Starting phenix.real_space_refine (version: dev) on Mon May 16 17:34:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/05_2022/3jby_6488.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/05_2022/3jby_6488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/05_2022/3jby_6488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/05_2022/3jby_6488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/05_2022/3jby_6488.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/05_2022/3jby_6488.pdb" } resolution = 3.7 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= 0.008 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 490": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "C GLU 1005": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 16846 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 19, 'CIS': 4, 'TRANS': 524, 'PCIS': 2} Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 22, 'CIS': 9, 'TRANS': 317, 'PCIS': 2} Chain: "C" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 19, 'CIS': 4, 'TRANS': 524, 'PCIS': 2} Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 22, 'CIS': 9, 'TRANS': 317, 'PCIS': 2} Chain: "E" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 639 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 639 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "J" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 1, ' CA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 1, ' CA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2107 SG CYS A 749 96.116 79.954 64.147 1.00 7.90 S ATOM 9256 SG CYS C 749 56.429 25.315 64.298 1.00 9.51 S Time building chain proxies: 9.80, per 1000 atoms: 0.58 Number of scatterers: 16846 At special positions: 0 Unit cell: (153.75, 107.01, 121.77, 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 4 19.99 S 106 16.00 P 124 15.00 O 3430 8.00 N 2978 7.00 C 10202 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: 6.97 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 19 sheets defined 34.6% alpha, 23.2% beta 34 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 524 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 686 through 707 removed outlier: 3.938A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 4.564A pdb=" N GLU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.513A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 799 removed outlier: 3.747A pdb=" N ASP A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 835 removed outlier: 3.510A pdb=" N CYS A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.802A pdb=" N MET A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 894 through 917 removed outlier: 3.755A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 951 removed outlier: 3.698A pdb=" N TYR A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 980 through 996 removed outlier: 3.600A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 4.616A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A1008 " --> pdb=" O PHE A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1024 removed outlier: 3.520A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 524 removed outlier: 3.547A pdb=" N ASN C 524 " --> pdb=" O HIS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 529 removed outlier: 3.987A pdb=" N GLU C 528 " --> pdb=" O ALA C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 600 removed outlier: 4.995A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.755A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 757 through 762 Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 3.512A pdb=" N CYS C 818 " --> pdb=" O ASP C 814 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.681A pdb=" N ALA C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 888 " --> pdb=" O ALA C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 917 Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 946 through 951 removed outlier: 3.522A pdb=" N TYR C 950 " --> pdb=" O PHE C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 993 removed outlier: 4.642A pdb=" N GLY C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.519A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 3.583A pdb=" N GLN C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C1027 " --> pdb=" O LYS C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id= A, first strand: chain 'A' and resid 536 through 539 removed outlier: 3.531A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 677 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 536 through 539 removed outlier: 3.531A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.819A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.568A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.787A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 141 through 147 Processing sheet with id= G, first strand: chain 'B' and resid 159 through 161 Processing sheet with id= H, first strand: chain 'B' and resid 209 through 212 Processing sheet with id= I, first strand: chain 'B' and resid 263 through 265 Processing sheet with id= J, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.574A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.574A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 2 through 6 removed outlier: 3.906A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.547A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 76 through 80 removed outlier: 4.490A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.773A pdb=" N GLU D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 141 through 147 Processing sheet with id= Q, first strand: chain 'D' and resid 159 through 161 Processing sheet with id= R, first strand: chain 'D' and resid 209 through 212 Processing sheet with id= S, first strand: chain 'D' and resid 263 through 265 removed outlier: 4.088A pdb=" N CYS D 287 " --> pdb=" O ARG D 302 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 6.88 Time building geometry restraints manager: 7.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2888 1.32 - 1.45: 6125 1.45 - 1.59: 8094 1.59 - 1.72: 201 1.72 - 1.86: 158 Bond restraints: 17466 Sorted by residual: bond pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 1.517 1.576 -0.059 9.30e-03 1.16e+04 4.03e+01 bond pdb=" C1' DG F 15 " pdb=" N9 DG F 15 " ideal model delta sigma weight residual 1.460 1.342 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 1.517 1.568 -0.051 9.30e-03 1.16e+04 2.97e+01 bond pdb=" C SER A 985 " pdb=" N GLY A 986 " ideal model delta sigma weight residual 1.333 1.402 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA ASN C 983 " pdb=" C ASN C 983 " ideal model delta sigma weight residual 1.525 1.479 0.046 1.02e-02 9.61e+03 2.02e+01 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 95.29 - 103.20: 417 103.20 - 111.11: 7398 111.11 - 119.03: 7295 119.03 - 126.94: 8538 126.94 - 134.85: 488 Bond angle restraints: 24136 Sorted by residual: angle pdb=" N PRO D 339 " pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 110.70 121.88 -11.18 1.22e+00 6.72e-01 8.40e+01 angle pdb=" N ARG A 999 " pdb=" CA ARG A 999 " pdb=" C ARG A 999 " ideal model delta sigma weight residual 111.14 120.34 -9.20 1.08e+00 8.57e-01 7.26e+01 angle pdb=" C THR D 338 " pdb=" N PRO D 339 " pdb=" CA PRO D 339 " ideal model delta sigma weight residual 120.38 128.86 -8.48 1.03e+00 9.43e-01 6.77e+01 angle pdb=" N PRO B 339 " pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 110.70 120.21 -9.51 1.22e+00 6.72e-01 6.07e+01 angle pdb=" N ARG C 999 " pdb=" CA ARG C 999 " pdb=" C ARG C 999 " ideal model delta sigma weight residual 111.40 119.25 -7.85 1.22e+00 6.72e-01 4.15e+01 ... (remaining 24131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 9127 29.34 - 58.68: 897 58.68 - 88.02: 44 88.02 - 117.35: 6 117.35 - 146.69: 4 Dihedral angle restraints: 10078 sinusoidal: 4866 harmonic: 5212 Sorted by residual: dihedral pdb=" CA ASP A 658 " pdb=" C ASP A 658 " pdb=" N GLY A 659 " pdb=" CA GLY A 659 " ideal model delta harmonic sigma weight residual 180.00 137.23 42.77 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ASP C 658 " pdb=" C ASP C 658 " pdb=" N GLY C 659 " pdb=" CA GLY C 659 " ideal model delta harmonic sigma weight residual 180.00 142.38 37.62 0 5.00e+00 4.00e-02 5.66e+01 dihedral pdb=" CA PHE A1004 " pdb=" C PHE A1004 " pdb=" N GLU A1005 " pdb=" CA GLU A1005 " ideal model delta harmonic sigma weight residual -180.00 -145.84 -34.16 0 5.00e+00 4.00e-02 4.67e+01 ... (remaining 10075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1802 0.065 - 0.129: 655 0.129 - 0.193: 152 0.193 - 0.258: 20 0.258 - 0.322: 7 Chirality restraints: 2636 Sorted by residual: chirality pdb=" CB ILE D 272 " pdb=" CA ILE D 272 " pdb=" CG1 ILE D 272 " pdb=" CG2 ILE D 272 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR C 493 " pdb=" N THR C 493 " pdb=" C THR C 493 " pdb=" CB THR C 493 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' DG H 7 " pdb=" C4' DG H 7 " pdb=" O3' DG H 7 " pdb=" C2' DG H 7 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2633 not shown) Planarity restraints: 2690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG F 1 " 0.033 2.00e-02 2.50e+03 2.58e-02 1.99e+01 pdb=" N9 DG F 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG F 1 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG F 1 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG F 1 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG F 1 " -0.046 2.00e-02 2.50e+03 pdb=" O6 DG F 1 " 0.047 2.00e-02 2.50e+03 pdb=" N1 DG F 1 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DG F 1 " -0.039 2.00e-02 2.50e+03 pdb=" N2 DG F 1 " 0.026 2.00e-02 2.50e+03 pdb=" N3 DG F 1 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG F 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 1 " 0.047 2.00e-02 2.50e+03 2.53e-02 1.92e+01 pdb=" N9 DG G 1 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DG G 1 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG G 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG G 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG G 1 " -0.033 2.00e-02 2.50e+03 pdb=" O6 DG G 1 " 0.047 2.00e-02 2.50e+03 pdb=" N1 DG G 1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG G 1 " -0.024 2.00e-02 2.50e+03 pdb=" N2 DG G 1 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DG G 1 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DG G 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 15 " -0.057 2.00e-02 2.50e+03 2.23e-02 1.49e+01 pdb=" N9 DG G 15 " 0.037 2.00e-02 2.50e+03 pdb=" C8 DG G 15 " 0.020 2.00e-02 2.50e+03 pdb=" N7 DG G 15 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG G 15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG G 15 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG G 15 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG G 15 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG G 15 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG G 15 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG G 15 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DG G 15 " 0.005 2.00e-02 2.50e+03 ... (remaining 2687 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 276 2.59 - 3.17: 15173 3.17 - 3.75: 27503 3.75 - 4.32: 37786 4.32 - 4.90: 59813 Nonbonded interactions: 140551 Sorted by model distance: nonbonded pdb=" NE2 GLN A 858 " pdb=" O ALA A 887 " model vdw 2.015 2.520 nonbonded pdb=" OE2 GLU C 981 " pdb=" N2 DG F 15 " model vdw 2.100 2.520 nonbonded pdb=" OG SER C 760 " pdb=" O ASP C 951 " model vdw 2.116 2.440 nonbonded pdb=" NZ LYS A 508 " pdb=" OP1 DG F 5 " model vdw 2.133 2.520 nonbonded pdb=" O3' DA J 16 " pdb="CA CA C1103 " model vdw 2.175 2.510 ... (remaining 140546 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' } 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 4 9.91 5 Zn 2 6.06 5 P 124 5.49 5 S 106 5.16 5 C 10202 2.51 5 N 2978 2.21 5 O 3430 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 3.240 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.140 Process input model: 52.390 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.015 0.129 17466 Z= 0.970 Angle : 1.572 13.709 24136 Z= 0.846 Chirality : 0.070 0.322 2636 Planarity : 0.009 0.090 2690 Dihedral : 20.723 146.691 6726 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.48 % Rotamer Outliers : 5.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.15), residues: 1794 helix: -3.34 (0.14), residues: 540 sheet: -1.16 (0.26), residues: 314 loop : -2.20 (0.15), residues: 940 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 453 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 22 residues processed: 510 average time/residue: 0.3160 time to fit residues: 231.3693 Evaluate side-chains 265 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 243 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1852 time to fit residues: 9.4755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 278 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN C 910 GLN C 937 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 17466 Z= 0.279 Angle : 0.766 11.240 24136 Z= 0.409 Chirality : 0.045 0.275 2636 Planarity : 0.007 0.114 2690 Dihedral : 22.613 154.254 3208 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.16 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: -1.92 (0.17), residues: 1794 helix: -1.01 (0.20), residues: 554 sheet: -0.38 (0.27), residues: 316 loop : -1.75 (0.16), residues: 924 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 299 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 27 residues processed: 339 average time/residue: 0.2955 time to fit residues: 150.3249 Evaluate side-chains 252 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 225 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1796 time to fit residues: 10.9434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 64 ASN B 65 ASN C 524 ASN ** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 17466 Z= 0.240 Angle : 0.702 11.682 24136 Z= 0.371 Chirality : 0.042 0.291 2636 Planarity : 0.006 0.102 2690 Dihedral : 22.500 157.128 3208 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.01 % Favored : 96.77 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: -1.06 (0.18), residues: 1794 helix: 0.13 (0.22), residues: 546 sheet: 0.08 (0.27), residues: 316 loop : -1.51 (0.17), residues: 932 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 268 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 17 residues processed: 294 average time/residue: 0.2870 time to fit residues: 126.8376 Evaluate side-chains 237 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 220 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1631 time to fit residues: 7.5601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 116 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 17466 Z= 0.284 Angle : 0.697 12.724 24136 Z= 0.368 Chirality : 0.043 0.298 2636 Planarity : 0.006 0.102 2690 Dihedral : 22.507 158.812 3208 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.68 % Favored : 96.10 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: -0.75 (0.19), residues: 1794 helix: 0.54 (0.22), residues: 552 sheet: 0.11 (0.27), residues: 328 loop : -1.40 (0.18), residues: 914 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 240 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 32 residues processed: 274 average time/residue: 0.2806 time to fit residues: 119.3162 Evaluate side-chains 245 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 213 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1591 time to fit residues: 11.7038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN A 766 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 HIS ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.108 17466 Z= 0.321 Angle : 0.710 12.343 24136 Z= 0.373 Chirality : 0.043 0.288 2636 Planarity : 0.006 0.113 2690 Dihedral : 22.548 160.654 3208 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.46 % Favored : 95.26 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: -0.76 (0.18), residues: 1794 helix: 0.61 (0.22), residues: 560 sheet: -0.06 (0.27), residues: 340 loop : -1.43 (0.18), residues: 894 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 251 average time/residue: 0.2653 time to fit residues: 102.0906 Evaluate side-chains 231 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1587 time to fit residues: 8.5535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.110 17466 Z= 0.334 Angle : 0.719 11.439 24136 Z= 0.377 Chirality : 0.043 0.289 2636 Planarity : 0.006 0.119 2690 Dihedral : 22.553 161.972 3208 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.68 % Favored : 94.98 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: 1794 helix: 0.69 (0.22), residues: 550 sheet: -0.06 (0.26), residues: 338 loop : -1.33 (0.18), residues: 906 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 1.772 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 241 average time/residue: 0.2830 time to fit residues: 104.6037 Evaluate side-chains 226 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.914 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1686 time to fit residues: 9.6054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN A 687 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.122 17466 Z= 0.249 Angle : 0.684 11.241 24136 Z= 0.357 Chirality : 0.041 0.196 2636 Planarity : 0.005 0.086 2690 Dihedral : 22.410 163.059 3208 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.57 % Favored : 95.09 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: -0.53 (0.19), residues: 1794 helix: 0.85 (0.23), residues: 550 sheet: 0.12 (0.27), residues: 326 loop : -1.29 (0.19), residues: 918 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 234 average time/residue: 0.2720 time to fit residues: 97.9799 Evaluate side-chains 217 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 207 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1460 time to fit residues: 4.9344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.136 17466 Z= 0.213 Angle : 0.689 12.193 24136 Z= 0.357 Chirality : 0.040 0.165 2636 Planarity : 0.006 0.133 2690 Dihedral : 22.188 164.105 3208 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.57 % Favored : 95.15 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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 (0.19), residues: 1794 helix: 1.00 (0.23), residues: 548 sheet: 0.33 (0.28), residues: 326 loop : -1.23 (0.19), residues: 920 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 227 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 234 average time/residue: 0.2946 time to fit residues: 106.0581 Evaluate side-chains 210 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1769 time to fit residues: 5.5816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 102 optimal weight: 0.0040 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 17466 Z= 0.244 Angle : 0.703 17.169 24136 Z= 0.361 Chirality : 0.041 0.188 2636 Planarity : 0.006 0.124 2690 Dihedral : 22.189 164.863 3208 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.57 % Favored : 95.15 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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 (0.19), residues: 1794 helix: 1.03 (0.23), residues: 552 sheet: 0.37 (0.28), residues: 326 loop : -1.22 (0.19), residues: 916 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 210 average time/residue: 0.2896 time to fit residues: 92.8353 Evaluate side-chains 198 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1557 time to fit residues: 4.0540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 17466 Z= 0.207 Angle : 0.696 18.268 24136 Z= 0.355 Chirality : 0.040 0.241 2636 Planarity : 0.006 0.108 2690 Dihedral : 22.013 166.480 3208 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.40 % Favored : 95.32 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: -0.24 (0.19), residues: 1794 helix: 1.06 (0.23), residues: 550 sheet: 0.50 (0.29), residues: 326 loop : -1.18 (0.19), residues: 918 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 222 average time/residue: 0.3308 time to fit residues: 114.9598 Evaluate side-chains 213 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 2.062 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2683 time to fit residues: 4.4402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 0.0470 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 0.0070 chunk 150 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 99 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 = 0.3678 r_free = 0.3678 target = 0.123547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099005 restraints weight = 33119.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101827 restraints weight = 17926.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.103709 restraints weight = 12162.980| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.428 17466 Z= 0.268 Angle : 0.723 20.630 24136 Z= 0.377 Chirality : 0.040 0.271 2636 Planarity : 0.006 0.153 2690 Dihedral : 21.894 167.359 3208 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.63 % Favored : 95.09 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: -0.23 (0.19), residues: 1794 helix: 1.10 (0.23), residues: 550 sheet: 0.55 (0.28), residues: 340 loop : -1.26 (0.19), residues: 904 =============================================================================== Job complete usr+sys time: 3008.32 seconds wall clock time: 56 minutes 4.44 seconds (3364.44 seconds total)