Starting phenix.real_space_refine (version: dev) on Wed Apr 6 10:31:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/04_2022/6cg0_7470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/04_2022/6cg0_7470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/04_2022/6cg0_7470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/04_2022/6cg0_7470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/04_2022/6cg0_7470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/04_2022/6cg0_7470.pdb" } resolution = 3.17 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= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A ARG 828": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A PHE 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 393": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 617": "OE1" <-> "OE2" Residue "C PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 696": "NH1" <-> "NH2" Residue "C PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 756": "NH1" <-> "NH2" Residue "C GLU 758": "OE1" <-> "OE2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 828": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 949": "NH1" <-> "NH2" Residue "C GLU 959": "OE1" <-> "OE2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 20080 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4921 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 588} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4944 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 590} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2664 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2649 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 342, 2649 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2698 Chain: "B" Number of atoms: 2672 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2662 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 342, 2662 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2717 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 947 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain: "I" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1225 Classifications: {'DNA': 60} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 59} Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 610 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "M" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 845 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "N" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 538 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' CA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' CA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2590 SG CYS A 727 97.086 23.425 71.510 1.00 75.71 S ATOM 2611 SG CYS A 730 98.249 20.598 69.684 1.00 74.45 S ATOM 7542 SG CYS C 727 61.203 83.048 69.025 1.00 71.59 S ATOM 7563 SG CYS C 730 60.014 85.872 67.139 1.00 74.40 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 Time building chain proxies: 13.21, per 1000 atoms: 0.66 Number of scatterers: 20080 At special positions: 0 Unit cell: (159.43, 109.14, 182.97, 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) Zn 2 29.99 Ca 2 19.99 S 109 16.00 P 209 15.00 O 4181 8.00 N 3547 7.00 C 12030 6.00 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=0, symmetry=0 Time building additional restraints: 8.61 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " Number of angles added : 4 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3730 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 22 sheets defined 40.2% alpha, 18.7% beta 90 base pairs and 154 stacking pairs defined. Time for finding SS restraints: 6.58 Creating SS restraints... Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.582A pdb=" N LEU A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 removed outlier: 3.573A pdb=" N VAL A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 455 Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.878A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.509A pdb=" N MET A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.819A pdb=" N CYS A 651 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 648 through 652' Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.522A pdb=" N GLY A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 822 through 841 removed outlier: 3.672A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 859 through 867 Processing helix chain 'A' and resid 873 through 895 removed outlier: 3.640A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 934 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.659A pdb=" N GLN A 962 " --> pdb=" O SER A 958 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.584A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1004 removed outlier: 3.900A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 420 removed outlier: 5.413A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 442 removed outlier: 3.758A pdb=" N VAL C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 457 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.509A pdb=" N LEU C 503 " --> pdb=" O PRO C 499 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 581 removed outlier: 5.288A pdb=" N GLU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.678A pdb=" N CYS C 651 " --> pdb=" O SER C 648 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS C 652 " --> pdb=" O GLU C 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 648 through 652' Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 738 removed outlier: 3.523A pdb=" N SER C 738 " --> pdb=" O ARG C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 812 Processing helix chain 'C' and resid 822 through 842 removed outlier: 3.756A pdb=" N ARG C 826 " --> pdb=" O SER C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 873 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.532A pdb=" N CYS C 902 " --> pdb=" O PRO C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 924 through 927 Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.813A pdb=" N HIS C 937 " --> pdb=" O THR C 933 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 942 " --> pdb=" O LYS C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.611A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 996 Processing helix chain 'C' and resid 999 through 1004 Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.742A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.735A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.559A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.508A pdb=" N LYS B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 27 Processing helix chain 'N' and resid 41 through 48 removed outlier: 4.199A pdb=" N CYS N 45 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER N 46 " --> pdb=" O LYS N 43 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU N 47 " --> pdb=" O LYS N 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG N 48 " --> pdb=" O CYS N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 117 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 121 through 136 removed outlier: 3.773A pdb=" N VAL N 125 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 3.771A pdb=" N GLU A 518 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 688 " --> pdb=" O GLU A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 536 removed outlier: 5.661A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 536 removed outlier: 5.661A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AA5, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.677A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 703 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.677A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 703 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.607A pdb=" N ARG D 349 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 22 through 24 removed outlier: 4.131A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.654A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 78 through 81 removed outlier: 3.697A pdb=" N CYS D 78 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.033A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB4, first strand: chain 'D' and resid 208 through 211 removed outlier: 4.259A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 267 removed outlier: 7.256A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.735A pdb=" N SER B 2 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.477A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 56 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.489A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 78 through 80 removed outlier: 4.218A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.831A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AC3, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.526A pdb=" N ILE B 218 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 248 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.679A pdb=" N VAL B 272 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 224 hydrogen bonds 444 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 154 stacking parallelities Total time for adding SS restraints: 10.46 Time building geometry restraints manager: 9.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3060 1.32 - 1.45: 6618 1.45 - 1.57: 10699 1.57 - 1.69: 415 1.69 - 1.81: 165 Bond restraints: 20957 Sorted by residual: bond pdb=" C LYS A 890 " pdb=" O LYS A 890 " ideal model delta sigma weight residual 1.244 1.228 0.016 1.00e-02 1.00e+04 2.53e+00 bond pdb=" C5 DT F 12 " pdb=" C7 DT F 12 " ideal model delta sigma weight residual 1.500 1.472 0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" N3 DT F 12 " pdb=" C4 DT F 12 " ideal model delta sigma weight residual 1.383 1.357 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" CA SER C 460 " pdb=" C SER C 460 " ideal model delta sigma weight residual 1.531 1.518 0.014 1.08e-02 8.57e+03 1.63e+00 bond pdb=" N9 DA L 35 " pdb=" C4 DA L 35 " ideal model delta sigma weight residual 1.376 1.401 -0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 20952 not shown) Histogram of bond angle deviations from ideal: 97.64 - 104.91: 1126 104.91 - 112.18: 10912 112.18 - 119.45: 6398 119.45 - 126.72: 9956 126.72 - 133.99: 844 Bond angle restraints: 29236 Sorted by residual: angle pdb=" C PRO C 521 " pdb=" N PRO C 522 " pdb=" CA PRO C 522 " ideal model delta sigma weight residual 119.84 127.93 -8.09 1.25e+00 6.40e-01 4.19e+01 angle pdb=" N TYR A 559 " pdb=" CA TYR A 559 " pdb=" C TYR A 559 " ideal model delta sigma weight residual 111.07 117.84 -6.77 1.07e+00 8.73e-01 4.00e+01 angle pdb=" N TYR C 725 " pdb=" CA TYR C 725 " pdb=" C TYR C 725 " ideal model delta sigma weight residual 109.25 100.47 8.78 1.53e+00 4.27e-01 3.29e+01 angle pdb=" N TYR A 725 " pdb=" CA TYR A 725 " pdb=" C TYR A 725 " ideal model delta sigma weight residual 108.23 99.80 8.43 1.72e+00 3.38e-01 2.40e+01 angle pdb=" N ARG A 875 " pdb=" CA ARG A 875 " pdb=" C ARG A 875 " ideal model delta sigma weight residual 111.28 106.08 5.20 1.09e+00 8.42e-01 2.28e+01 ... (remaining 29231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 10809 34.69 - 69.38: 992 69.38 - 104.07: 22 104.07 - 138.76: 0 138.76 - 173.45: 2 Dihedral angle restraints: 11825 sinusoidal: 6041 harmonic: 5784 Sorted by residual: dihedral pdb=" C4' DC J 9 " pdb=" C3' DC J 9 " pdb=" O3' DC J 9 " pdb=" P DT J 10 " ideal model delta sinusoidal sigma weight residual 220.00 46.55 173.45 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C4' DC I 9 " pdb=" C3' DC I 9 " pdb=" O3' DC I 9 " pdb=" P DT I 10 " ideal model delta sinusoidal sigma weight residual 220.00 72.06 147.94 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 11822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2771 0.056 - 0.112: 371 0.112 - 0.167: 56 0.167 - 0.223: 6 0.223 - 0.279: 5 Chirality restraints: 3209 Sorted by residual: chirality pdb=" CA TYR C 935 " pdb=" N TYR C 935 " pdb=" C TYR C 935 " pdb=" CB TYR C 935 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA TYR A 559 " pdb=" N TYR A 559 " pdb=" C TYR A 559 " pdb=" CB TYR A 559 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA TRP A 893 " pdb=" N TRP A 893 " pdb=" C TRP A 893 " pdb=" CB TRP A 893 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3206 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 46 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C PHE D 46 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE D 46 " 0.027 2.00e-02 2.50e+03 pdb=" N AHIS D 47 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 46 " 0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C PHE D 46 " -0.064 2.00e-02 2.50e+03 pdb=" O PHE D 46 " 0.024 2.00e-02 2.50e+03 pdb=" N BHIS D 47 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT F 12 " 0.021 2.00e-02 2.50e+03 1.99e-02 9.95e+00 pdb=" N1 DT F 12 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DT F 12 " -0.021 2.00e-02 2.50e+03 pdb=" O2 DT F 12 " -0.024 2.00e-02 2.50e+03 pdb=" N3 DT F 12 " 0.045 2.00e-02 2.50e+03 pdb=" C4 DT F 12 " -0.007 2.00e-02 2.50e+03 pdb=" O4 DT F 12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DT F 12 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DT F 12 " -0.017 2.00e-02 2.50e+03 pdb=" C6 DT F 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1888 2.74 - 3.28: 18847 3.28 - 3.82: 34484 3.82 - 4.36: 40314 4.36 - 4.90: 65304 Nonbonded interactions: 160837 Sorted by model distance: nonbonded pdb=" OG1 THR D 308 " pdb=" OD1 ASP D 310 " model vdw 2.205 2.440 nonbonded pdb=" OE2 GLU C 811 " pdb=" OH TYR C 926 " model vdw 2.206 2.440 nonbonded pdb=" O LEU C 462 " pdb=" NE2 GLN C 498 " model vdw 2.224 2.520 nonbonded pdb=" OE2 GLU A 547 " pdb=" NH1 ARG B 159 " model vdw 2.226 2.520 nonbonded pdb=" NZ LYS B 97 " pdb=" OH TYR B 161 " model vdw 2.244 2.520 ... (remaining 160832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 395 through 417 or (resid 418 through 419 and (name N or n \ ame CA or name C or name O or name CB )) or resid 420 through 439 or (resid 440 \ through 441 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 2 through 1006 or (resid 1007 and (name N or name CA or name C or name O or name \ CB )) or resid 1101 through 1102)) selection = (chain 'C' and ((resid 395 and (name N or name CA or name C or name O or name CB \ )) or resid 396 or (resid 397 and (name N or name CA or name C or name O or nam \ e CB )) or resid 398 through 523 or (resid 524 and (name N or name CA or name C \ or name O or name CB )) or resid 525 through 689 or (resid 690 and (name N or na \ me CA or name C or name O or name CB )) or resid 691 through 1007 or resid 1101 \ through 1102)) } ncs_group { reference = (chain 'B' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 46 or resid 48 through 118 or (resid 119 and (name N or nam \ e CA or name C or name O or name CB )) or resid 120 through 187 or (resid 188 an \ d (name N or name CA or name C or name O or name CB )) or resid 189 through 247 \ or resid 249 through 334 or (resid 335 and (name N or name CA or name C or name \ O or name CB )) or resid 341 through 351)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 81 or resid 88 through 24 \ 7 or resid 249 through 351)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 209 5.49 5 S 109 5.16 5 C 12030 2.51 5 N 3547 2.21 5 O 4181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.520 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: 6.450 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.180 Process input model: 67.210 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20957 Z= 0.171 Angle : 0.601 8.781 29236 Z= 0.385 Chirality : 0.041 0.279 3209 Planarity : 0.004 0.056 3027 Dihedral : 20.011 173.451 8095 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.49 % Favored : 97.41 % Rotamer Outliers : 4.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.17), residues: 1974 helix: -0.47 (0.18), residues: 687 sheet: -1.89 (0.26), residues: 361 loop : -2.45 (0.18), residues: 926 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 153 time to evaluate : 2.079 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 28 residues processed: 216 average time/residue: 0.4804 time to fit residues: 141.1803 Evaluate side-chains 104 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 76 time to evaluate : 2.000 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4339 time to fit residues: 19.2528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 482 HIS A 495 GLN A 505 ASN A 800 ASN A 850 ASN A 978 GLN A 990 HIS A1000 GLN ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS C 495 GLN ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 GLN C 860 GLN C 962 GLN C 978 GLN D 89 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 222 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 20957 Z= 0.173 Angle : 0.540 10.665 29236 Z= 0.301 Chirality : 0.038 0.156 3209 Planarity : 0.004 0.055 3027 Dihedral : 23.684 173.317 4268 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 1974 helix: 0.96 (0.20), residues: 702 sheet: -1.20 (0.27), residues: 354 loop : -1.92 (0.18), residues: 918 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.983 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.3000 time to fit residues: 45.4615 Evaluate side-chains 78 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1948 time to fit residues: 4.1126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 212 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 157 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A 800 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 GLN C 961 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.077 20957 Z= 0.435 Angle : 0.653 8.978 29236 Z= 0.358 Chirality : 0.043 0.185 3209 Planarity : 0.005 0.058 3027 Dihedral : 24.192 173.264 4268 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1974 helix: 1.10 (0.20), residues: 705 sheet: -0.88 (0.27), residues: 357 loop : -1.74 (0.19), residues: 912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 2.018 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 0.3219 time to fit residues: 45.6315 Evaluate side-chains 79 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1948 time to fit residues: 5.3905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 131 optimal weight: 0.3980 chunk 197 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 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 962 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 GLN ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20957 Z= 0.210 Angle : 0.544 14.129 29236 Z= 0.299 Chirality : 0.039 0.150 3209 Planarity : 0.004 0.046 3027 Dihedral : 23.928 173.983 4268 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 1974 helix: 1.43 (0.20), residues: 712 sheet: -0.63 (0.27), residues: 358 loop : -1.48 (0.20), residues: 904 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 81 average time/residue: 0.3394 time to fit residues: 44.8601 Evaluate side-chains 73 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4086 time to fit residues: 4.5707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 0.0070 chunk 178 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 0.2980 chunk 187 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 20957 Z= 0.161 Angle : 0.501 8.579 29236 Z= 0.278 Chirality : 0.037 0.147 3209 Planarity : 0.003 0.043 3027 Dihedral : 23.814 173.942 4268 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1974 helix: 1.67 (0.21), residues: 712 sheet: -0.30 (0.28), residues: 354 loop : -1.27 (0.20), residues: 908 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 2.002 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 82 average time/residue: 0.2807 time to fit residues: 38.9888 Evaluate side-chains 76 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1969 time to fit residues: 3.6776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A1006 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 20957 Z= 0.329 Angle : 0.593 17.823 29236 Z= 0.322 Chirality : 0.041 0.165 3209 Planarity : 0.004 0.045 3027 Dihedral : 24.144 173.532 4268 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 1974 helix: 1.52 (0.20), residues: 719 sheet: -0.30 (0.27), residues: 364 loop : -1.28 (0.20), residues: 891 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 1.943 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.3077 time to fit residues: 39.6881 Evaluate side-chains 75 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 2.412 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2691 time to fit residues: 5.4093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 119 optimal weight: 0.2980 chunk 152 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20957 Z= 0.147 Angle : 0.505 9.334 29236 Z= 0.278 Chirality : 0.037 0.145 3209 Planarity : 0.003 0.043 3027 Dihedral : 23.863 173.858 4268 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1974 helix: 1.73 (0.21), residues: 716 sheet: -0.07 (0.28), residues: 359 loop : -1.13 (0.20), residues: 899 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.972 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.2977 time to fit residues: 36.8353 Evaluate side-chains 72 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2623 time to fit residues: 3.3795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20957 Z= 0.176 Angle : 0.527 17.999 29236 Z= 0.284 Chirality : 0.038 0.190 3209 Planarity : 0.003 0.044 3027 Dihedral : 23.895 173.932 4268 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1974 helix: 1.78 (0.20), residues: 718 sheet: 0.07 (0.28), residues: 359 loop : -1.06 (0.20), residues: 897 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 2.064 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.3022 time to fit residues: 36.7769 Evaluate side-chains 70 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 127 optimal weight: 0.0980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20957 Z= 0.197 Angle : 0.520 11.321 29236 Z= 0.285 Chirality : 0.038 0.144 3209 Planarity : 0.003 0.043 3027 Dihedral : 23.893 173.752 4268 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1974 helix: 1.79 (0.20), residues: 718 sheet: 0.15 (0.28), residues: 361 loop : -1.03 (0.21), residues: 895 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 2.181 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.2985 time to fit residues: 36.9959 Evaluate side-chains 71 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2251 time to fit residues: 3.4950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 4.9990 chunk 125 optimal weight: 0.0870 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20957 Z= 0.169 Angle : 0.532 19.856 29236 Z= 0.285 Chirality : 0.037 0.180 3209 Planarity : 0.003 0.043 3027 Dihedral : 23.878 173.665 4268 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1974 helix: 1.80 (0.20), residues: 718 sheet: 0.20 (0.28), residues: 361 loop : -1.02 (0.21), residues: 895 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 2.144 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.3142 time to fit residues: 37.6274 Evaluate side-chains 68 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 158 optimal weight: 0.0010 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.085754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056665 restraints weight = 109513.869| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.23 r_work: 0.3066 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work: 0.3047 rms_B_bonded: 3.01 restraints_weight: 0.1250 r_work: 0.3037 rms_B_bonded: 3.06 restraints_weight: 0.0625 r_work: 0.3027 rms_B_bonded: 3.14 restraints_weight: 0.0312 r_work: 0.3017 rms_B_bonded: 3.23 restraints_weight: 0.0156 r_work: 0.3006 rms_B_bonded: 3.35 restraints_weight: 0.0078 r_work: 0.2995 rms_B_bonded: 3.49 restraints_weight: 0.0039 r_work: 0.2984 rms_B_bonded: 3.65 restraints_weight: 0.0020 r_work: 0.2972 rms_B_bonded: 3.83 restraints_weight: 0.0010 r_work: 0.2960 rms_B_bonded: 4.04 restraints_weight: 0.0005 r_work: 0.2947 rms_B_bonded: 4.27 restraints_weight: 0.0002 r_work: 0.2934 rms_B_bonded: 4.52 restraints_weight: 0.0001 r_work: 0.2920 rms_B_bonded: 4.80 restraints_weight: 0.0001 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 20957 Z= 0.133 Angle : 0.495 9.703 29236 Z= 0.271 Chirality : 0.037 0.141 3209 Planarity : 0.003 0.042 3027 Dihedral : 23.725 173.389 4268 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1974 helix: 1.92 (0.20), residues: 714 sheet: 0.34 (0.29), residues: 355 loop : -0.99 (0.20), residues: 905 =============================================================================== Job complete usr+sys time: 3122.10 seconds wall clock time: 58 minutes 10.76 seconds (3490.76 seconds total)