Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 07:16:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/08_2023/6cg0_7470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/08_2023/6cg0_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_7470/08_2023/6cg0_7470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/08_2023/6cg0_7470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/08_2023/6cg0_7470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cg0_7470/08_2023/6cg0_7470.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: {' CA': 1, ' ZN': 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: {' CA': 1, ' ZN': 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: 12.54, per 1000 atoms: 0.62 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: 8.86 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal 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: 7.58 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: 10.18 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 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: 1.670 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: 6.590 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 66.310 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 15.24 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 : 2.101 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 28 residues processed: 216 average time/residue: 0.5227 time to fit residues: 152.9238 Evaluate side-chains 104 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 76 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4456 time to fit residues: 19.5284 ------------------------------------------------------------------------------- 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: 0.8417 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 : 8.80 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 : 1.965 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.2993 time to fit residues: 45.3290 Evaluate side-chains 78 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 1.944 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2002 time to fit residues: 4.3358 ------------------------------------------------------------------------------- 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: 4.9990 chunk 133 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 157 optimal weight: 0.1980 overall best weight: 3.0388 ------------------------------------------------------------------------------- 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: 0.8546 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 20957 Z= 0.360 Angle : 0.615 8.395 29236 Z= 0.339 Chirality : 0.041 0.178 3209 Planarity : 0.004 0.057 3027 Dihedral : 24.073 173.007 4268 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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: -0.68 (0.19), residues: 1974 helix: 1.22 (0.20), residues: 704 sheet: -0.84 (0.27), residues: 353 loop : -1.66 (0.19), residues: 917 *********************** 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 : 2.005 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 87 average time/residue: 0.3298 time to fit residues: 46.1906 Evaluate side-chains 76 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.988 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1850 time to fit residues: 4.2921 ------------------------------------------------------------------------------- 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: 0.4980 chunk 21 optimal weight: 0.3980 chunk 93 optimal weight: 0.4980 chunk 131 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A 962 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 GLN C 800 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2555 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= 0.149 Angle : 0.514 13.183 29236 Z= 0.284 Chirality : 0.038 0.149 3209 Planarity : 0.003 0.045 3027 Dihedral : 23.804 173.364 4268 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.19), residues: 1974 helix: 1.53 (0.20), residues: 711 sheet: -0.55 (0.27), residues: 354 loop : -1.41 (0.20), residues: 909 *********************** 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 81 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 1.945 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 81 average time/residue: 0.3087 time to fit residues: 41.5067 Evaluate side-chains 75 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1705 time to fit residues: 3.2029 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 800 ASN ** 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: 0.8537 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 20957 Z= 0.289 Angle : 0.565 10.991 29236 Z= 0.310 Chirality : 0.040 0.157 3209 Planarity : 0.004 0.066 3027 Dihedral : 24.047 173.321 4268 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: 1.62 (0.21), residues: 706 sheet: -0.37 (0.27), residues: 358 loop : -1.29 (0.20), residues: 910 *********************** 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 79 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 2.048 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 77 average time/residue: 0.3408 time to fit residues: 43.9777 Evaluate side-chains 74 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 2.177 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3166 time to fit residues: 4.2467 ------------------------------------------------------------------------------- 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: 0.9980 chunk 188 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 520 GLN ** 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: 0.8499 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20957 Z= 0.172 Angle : 0.525 17.279 29236 Z= 0.286 Chirality : 0.038 0.153 3209 Planarity : 0.003 0.045 3027 Dihedral : 23.887 173.665 4268 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.58 % 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: 0.13 (0.19), residues: 1974 helix: 1.74 (0.21), residues: 706 sheet: -0.18 (0.27), residues: 359 loop : -1.16 (0.20), residues: 909 *********************** 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 79 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 2.041 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 76 average time/residue: 0.2737 time to fit residues: 36.4482 Evaluate side-chains 74 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1978 time to fit residues: 4.0328 ------------------------------------------------------------------------------- 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: 3.9990 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 208 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 126 optimal weight: 0.0060 chunk 96 optimal weight: 6.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- 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 520 GLN ** 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: 0.8492 moved from start: 0.2923 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= 0.164 Angle : 0.505 9.470 29236 Z= 0.279 Chirality : 0.037 0.145 3209 Planarity : 0.003 0.043 3027 Dihedral : 23.857 173.542 4268 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.41 % 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: 0.26 (0.20), residues: 1974 helix: 1.79 (0.20), residues: 709 sheet: -0.03 (0.28), residues: 354 loop : -1.06 (0.20), residues: 911 *********************** 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 75 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 1.823 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 73 average time/residue: 0.2896 time to fit residues: 36.6673 Evaluate side-chains 71 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2342 time to fit residues: 2.9972 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 HIS ** 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: 0.8496 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20957 Z= 0.183 Angle : 0.527 17.777 29236 Z= 0.287 Chirality : 0.038 0.145 3209 Planarity : 0.003 0.043 3027 Dihedral : 23.858 173.512 4268 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 0.32 (0.20), residues: 1974 helix: 1.80 (0.20), residues: 709 sheet: 0.07 (0.28), residues: 361 loop : -1.03 (0.20), residues: 904 *********************** 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 71 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 2.159 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 70 average time/residue: 0.2828 time to fit residues: 35.0552 Evaluate side-chains 68 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5839 ------------------------------------------------------------------------------- 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: 4.9990 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 520 GLN ** 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: 0.8513 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 20957 Z= 0.225 Angle : 0.532 10.447 29236 Z= 0.292 Chirality : 0.038 0.145 3209 Planarity : 0.003 0.043 3027 Dihedral : 23.919 173.365 4268 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.35 % 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: 1.80 (0.20), residues: 710 sheet: 0.06 (0.28), residues: 367 loop : -0.98 (0.21), residues: 897 *********************** 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 72 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.980 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 69 average time/residue: 0.2828 time to fit residues: 34.3829 Evaluate side-chains 69 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 1.964 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2298 time to fit residues: 3.5390 ------------------------------------------------------------------------------- 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: 0.0050 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 0.0370 overall best weight: 0.7474 ------------------------------------------------------------------------------- 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 520 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3098 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= 0.150 Angle : 0.520 18.020 29236 Z= 0.281 Chirality : 0.037 0.156 3209 Planarity : 0.003 0.042 3027 Dihedral : 23.787 173.221 4268 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 0.47 (0.20), residues: 1974 helix: 1.88 (0.21), residues: 710 sheet: 0.28 (0.28), residues: 361 loop : -0.97 (0.21), residues: 903 ********************** 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 71 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 2.087 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.2818 time to fit residues: 34.3789 Evaluate side-chains 68 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.781 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3250 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 0.8980 chunk 158 optimal weight: 0.0010 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 0.0040 chunk 71 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.085737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056489 restraints weight = 109347.484| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.26 r_work: 0.2925 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3153 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= 0.135 Angle : 0.498 11.035 29236 Z= 0.273 Chirality : 0.037 0.142 3209 Planarity : 0.003 0.041 3027 Dihedral : 23.717 172.963 4268 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 0.58 (0.20), residues: 1974 helix: 1.94 (0.20), residues: 710 sheet: 0.41 (0.29), residues: 356 loop : -0.90 (0.20), residues: 908 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.46 seconds wall clock time: 65 minutes 41.49 seconds (3941.49 seconds total)