Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 05:39:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuf_10930/04_2023/6yuf_10930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuf_10930/04_2023/6yuf_10930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuf_10930/04_2023/6yuf_10930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuf_10930/04_2023/6yuf_10930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuf_10930/04_2023/6yuf_10930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuf_10930/04_2023/6yuf_10930_updated.pdb" } resolution = 3.94 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= 0.003 sd= 0.065 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 68 5.49 5 S 72 5.16 5 Be 2 3.05 5 C 12233 2.51 5 N 3307 2.21 5 O 3840 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 24": "OE1" <-> "OE2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B GLU 585": "OE1" <-> "OE2" Residue "B ASP 593": "OD1" <-> "OD2" Residue "B ASP 608": "OD1" <-> "OD2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 276": "NH1" <-> "NH2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 463": "NH1" <-> "NH2" Residue "D GLU 474": "OE1" <-> "OE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ARG 494": "NH1" <-> "NH2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D GLU 558": "OE1" <-> "OE2" Residue "D ARG 561": "NH1" <-> "NH2" Residue "D PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 801": "NH1" <-> "NH2" Residue "D ARG 814": "NH1" <-> "NH2" Residue "D ARG 850": "NH1" <-> "NH2" Residue "D GLU 906": "OE1" <-> "OE2" Residue "D ARG 948": "NH1" <-> "NH2" Residue "D ARG 965": "NH1" <-> "NH2" Residue "D ARG 993": "NH1" <-> "NH2" Residue "D TYR 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1032": "NH1" <-> "NH2" Residue "D ARG 1051": "NH1" <-> "NH2" Residue "D ARG 1060": "NH1" <-> "NH2" Residue "D ARG 1085": "NH1" <-> "NH2" Residue "D GLU 1088": "OE1" <-> "OE2" Residue "D ARG 1094": "NH1" <-> "NH2" Residue "D ARG 1122": "NH1" <-> "NH2" Residue "D ARG 1159": "NH1" <-> "NH2" Residue "D ARG 1165": "NH1" <-> "NH2" Residue "D ARG 1213": "NH1" <-> "NH2" Residue "D ARG 1217": "NH1" <-> "NH2" Residue "D ARG 1321": "NH1" <-> "NH2" Residue "D ARG 1342": "NH1" <-> "NH2" Residue "D ARG 1360": "NH1" <-> "NH2" Residue "D ARG 1373": "NH1" <-> "NH2" Residue "D GLU 1397": "OE1" <-> "OE2" Residue "D GLU 1405": "OE1" <-> "OE2" Residue "D ARG 1518": "NH1" <-> "NH2" Residue "A ARG 3": "NH1" <-> "NH2" Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 1066": "NH1" <-> "NH2" Residue "A ARG 1125": "NH1" <-> "NH2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1179": "NH1" <-> "NH2" Residue "A PHE 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1209": "NH1" <-> "NH2" Residue "A ARG 1217": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 976": "OE1" <-> "OE2" Residue "C ARG 992": "NH1" <-> "NH2" Residue "C ARG 996": "NH1" <-> "NH2" Residue "C ARG 997": "NH1" <-> "NH2" Residue "C ARG 1012": "NH1" <-> "NH2" Residue "C GLU 1015": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1040": "NH1" <-> "NH2" Residue "C ARG 1047": "NH1" <-> "NH2" Residue "C ARG 1048": "NH1" <-> "NH2" Residue "C ARG 1081": "NH1" <-> "NH2" Residue "C GLU 1090": "OE1" <-> "OE2" Residue "C ARG 1115": "NH1" <-> "NH2" Residue "C GLU 1187": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19528 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1195 Classifications: {'peptide': 152} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Chain: "D" Number of atoms: 10247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1272, 10247 Classifications: {'peptide': 1272} Link IDs: {'PTRANS': 36, 'TRANS': 1235} Chain breaks: 4 Chain: "A" Number of atoms: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3047 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 13, 'TRANS': 370} Chain breaks: 2 Chain: "C" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3665 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 10, 'TRANS': 445} Chain breaks: 2 Chain: "X" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "Y" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 654 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.64, per 1000 atoms: 0.54 Number of scatterers: 19528 At special positions: 0 Unit cell: (129.71, 130.8, 179.85, 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 72 16.00 P 68 15.00 F 6 9.00 O 3840 8.00 N 3307 7.00 C 12233 6.00 Be 2 4.00 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.36 Conformation dependent library (CDL) restraints added in 2.7 seconds 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 8 sheets defined 57.2% alpha, 4.3% beta 31 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 7.33 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 55 through 87 Processing helix chain 'B' and resid 555 through 562 Processing helix chain 'B' and resid 569 through 574 Processing helix chain 'B' and resid 585 through 599 Processing helix chain 'D' and resid 216 through 239 Processing helix chain 'D' and resid 261 through 277 removed outlier: 3.779A pdb=" N ARG D 276 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 290 through 300 Processing helix chain 'D' and resid 321 through 339 removed outlier: 3.582A pdb=" N PHE D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 Processing helix chain 'D' and resid 367 through 375 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 387 through 410 Processing helix chain 'D' and resid 416 through 438 Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 445 through 464 Proline residue: D 453 - end of helix removed outlier: 4.503A pdb=" N GLN D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 457 " --> pdb=" O PRO D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 476 removed outlier: 5.755A pdb=" N ASP D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE D 472 " --> pdb=" O ARG D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 481 No H-bonds generated for 'chain 'D' and resid 479 through 481' Processing helix chain 'D' and resid 487 through 490 No H-bonds generated for 'chain 'D' and resid 487 through 490' Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.897A pdb=" N VAL D 509 " --> pdb=" O THR D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 575 removed outlier: 4.546A pdb=" N VAL D 548 " --> pdb=" O HIS D 544 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 551 " --> pdb=" O THR D 547 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU D 558 " --> pdb=" O LYS D 554 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR D 560 " --> pdb=" O ARG D 556 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG D 561 " --> pdb=" O HIS D 557 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 566 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 568 " --> pdb=" O ASN D 564 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR D 569 " --> pdb=" O HIS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 601 removed outlier: 3.838A pdb=" N THR D 590 " --> pdb=" O PHE D 586 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 591 " --> pdb=" O ALA D 587 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 595 " --> pdb=" O LYS D 591 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 601 " --> pdb=" O LEU D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 625 removed outlier: 4.043A pdb=" N GLN D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE D 616 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET D 622 " --> pdb=" O MET D 618 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 625 " --> pdb=" O VAL D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 648 removed outlier: 4.141A pdb=" N LEU D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 644 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS D 647 " --> pdb=" O LEU D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 685 removed outlier: 4.070A pdb=" N GLU D 683 " --> pdb=" O THR D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 694 No H-bonds generated for 'chain 'D' and resid 691 through 694' Processing helix chain 'D' and resid 703 through 711 removed outlier: 3.678A pdb=" N LEU D 706 " --> pdb=" O GLU D 703 " (cutoff:3.500A) Proline residue: D 707 - end of helix removed outlier: 3.509A pdb=" N ASN D 711 " --> pdb=" O TYR D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 722 Processing helix chain 'D' and resid 732 through 744 removed outlier: 4.836A pdb=" N GLN D 742 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS D 743 " --> pdb=" O LYS D 739 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D 744 " --> pdb=" O ASN D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 770 removed outlier: 3.788A pdb=" N PHE D 764 " --> pdb=" O ASP D 760 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 767 " --> pdb=" O ILE D 763 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU D 768 " --> pdb=" O PHE D 764 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR D 769 " --> pdb=" O ILE D 765 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N HIS D 770 " --> pdb=" O ILE D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 775 No H-bonds generated for 'chain 'D' and resid 772 through 775' Processing helix chain 'D' and resid 777 through 787 removed outlier: 4.904A pdb=" N LEU D 783 " --> pdb=" O PHE D 779 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE D 784 " --> pdb=" O PHE D 780 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 806 removed outlier: 3.695A pdb=" N LEU D 800 " --> pdb=" O ARG D 796 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN D 805 " --> pdb=" O ARG D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 815 Processing helix chain 'D' and resid 817 through 828 removed outlier: 3.570A pdb=" N LYS D 826 " --> pdb=" O GLN D 822 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER D 827 " --> pdb=" O ILE D 823 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN D 828 " --> pdb=" O ILE D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 832 through 848 removed outlier: 3.907A pdb=" N ASP D 836 " --> pdb=" O ALA D 832 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR D 837 " --> pdb=" O ILE D 833 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 846 " --> pdb=" O LEU D 842 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 848 " --> pdb=" O THR D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 863 Proline residue: D 854 - end of helix removed outlier: 4.593A pdb=" N GLY D 858 " --> pdb=" O GLN D 855 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D 861 " --> pdb=" O GLY D 858 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER D 862 " --> pdb=" O CYS D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 885 removed outlier: 4.279A pdb=" N LYS D 877 " --> pdb=" O LYS D 873 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 881 " --> pdb=" O LYS D 877 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 884 " --> pdb=" O CYS D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 902 removed outlier: 4.169A pdb=" N ASP D 894 " --> pdb=" O ASN D 890 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 898 " --> pdb=" O ASP D 894 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG D 902 " --> pdb=" O LYS D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 922 removed outlier: 4.828A pdb=" N LEU D 915 " --> pdb=" O SER D 911 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU D 916 " --> pdb=" O GLU D 912 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 918 " --> pdb=" O SER D 914 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 950 No H-bonds generated for 'chain 'D' and resid 947 through 950' Processing helix chain 'D' and resid 952 through 955 No H-bonds generated for 'chain 'D' and resid 952 through 955' Processing helix chain 'D' and resid 965 through 977 removed outlier: 4.419A pdb=" N VAL D 970 " --> pdb=" O HIS D 966 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 972 " --> pdb=" O LEU D 968 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS D 974 " --> pdb=" O VAL D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 1004 removed outlier: 3.635A pdb=" N GLN D 991 " --> pdb=" O THR D 987 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D1000 " --> pdb=" O LEU D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1032 removed outlier: 3.665A pdb=" N THR D1026 " --> pdb=" O GLU D1022 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D1029 " --> pdb=" O SER D1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1051 removed outlier: 4.945A pdb=" N LEU D1046 " --> pdb=" O TYR D1042 " (cutoff:3.500A) Proline residue: D1048 - end of helix removed outlier: 3.757A pdb=" N ARG D1051 " --> pdb=" O LYS D1047 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1073 removed outlier: 3.935A pdb=" N PHE D1061 " --> pdb=" O GLU D1058 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D1066 " --> pdb=" O TYR D1063 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA D1067 " --> pdb=" O TYR D1064 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D1073 " --> pdb=" O ARG D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1094 removed outlier: 3.849A pdb=" N GLU D1088 " --> pdb=" O LEU D1084 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER D1089 " --> pdb=" O ARG D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1117 removed outlier: 3.892A pdb=" N MET D1104 " --> pdb=" O THR D1100 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU D1105 " --> pdb=" O ALA D1101 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D1106 " --> pdb=" O THR D1102 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL D1107 " --> pdb=" O LEU D1103 " (cutoff:3.500A) Proline residue: D1108 - end of helix removed outlier: 4.560A pdb=" N SER D1112 " --> pdb=" O PRO D1108 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR D1115 " --> pdb=" O CYS D1111 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG D1116 " --> pdb=" O SER D1112 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1138 removed outlier: 4.833A pdb=" N VAL D1127 " --> pdb=" O LEU D1123 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D1138 " --> pdb=" O LEU D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1148 through 1151 No H-bonds generated for 'chain 'D' and resid 1148 through 1151' Processing helix chain 'D' and resid 1153 through 1160 removed outlier: 3.894A pdb=" N TYR D1160 " --> pdb=" O LEU D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1168 through 1171 No H-bonds generated for 'chain 'D' and resid 1168 through 1171' Processing helix chain 'D' and resid 1184 through 1195 removed outlier: 3.633A pdb=" N LYS D1194 " --> pdb=" O GLY D1190 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU D1195 " --> pdb=" O TYR D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1217 removed outlier: 4.750A pdb=" N ASN D1210 " --> pdb=" O HIS D1206 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS D1215 " --> pdb=" O MET D1211 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG D1217 " --> pdb=" O ARG D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1221 through 1223 No H-bonds generated for 'chain 'D' and resid 1221 through 1223' Processing helix chain 'D' and resid 1225 through 1237 removed outlier: 3.593A pdb=" N THR D1230 " --> pdb=" O LEU D1226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D1236 " --> pdb=" O ASP D1232 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU D1237 " --> pdb=" O MET D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1240 through 1258 removed outlier: 3.621A pdb=" N VAL D1245 " --> pdb=" O ASN D1241 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D1249 " --> pdb=" O VAL D1245 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D1256 " --> pdb=" O GLU D1252 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP D1257 " --> pdb=" O LEU D1253 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D1258 " --> pdb=" O LEU D1254 " (cutoff:3.500A) Processing helix chain 'D' and resid 1263 through 1268 Processing helix chain 'D' and resid 1296 through 1298 No H-bonds generated for 'chain 'D' and resid 1296 through 1298' Processing helix chain 'D' and resid 1300 through 1303 No H-bonds generated for 'chain 'D' and resid 1300 through 1303' Processing helix chain 'D' and resid 1308 through 1316 removed outlier: 3.645A pdb=" N LEU D1312 " --> pdb=" O LEU D1308 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP D1313 " --> pdb=" O PRO D1309 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS D1315 " --> pdb=" O ILE D1311 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE D1316 " --> pdb=" O LEU D1312 " (cutoff:3.500A) Processing helix chain 'D' and resid 1320 through 1336 removed outlier: 4.403A pdb=" N ILE D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D1334 " --> pdb=" O LEU D1330 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS D1335 " --> pdb=" O LYS D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1341 through 1347 removed outlier: 4.826A pdb=" N SER D1346 " --> pdb=" O ARG D1342 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR D1347 " --> pdb=" O MET D1343 " (cutoff:3.500A) Processing helix chain 'D' and resid 1349 through 1351 No H-bonds generated for 'chain 'D' and resid 1349 through 1351' Processing helix chain 'D' and resid 1357 through 1373 removed outlier: 4.945A pdb=" N GLU D1361 " --> pdb=" O GLU D1358 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA D1363 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D1370 " --> pdb=" O HIS D1367 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS D1371 " --> pdb=" O THR D1368 " (cutoff:3.500A) Processing helix chain 'D' and resid 1381 through 1392 removed outlier: 4.125A pdb=" N ALA D1386 " --> pdb=" O ALA D1383 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D1389 " --> pdb=" O ALA D1386 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE D1390 " --> pdb=" O ASP D1387 " (cutoff:3.500A) Processing helix chain 'D' and resid 1412 through 1416 Processing helix chain 'D' and resid 1424 through 1435 removed outlier: 3.970A pdb=" N ILE D1429 " --> pdb=" O ARG D1425 " (cutoff:3.500A) Proline residue: D1435 - end of helix Processing helix chain 'D' and resid 1448 through 1462 removed outlier: 3.588A pdb=" N VAL D1454 " --> pdb=" O LYS D1450 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D1459 " --> pdb=" O SER D1455 " (cutoff:3.500A) Processing helix chain 'D' and resid 1471 through 1485 removed outlier: 3.978A pdb=" N ILE D1475 " --> pdb=" O GLU D1471 " (cutoff:3.500A) Processing helix chain 'D' and resid 1487 through 1492 removed outlier: 4.953A pdb=" N GLY D1492 " --> pdb=" O PRO D1488 " (cutoff:3.500A) Processing helix chain 'D' and resid 1504 through 1524 removed outlier: 3.510A pdb=" N ILE D1508 " --> pdb=" O ILE D1504 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN D1509 " --> pdb=" O LEU D1505 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D1513 " --> pdb=" O ASN D1509 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D1514 " --> pdb=" O LEU D1510 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D1515 " --> pdb=" O CYS D1511 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE D1524 " --> pdb=" O ILE D1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 124 through 134 removed outlier: 4.833A pdb=" N GLU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 172 through 205 removed outlier: 3.574A pdb=" N GLU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1077 Processing helix chain 'A' and resid 1081 through 1089 Processing helix chain 'A' and resid 1134 through 1151 removed outlier: 3.719A pdb=" N TYR A1151 " --> pdb=" O ALA A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1181 Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 4.929A pdb=" N LYS A1200 " --> pdb=" O GLN A1196 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 48 Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 166 through 237 removed outlier: 3.826A pdb=" N ASN C 218 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 966 Processing helix chain 'C' and resid 974 through 1035 Processing helix chain 'C' and resid 1099 through 1116 Processing helix chain 'C' and resid 1133 through 1149 Processing helix chain 'C' and resid 1162 through 1164 No H-bonds generated for 'chain 'C' and resid 1162 through 1164' Processing helix chain 'C' and resid 1186 through 1190 Processing sheet with id= A, first strand: chain 'D' and resid 248 through 250 Processing sheet with id= B, first strand: chain 'A' and resid 18 through 21 removed outlier: 7.231A pdb=" N MET A 92 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU A 7 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS A 90 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL A 9 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYR A 88 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 114 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1218 through 1222 removed outlier: 6.506A pdb=" N PHE A1157 " --> pdb=" O VAL A1189 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A1191 " --> pdb=" O PHE A1157 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A1159 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1099 through 1103 Processing sheet with id= E, first strand: chain 'C' and resid 5 through 9 removed outlier: 3.868A pdb=" N LYS C 5 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 78 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG C 99 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.373A pdb=" N ASN C1122 " --> pdb=" O ILE C1153 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR C1155 " --> pdb=" O ASN C1122 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU C1124 " --> pdb=" O THR C1155 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 1040 through 1044 removed outlier: 3.646A pdb=" N GLU C1042 " --> pdb=" O ARG C1081 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 1170 through 1174 removed outlier: 3.799A pdb=" N GLY C1170 " --> pdb=" O GLU C1181 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 8.53 Time building geometry restraints manager: 9.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.02: 2 1.02 - 1.24: 2078 1.24 - 1.46: 7918 1.46 - 1.68: 9876 1.68 - 1.89: 113 Bond restraints: 19987 Sorted by residual: bond pdb=" CD GLN C 9 " pdb=" NE2 GLN C 9 " ideal model delta sigma weight residual 1.328 0.800 0.528 2.10e-02 2.27e+03 6.33e+02 bond pdb=" CB GLN C 9 " pdb=" CG GLN C 9 " ideal model delta sigma weight residual 1.520 1.093 0.427 3.00e-02 1.11e+03 2.03e+02 bond pdb=" O5' ADP C1202 " pdb=" PA ADP C1202 " ideal model delta sigma weight residual 1.610 1.895 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" O5' ADP A1302 " pdb=" PA ADP A1302 " ideal model delta sigma weight residual 1.610 1.894 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" CG1 ILE D1520 " pdb=" CD1 ILE D1520 " ideal model delta sigma weight residual 1.513 0.998 0.515 3.90e-02 6.57e+02 1.74e+02 ... (remaining 19982 not shown) Histogram of bond angle deviations from ideal: 68.85 - 85.14: 5 85.14 - 101.43: 111 101.43 - 117.73: 15209 117.73 - 134.02: 11909 134.02 - 150.31: 12 Bond angle restraints: 27246 Sorted by residual: angle pdb=" CG GLN C 9 " pdb=" CD GLN C 9 " pdb=" NE2 GLN C 9 " ideal model delta sigma weight residual 116.40 93.95 22.45 1.50e+00 4.44e-01 2.24e+02 angle pdb=" NE ARG C 220 " pdb=" CZ ARG C 220 " pdb=" NH2 ARG C 220 " ideal model delta sigma weight residual 119.20 105.85 13.35 9.00e-01 1.23e+00 2.20e+02 angle pdb=" CG MET D1211 " pdb=" SD MET D1211 " pdb=" CE MET D1211 " ideal model delta sigma weight residual 100.90 68.85 32.05 2.20e+00 2.07e-01 2.12e+02 angle pdb=" NE ARG C 220 " pdb=" CZ ARG C 220 " pdb=" NH1 ARG C 220 " ideal model delta sigma weight residual 121.50 134.07 -12.57 1.00e+00 1.00e+00 1.58e+02 angle pdb=" CG GLN C 9 " pdb=" CD GLN C 9 " pdb=" OE1 GLN C 9 " ideal model delta sigma weight residual 120.80 142.74 -21.94 2.00e+00 2.50e-01 1.20e+02 ... (remaining 27241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 11444 33.75 - 67.50: 531 67.50 - 101.26: 35 101.26 - 135.01: 1 135.01 - 168.76: 4 Dihedral angle restraints: 12015 sinusoidal: 5311 harmonic: 6704 Sorted by residual: dihedral pdb=" CA SER D1178 " pdb=" C SER D1178 " pdb=" N PRO D1179 " pdb=" CA PRO D1179 " ideal model delta harmonic sigma weight residual -180.00 -142.80 -37.20 0 5.00e+00 4.00e-02 5.54e+01 dihedral pdb=" CA LYS D 722 " pdb=" C LYS D 722 " pdb=" N VAL D 723 " pdb=" CA VAL D 723 " ideal model delta harmonic sigma weight residual -180.00 -145.18 -34.82 0 5.00e+00 4.00e-02 4.85e+01 dihedral pdb=" O1B ADP C1202 " pdb=" O3A ADP C1202 " pdb=" PB ADP C1202 " pdb=" PA ADP C1202 " ideal model delta sinusoidal sigma weight residual 300.00 132.53 167.47 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 12012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 3114 0.238 - 0.476: 40 0.476 - 0.713: 2 0.713 - 0.951: 2 0.951 - 1.189: 1 Chirality restraints: 3159 Sorted by residual: chirality pdb=" CG LEU D1189 " pdb=" CB LEU D1189 " pdb=" CD1 LEU D1189 " pdb=" CD2 LEU D1189 " both_signs ideal model delta sigma weight residual False -2.59 -1.40 -1.19 2.00e-01 2.50e+01 3.53e+01 chirality pdb=" CG LEU C 964 " pdb=" CB LEU C 964 " pdb=" CD1 LEU C 964 " pdb=" CD2 LEU C 964 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CG LEU D 999 " pdb=" CB LEU D 999 " pdb=" CD1 LEU D 999 " pdb=" CD2 LEU D 999 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 ... (remaining 3156 not shown) Planarity restraints: 3214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 922 " -0.009 2.00e-02 2.50e+03 6.10e-02 9.30e+01 pdb=" CG TRP D 922 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 922 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP D 922 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP D 922 " 0.102 2.00e-02 2.50e+03 pdb=" CE2 TRP D 922 " -0.056 2.00e-02 2.50e+03 pdb=" CE3 TRP D 922 " -0.035 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 922 " -0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 922 " 0.085 2.00e-02 2.50e+03 pdb=" CH2 TRP D 922 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 85 " 0.225 9.50e-02 1.11e+02 1.27e-01 8.01e+01 pdb=" NE ARG B 85 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 85 " 0.146 2.00e-02 2.50e+03 pdb=" NH1 ARG B 85 " -0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG B 85 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1149 " 0.089 2.00e-02 2.50e+03 6.81e-02 6.95e+01 pdb=" CG HIS A1149 " -0.119 2.00e-02 2.50e+03 pdb=" ND1 HIS A1149 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS A1149 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A1149 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS A1149 " 0.062 2.00e-02 2.50e+03 ... (remaining 3211 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 393 2.61 - 3.18: 18156 3.18 - 3.75: 32028 3.75 - 4.33: 41513 4.33 - 4.90: 62184 Nonbonded interactions: 154274 Sorted by model distance: nonbonded pdb=" OE1 GLN C 141 " pdb=" F3 BEF C1201 " model vdw 2.033 2.390 nonbonded pdb=" O ARG C 143 " pdb=" OG SER C 146 " model vdw 2.110 2.440 nonbonded pdb=" O GLN D 502 " pdb=" OG SER D 505 " model vdw 2.160 2.440 nonbonded pdb=" O THR D 272 " pdb=" OG SER D 275 " model vdw 2.162 2.440 nonbonded pdb=" NH2 ARG D 801 " pdb=" OD1 ASN D 804 " model vdw 2.182 2.520 ... (remaining 154269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.720 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 58.540 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.018 0.528 19987 Z= 1.125 Angle : 1.710 34.008 27246 Z= 0.886 Chirality : 0.082 1.189 3159 Planarity : 0.011 0.179 3214 Dihedral : 18.028 168.761 7635 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.16), residues: 2238 helix: -1.64 (0.13), residues: 1189 sheet: -1.87 (0.44), residues: 128 loop : -3.04 (0.19), residues: 921 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 247 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 252 average time/residue: 0.3380 time to fit residues: 131.6874 Evaluate side-chains 169 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3891 time to fit residues: 4.9621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 ASN ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 ASN ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1059 GLN D1336 GLN A 167 GLN C 34 ASN ** C1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 19987 Z= 0.207 Angle : 0.709 11.846 27246 Z= 0.369 Chirality : 0.043 0.232 3159 Planarity : 0.005 0.077 3214 Dihedral : 17.944 171.167 3090 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.17), residues: 2238 helix: -0.63 (0.14), residues: 1210 sheet: -1.59 (0.43), residues: 129 loop : -2.75 (0.19), residues: 899 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 239 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 254 average time/residue: 0.3155 time to fit residues: 125.9714 Evaluate side-chains 195 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1954 time to fit residues: 8.4166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 ASN B 576 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1193 GLN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 GLN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 19987 Z= 0.330 Angle : 0.751 12.393 27246 Z= 0.397 Chirality : 0.045 0.230 3159 Planarity : 0.005 0.082 3214 Dihedral : 17.769 174.876 3090 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.25 % Favored : 90.71 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2238 helix: -0.44 (0.14), residues: 1224 sheet: -1.57 (0.43), residues: 135 loop : -2.71 (0.20), residues: 879 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 194 time to evaluate : 2.357 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 226 average time/residue: 0.3097 time to fit residues: 111.6648 Evaluate side-chains 198 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 2.531 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1979 time to fit residues: 12.5957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 60 optimal weight: 0.0470 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 GLN D 222 GLN D 518 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN C 9 GLN C 979 ASN ** C1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19987 Z= 0.196 Angle : 0.667 10.901 27246 Z= 0.343 Chirality : 0.042 0.225 3159 Planarity : 0.004 0.076 3214 Dihedral : 17.513 172.526 3090 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.18), residues: 2238 helix: -0.14 (0.15), residues: 1230 sheet: -1.31 (0.45), residues: 126 loop : -2.44 (0.20), residues: 882 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 213 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 236 average time/residue: 0.2874 time to fit residues: 108.6996 Evaluate side-chains 192 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 2.314 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1969 time to fit residues: 6.7838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 154 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN D 518 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 19987 Z= 0.283 Angle : 0.718 10.582 27246 Z= 0.374 Chirality : 0.044 0.219 3159 Planarity : 0.005 0.079 3214 Dihedral : 17.506 174.492 3090 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.16 % Favored : 90.80 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.18), residues: 2238 helix: -0.10 (0.15), residues: 1223 sheet: -1.28 (0.48), residues: 116 loop : -2.51 (0.20), residues: 899 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 221 average time/residue: 0.3142 time to fit residues: 111.6316 Evaluate side-chains 196 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 2.392 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1870 time to fit residues: 8.6822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 223 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 103 optimal weight: 0.0050 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 518 GLN ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19987 Z= 0.179 Angle : 0.671 11.768 27246 Z= 0.339 Chirality : 0.041 0.223 3159 Planarity : 0.004 0.074 3214 Dihedral : 17.361 172.301 3090 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2238 helix: 0.10 (0.15), residues: 1220 sheet: -1.11 (0.50), residues: 112 loop : -2.31 (0.21), residues: 906 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 213 time to evaluate : 2.513 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 227 average time/residue: 0.3330 time to fit residues: 119.4274 Evaluate side-chains 191 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 2.557 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1695 time to fit residues: 5.5147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 222 optimal weight: 0.0670 chunk 139 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 518 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1512 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19987 Z= 0.187 Angle : 0.684 12.299 27246 Z= 0.343 Chirality : 0.042 0.217 3159 Planarity : 0.004 0.072 3214 Dihedral : 17.269 173.122 3090 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2238 helix: 0.19 (0.15), residues: 1217 sheet: -0.94 (0.51), residues: 112 loop : -2.20 (0.21), residues: 909 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 204 time to evaluate : 2.540 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 219 average time/residue: 0.3132 time to fit residues: 108.7343 Evaluate side-chains 188 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1927 time to fit residues: 5.9683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 132 optimal weight: 0.0050 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1193 GLN C 977 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19987 Z= 0.180 Angle : 0.694 12.008 27246 Z= 0.343 Chirality : 0.041 0.220 3159 Planarity : 0.004 0.071 3214 Dihedral : 17.213 172.813 3090 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2238 helix: 0.30 (0.15), residues: 1212 sheet: -0.78 (0.52), residues: 112 loop : -2.11 (0.21), residues: 914 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 212 average time/residue: 0.3147 time to fit residues: 106.2645 Evaluate side-chains 187 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 183 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2212 time to fit residues: 4.7413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.0870 chunk 194 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 0.0970 chunk 136 optimal weight: 0.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19987 Z= 0.196 Angle : 0.721 15.335 27246 Z= 0.355 Chirality : 0.042 0.256 3159 Planarity : 0.004 0.071 3214 Dihedral : 17.184 173.138 3090 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2238 helix: 0.35 (0.15), residues: 1212 sheet: -0.80 (0.52), residues: 112 loop : -2.08 (0.21), residues: 914 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 195 average time/residue: 0.3126 time to fit residues: 98.0781 Evaluate side-chains 187 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2344 time to fit residues: 4.8603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 211 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19987 Z= 0.205 Angle : 0.727 14.788 27246 Z= 0.358 Chirality : 0.042 0.277 3159 Planarity : 0.004 0.072 3214 Dihedral : 17.170 173.258 3090 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2238 helix: 0.34 (0.15), residues: 1212 sheet: -0.84 (0.52), residues: 112 loop : -2.07 (0.21), residues: 914 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 191 average time/residue: 0.2961 time to fit residues: 91.6730 Evaluate side-chains 187 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 2.476 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2178 time to fit residues: 5.3117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.094736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.080751 restraints weight = 87075.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.082433 restraints weight = 52751.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.083530 restraints weight = 36901.473| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19987 Z= 0.190 Angle : 0.719 15.010 27246 Z= 0.353 Chirality : 0.042 0.330 3159 Planarity : 0.004 0.071 3214 Dihedral : 17.137 172.969 3090 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2238 helix: 0.39 (0.15), residues: 1207 sheet: -0.82 (0.52), residues: 112 loop : -2.06 (0.21), residues: 919 =============================================================================== Job complete usr+sys time: 3336.44 seconds wall clock time: 62 minutes 44.06 seconds (3764.06 seconds total)