t0) REVERT: F 509 GLN cc_start: 0.8470 (tt0) cc_final: 0.8251 (tt0) REVERT: F 655 MET cc_start: 0.7519 (mmm) cc_final: 0.5521 (ptm) REVERT: F 918 LYS cc_start: 0.8712 (tttt) cc_final: 0.8455 (tttp) outliers start: 52 outliers final: 34 residues processed: 318 average time/residue: 0.1986 time to fit residues: 94.2926 Evaluate side-chains 307 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 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 D residue 783 SER Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain F residue 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 778 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 294 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 295 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 275 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** E 575 GLN F 433 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107543 restraints weight = 34505.256| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.28 r_work: 0.2934 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25199 Z= 0.154 Angle : 0.561 10.962 34123 Z= 0.282 Chirality : 0.043 0.155 3909 Planarity : 0.004 0.052 4358 Dihedral : 10.566 88.020 3670 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.96 % Allowed : 12.72 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3095 helix: 1.30 (0.14), residues: 1340 sheet: -0.40 (0.26), residues: 418 loop : -1.74 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 422 TYR 0.018 0.002 TYR A 939 PHE 0.018 0.002 PHE C 820 TRP 0.008 0.001 TRP C 470 HIS 0.004 0.001 HIS E 843 Details of bonding type rmsd covalent geometry : bond 0.00372 (25193) covalent geometry : angle 0.56062 (34123) hydrogen bonds : bond 0.03707 ( 1057) hydrogen bonds : angle 4.57714 ( 3084) Misc. bond : bond 0.00041 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 283 time to evaluate : 0.943 Fit side-chains REVERT: A 420 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7908 (pttt) REVERT: A 424 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7897 (ttp-170) REVERT: A 609 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 922 ASP cc_start: 0.8488 (t0) cc_final: 0.8127 (t0) REVERT: B 482 ARG cc_start: 0.8239 (tmm160) cc_final: 0.8018 (tmm160) REVERT: B 484 GLN cc_start: 0.8653 (tt0) cc_final: 0.8374 (tt0) REVERT: B 597 ARG cc_start: 0.7077 (ptp-110) cc_final: 0.6710 (mmm-85) REVERT: B 778 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8517 (pp) REVERT: C 423 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7414 (tm-30) REVERT: C 424 ARG cc_start: 0.8797 (mtt180) cc_final: 0.8496 (mtt180) REVERT: C 459 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8338 (ttt-90) REVERT: D 770 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.6855 (p90) REVERT: D 915 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8139 (mp0) REVERT: D 922 ASP cc_start: 0.8605 (t70) cc_final: 0.8119 (t0) REVERT: E 421 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.4494 (m-80) REVERT: E 778 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8515 (pp) REVERT: F 509 GLN cc_start: 0.8384 (tt0) cc_final: 0.8133 (tt0) REVERT: F 655 MET cc_start: 0.7534 (mmm) cc_final: 0.5491 (ptm) REVERT: F 918 LYS cc_start: 0.8632 (tttt) cc_final: 0.8391 (tttp) outliers start: 52 outliers final: 38 residues processed: 318 average time/residue: 0.1940 time to fit residues: 92.1561 Evaluate side-chains 308 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 600 GLN Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 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 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 421 PHE Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain 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 209 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 268 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 286 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 832 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN F 433 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108596 restraints weight = 34484.663| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.28 r_work: 0.2937 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25199 Z= 0.155 Angle : 0.556 10.486 34123 Z= 0.280 Chirality : 0.043 0.156 3909 Planarity : 0.004 0.050 4358 Dihedral : 10.490 87.960 3670 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.11 % Allowed : 13.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3095 helix: 1.39 (0.14), residues: 1342 sheet: -0.32 (0.26), residues: 419 loop : -1.66 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 422 TYR 0.019 0.002 TYR A 939 PHE 0.019 0.002 PHE C 820 TRP 0.012 0.001 TRP A 770 HIS 0.004 0.001 HIS E 843 Details of bonding type rmsd covalent geometry : bond 0.00374 (25193) covalent geometry : angle 0.55582 (34123) hydrogen bonds : bond 0.03663 ( 1057) hydrogen bonds : angle 4.52275 ( 3084) Misc. bond : bond 0.00056 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 280 time to evaluate : 0.822 Fit side-chains REVERT: A 420 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7905 (pttt) REVERT: A 424 ARG cc_start: 0.8310 (ttm170) cc_final: 0.7902 (ttp-170) REVERT: A 609 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7681 (mt-10) REVERT: A 918 LYS cc_start: 0.8443 (mptt) cc_final: 0.8060 (ptpt) REVERT: A 922 ASP cc_start: 0.8544 (t0) cc_final: 0.7882 (t0) REVERT: B 484 GLN cc_start: 0.8696 (tt0) cc_final: 0.8425 (tt0) REVERT: B 597 ARG cc_start: 0.7135 (ptp-110) cc_final: 0.6757 (mmm-85) REVERT: B 778 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8508 (pp) REVERT: C 420 LYS cc_start: 0.7871 (tttm) cc_final: 0.7656 (tttm) REVERT: C 423 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7459 (tm-30) REVERT: C 424 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8500 (mtt180) REVERT: C 459 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8362 (ttt-90) REVERT: D 770 TRP cc_start: 0.7708 (OUTLIER) cc_final: 0.6758 (p90) REVERT: D 915 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8222 (mp0) REVERT: E 684 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8547 (mp) REVERT: E 778 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8473 (pp) REVERT: F 509 GLN cc_start: 0.8360 (tt0) cc_final: 0.8086 (tt0) REVERT: F 655 MET cc_start: 0.7561 (mmm) cc_final: 0.5464 (ptm) REVERT: F 918 LYS cc_start: 0.8646 (tttt) cc_final: 0.8381 (tttm) outliers start: 56 outliers final: 46 residues processed: 320 average time/residue: 0.1948 time to fit residues: 92.9559 Evaluate side-chains 319 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 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 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 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 85 optimal weight: 8.9990 chunk 97 optimal weight: 0.3980 chunk 234 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN B 484 GLN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 GLN D 477 ASN F 433 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110676 restraints weight = 34368.237| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.22 r_work: 0.2949 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25199 Z= 0.162 Angle : 0.562 10.366 34123 Z= 0.283 Chirality : 0.043 0.158 3909 Planarity : 0.004 0.050 4358 Dihedral : 10.444 88.386 3670 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.19 % Allowed : 13.66 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3095 helix: 1.43 (0.14), residues: 1343 sheet: -0.34 (0.26), residues: 422 loop : -1.61 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 562 TYR 0.020 0.002 TYR A 939 PHE 0.019 0.002 PHE C 820 TRP 0.014 0.001 TRP A 770 HIS 0.004 0.001 HIS E 843 Details of bonding type rmsd covalent geometry : bond 0.00392 (25193) covalent geometry : angle 0.56175 (34123) hydrogen bonds : bond 0.03711 ( 1057) hydrogen bonds : angle 4.51896 ( 3084) Misc. bond : bond 0.00071 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 0.957 Fit side-chains REVERT: A 420 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7923 (pttt) REVERT: A 424 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7882 (ttp-170) REVERT: A 609 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 918 LYS cc_start: 0.8431 (mptt) cc_final: 0.8057 (ptpt) REVERT: A 922 ASP cc_start: 0.8478 (t0) cc_final: 0.7805 (t0) REVERT: B 482 ARG cc_start: 0.8178 (tmm160) cc_final: 0.7964 (tmm160) REVERT: B 597 ARG cc_start: 0.7130 (ptp-110) cc_final: 0.6756 (mmm-85) REVERT: B 778 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8556 (pp) REVERT: C 423 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7462 (tm-30) REVERT: C 424 ARG cc_start: 0.8689 (mtt180) cc_final: 0.8362 (mtt180) REVERT: C 459 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8315 (ttt-90) REVERT: D 651 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8457 (t0) REVERT: D 770 TRP cc_start: 0.7687 (OUTLIER) cc_final: 0.6741 (p90) REVERT: D 915 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8184 (mp0) REVERT: E 684 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8551 (mp) REVERT: E 778 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8509 (pp) REVERT: F 509 GLN cc_start: 0.8338 (tt0) cc_final: 0.8062 (tt0) REVERT: F 655 MET cc_start: 0.7527 (mmm) cc_final: 0.5392 (ptm) REVERT: F 918 LYS cc_start: 0.8611 (tttt) cc_final: 0.8349 (tttm) outliers start: 58 outliers final: 44 residues processed: 317 average time/residue: 0.1950 time to fit residues: 92.5667 Evaluate side-chains 322 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 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 553 THR Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain 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 641 VAL Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 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 8 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 233 optimal weight: 0.0470 chunk 22 optimal weight: 7.9990 chunk 119 optimal weight: 0.0170 chunk 268 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 270 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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** D 477 ASN E 640 ASN F 433 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112132 restraints weight = 34354.363| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.28 r_work: 0.2991 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25199 Z= 0.093 Angle : 0.503 10.728 34123 Z= 0.252 Chirality : 0.040 0.147 3909 Planarity : 0.004 0.051 4358 Dihedral : 9.786 89.677 3670 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.89 % Allowed : 13.96 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3095 helix: 1.85 (0.14), residues: 1336 sheet: -0.16 (0.26), residues: 424 loop : -1.41 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 562 TYR 0.014 0.001 TYR E 492 PHE 0.018 0.001 PHE F 545 TRP 0.018 0.001 TRP A 770 HIS 0.002 0.000 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00210 (25193) covalent geometry : angle 0.50300 (34123) hydrogen bonds : bond 0.03003 ( 1057) hydrogen bonds : angle 4.30168 ( 3084) Misc. bond : bond 0.00038 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 1.009 Fit side-chains REVERT: A 424 ARG cc_start: 0.8342 (ttm170) cc_final: 0.7947 (ttp-170) REVERT: A 918 LYS cc_start: 0.8422 (mptt) cc_final: 0.8127 (ptpt) REVERT: A 922 ASP cc_start: 0.8500 (t0) cc_final: 0.7862 (t0) REVERT: B 579 LYS cc_start: 0.8494 (mttp) cc_final: 0.8245 (mtmm) REVERT: B 597 ARG cc_start: 0.6983 (ptp-110) cc_final: 0.6703 (mmm-85) REVERT: B 778 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8466 (pp) REVERT: C 423 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 424 ARG cc_start: 0.8541 (mtt180) cc_final: 0.8222 (mtt180) REVERT: C 651 ASP cc_start: 0.8295 (t0) cc_final: 0.8068 (t70) REVERT: D 557 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7526 (tm-30) REVERT: D 651 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8437 (t0) REVERT: D 770 TRP cc_start: 0.7699 (OUTLIER) cc_final: 0.6867 (p90) REVERT: D 785 ARG cc_start: 0.8589 (mtp-110) cc_final: 0.8089 (mtp180) REVERT: D 915 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8074 (mp0) REVERT: E 684 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8525 (mp) REVERT: E 778 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8446 (pp) REVERT: F 509 GLN cc_start: 0.8266 (tt0) cc_final: 0.7985 (tt0) REVERT: F 655 MET cc_start: 0.7509 (mmm) cc_final: 0.5444 (ptm) REVERT: F 918 LYS cc_start: 0.8623 (tttt) cc_final: 0.8324 (tttm) outliers start: 50 outliers final: 37 residues processed: 330 average time/residue: 0.1974 time to fit residues: 97.6700 Evaluate side-chains 319 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 A residue 832 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU 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 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 651 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 641 VAL 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 764 VAL Chi-restraints excluded: chain F residue 771 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 80 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 0.0570 chunk 300 optimal weight: 0.0770 chunk 180 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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** C 713 GLN D 433 HIS F 433 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111125 restraints weight = 34303.955| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.21 r_work: 0.3025 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 25199 Z= 0.097 Angle : 0.508 10.252 34123 Z= 0.253 Chirality : 0.040 0.152 3909 Planarity : 0.004 0.050 4358 Dihedral : 9.694 88.549 3670 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.70 % Allowed : 14.49 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3095 helix: 1.96 (0.14), residues: 1338 sheet: -0.04 (0.26), residues: 423 loop : -1.31 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 422 TYR 0.015 0.001 TYR E 492 PHE 0.023 0.001 PHE F 545 TRP 0.020 0.001 TRP A 770 HIS 0.002 0.000 HIS C 433 Details of bonding type rmsd covalent geometry : bond 0.00222 (25193) covalent geometry : angle 0.50839 (34123) hydrogen bonds : bond 0.03028 ( 1057) hydrogen bonds : angle 4.23736 ( 3084) Misc. bond : bond 0.00041 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 1.001 Fit side-chains REVERT: A 424 ARG cc_start: 0.8285 (ttm170) cc_final: 0.7968 (ttp-170) REVERT: A 616 ASN cc_start: 0.8550 (p0) cc_final: 0.8344 (p0) REVERT: A 922 ASP cc_start: 0.8595 (t0) cc_final: 0.8020 (t0) REVERT: B 778 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8467 (pp) REVERT: C 424 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8336 (mtt180) REVERT: D 494 MET cc_start: 0.7668 (mmm) cc_final: 0.7411 (mmt) REVERT: D 651 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8426 (t0) REVERT: D 770 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.6941 (p90) REVERT: D 785 ARG cc_start: 0.8586 (mtp-110) cc_final: 0.8093 (mtp180) REVERT: D 915 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8015 (mp0) REVERT: E 684 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8472 (mp) REVERT: E 778 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8414 (pp) REVERT: F 655 MET cc_start: 0.7518 (mmm) cc_final: 0.5809 (ptm) REVERT: F 918 LYS cc_start: 0.8603 (tttt) cc_final: 0.8310 (tttm) outliers start: 45 outliers final: 36 residues processed: 312 average time/residue: 0.1893 time to fit residues: 88.6863 Evaluate side-chains 315 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 641 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 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 641 VAL 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 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 172 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 chunk 238 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 186 optimal weight: 0.1980 chunk 28 optimal weight: 6.9990 chunk 199 optimal weight: 0.6980 chunk 290 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN C 713 GLN D 615 GLN F 433 HIS F 509 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111518 restraints weight = 34430.859| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.24 r_work: 0.2995 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25199 Z= 0.102 Angle : 0.521 9.943 34123 Z= 0.260 Chirality : 0.040 0.154 3909 Planarity : 0.004 0.050 4358 Dihedral : 9.633 88.222 3670 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.66 % Allowed : 14.60 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3095 helix: 1.99 (0.14), residues: 1337 sheet: 0.00 (0.26), residues: 425 loop : -1.27 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 482 TYR 0.014 0.001 TYR E 492 PHE 0.030 0.001 PHE C 545 TRP 0.020 0.001 TRP A 770 HIS 0.002 0.000 HIS C 433 Details of bonding type rmsd covalent geometry : bond 0.00236 (25193) covalent geometry : angle 0.52126 (34123) hydrogen bonds : bond 0.03068 ( 1057) hydrogen bonds : angle 4.21377 ( 3084) Misc. bond : bond 0.00049 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 0.890 Fit side-chains REVERT: A 424 ARG cc_start: 0.8368 (ttm170) cc_final: 0.7978 (ttp-170) REVERT: A 922 ASP cc_start: 0.8470 (t0) cc_final: 0.7858 (t0) REVERT: B 778 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8450 (pp) REVERT: C 424 ARG cc_start: 0.8423 (mtt180) cc_final: 0.8144 (mtt180) REVERT: D 494 MET cc_start: 0.7572 (mmm) cc_final: 0.7287 (mmt) REVERT: D 651 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8403 (t0) REVERT: D 770 TRP cc_start: 0.7636 (OUTLIER) cc_final: 0.6957 (p90) REVERT: D 785 ARG cc_start: 0.8586 (mtp-110) cc_final: 0.8070 (mtp180) REVERT: D 915 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7965 (mp0) REVERT: E 609 GLU cc_start: 0.6511 (tm-30) cc_final: 0.6274 (tm-30) REVERT: E 684 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8501 (mp) REVERT: E 778 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8352 (pp) REVERT: F 547 PHE cc_start: 0.7578 (p90) cc_final: 0.7244 (p90) REVERT: F 655 MET cc_start: 0.7414 (mmm) cc_final: 0.5366 (ptm) REVERT: F 918 LYS cc_start: 0.8608 (tttt) cc_final: 0.8316 (tttm) outliers start: 44 outliers final: 37 residues processed: 312 average time/residue: 0.1841 time to fit residues: 86.7520 Evaluate side-chains 313 residues out of total 2663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 651 ASP 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 641 VAL 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 566 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 281 optimal weight: 5.9990 chunk 304 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 156 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 713 GLN D 615 GLN F 433 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109477 restraints weight = 34318.626| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.24 r_work: 0.2968 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.003 0.064 25199 Z= 0.142 Angle : 0.545 9.762 34123 Z= 0.273 Chirality : 0.042 0.155 3909 Planarity : 0.004 0.049 4358 Dihedral : 9.813 87.886 3670 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.58 % Allowed : 14.94 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3095 helix: 1.87 (0.14), residues: 1338 sheet: -0.01 (0.26), residues: 425 loop : -1.30 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 482 TYR 0.018 0.002 TYR A 939 PHE 0.027 0.002 PHE C 545 TRP 0.020 0.001 TRP A 770 HIS 0.003 0.001 HIS E 843 Details of bonding type rmsd covalent geometry : bond 0.00343 (25193) covalent geometry : angle 0.54466 (34123) hydrogen bonds : bond 0.03354 ( 1057) hydrogen bonds : angle 4.27812 ( 3084) Misc. bond : bond 0.00085 ( 6) =============================================================================== Job complete usr+sys time: 5691.58 seconds wall clock time: 98 minutes 16.45 seconds (5896.45 seconds total)