Starting phenix.real_space_refine (version: dev) on Sun Dec 18 18:40:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/12_2022/3jby_6488.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/12_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_6488/12_2022/3jby_6488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/12_2022/3jby_6488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/12_2022/3jby_6488.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/12_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 Anisotropic ADP refinement not supported. Converting 16846 atoms to isotropic. 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-4807/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: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} 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: {' CA': 2, ' ZN': 1} 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: {' CA': 2, ' ZN': 1} 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: 9.74, 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: 8.73 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal 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: 5.84 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: 7.44 Time building geometry restraints manager: 8.59 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: 0.010 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 3.250 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.170 Process input model: 55.780 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.690 ------------------------------------------------------------------------------- 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 : 1.832 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: 0.3286 time to fit residues: 240.5916 Evaluate side-chains 265 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 243 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1793 time to fit residues: 9.2462 ------------------------------------------------------------------------------- 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: 0.8980 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: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** 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 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** D 171 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 17466 Z= 0.258 Angle : 0.767 11.797 24136 Z= 0.409 Chirality : 0.045 0.283 2636 Planarity : 0.006 0.075 2690 Dihedral : 22.635 154.917 3208 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.62 % Favored : 97.27 % Rotamer Outliers : 4.23 % 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: -1.82 (0.17), residues: 1794 helix: -0.86 (0.20), residues: 554 sheet: -0.34 (0.27), residues: 316 loop : -1.73 (0.17), 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 370 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 303 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 28 residues processed: 342 average time/residue: 0.2885 time to fit residues: 148.8306 Evaluate side-chains 259 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1784 time to fit residues: 11.2790 ------------------------------------------------------------------------------- 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: 0.3980 chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 171 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 629 HIS C 669 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN D 253 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 17466 Z= 0.293 Angle : 0.713 11.745 24136 Z= 0.377 Chirality : 0.043 0.285 2636 Planarity : 0.005 0.067 2690 Dihedral : 22.589 157.708 3208 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.23 % Favored : 96.54 % Rotamer Outliers : 3.85 % 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: -1.09 (0.18), residues: 1794 helix: 0.14 (0.21), residues: 552 sheet: -0.15 (0.27), residues: 336 loop : -1.50 (0.18), residues: 906 *********************** 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 309 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 248 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 288 average time/residue: 0.3010 time to fit residues: 129.8919 Evaluate side-chains 244 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 2.129 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1567 time to fit residues: 11.6478 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN C 669 ASN C 687 HIS C 822 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 17466 Z= 0.407 Angle : 0.753 12.159 24136 Z= 0.397 Chirality : 0.045 0.284 2636 Planarity : 0.006 0.074 2690 Dihedral : 22.790 159.222 3208 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.01 % Favored : 95.71 % Rotamer Outliers : 3.72 % 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: -1.12 (0.18), residues: 1794 helix: 0.20 (0.22), residues: 562 sheet: -0.24 (0.27), residues: 336 loop : -1.56 (0.17), residues: 896 *********************** 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 288 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 229 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 28 residues processed: 265 average time/residue: 0.2926 time to fit residues: 117.0589 Evaluate side-chains 231 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1626 time to fit residues: 10.7210 ------------------------------------------------------------------------------- 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: 1.9990 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN A 687 HIS A 766 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 17466 Z= 0.246 Angle : 0.688 12.180 24136 Z= 0.358 Chirality : 0.042 0.292 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.586 161.068 3208 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.48 % Rotamer Outliers : 2.40 % 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: -0.70 (0.19), residues: 1794 helix: 0.65 (0.22), residues: 544 sheet: -0.11 (0.27), residues: 336 loop : -1.30 (0.18), residues: 914 *********************** 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 260 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 222 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 23 residues processed: 246 average time/residue: 0.3018 time to fit residues: 112.1973 Evaluate side-chains 237 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1645 time to fit residues: 9.5903 ------------------------------------------------------------------------------- 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: 0.2980 chunk 165 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 85 optimal weight: 0.0000 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.6224 ------------------------------------------------------------------------------- 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 16 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: 0.8279 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 17466 Z= 0.176 Angle : 0.662 11.676 24136 Z= 0.342 Chirality : 0.040 0.290 2636 Planarity : 0.005 0.071 2690 Dihedral : 22.291 162.420 3208 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.96 % Favored : 95.76 % Rotamer Outliers : 2.02 % 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: -0.43 (0.19), residues: 1794 helix: 0.92 (0.23), residues: 546 sheet: 0.15 (0.28), residues: 316 loop : -1.19 (0.19), residues: 932 *********************** 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 283 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 269 average time/residue: 0.2975 time to fit residues: 120.7227 Evaluate side-chains 224 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1709 time to fit residues: 6.9201 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 102 optimal weight: 0.0020 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.7792 ------------------------------------------------------------------------------- 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 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: 0.8319 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 17466 Z= 0.224 Angle : 0.670 11.217 24136 Z= 0.347 Chirality : 0.041 0.291 2636 Planarity : 0.005 0.069 2690 Dihedral : 22.303 163.119 3208 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.48 % Rotamer Outliers : 2.08 % 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: -0.37 (0.19), residues: 1794 helix: 1.01 (0.23), residues: 548 sheet: 0.24 (0.28), residues: 326 loop : -1.23 (0.19), residues: 920 *********************** 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 258 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 239 average time/residue: 0.2944 time to fit residues: 107.1709 Evaluate side-chains 219 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1704 time to fit residues: 7.5763 ------------------------------------------------------------------------------- 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: 8.9990 chunk 109 optimal weight: 6.9990 chunk 55 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17466 Z= 0.183 Angle : 0.661 11.325 24136 Z= 0.341 Chirality : 0.040 0.172 2636 Planarity : 0.005 0.068 2690 Dihedral : 22.109 164.247 3208 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.35 % Favored : 95.37 % Rotamer Outliers : 0.95 % 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: -0.29 (0.19), residues: 1794 helix: 1.02 (0.23), residues: 548 sheet: 0.33 (0.28), residues: 330 loop : -1.17 (0.19), residues: 916 *********************** 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 249 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 234 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 242 average time/residue: 0.2936 time to fit residues: 108.5726 Evaluate side-chains 214 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 209 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1760 time to fit residues: 4.1437 ------------------------------------------------------------------------------- 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: 0.9990 chunk 175 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 134 optimal weight: 0.0010 chunk 52 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 GLN ** A 964 HIS ** 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17466 Z= 0.183 Angle : 0.667 11.301 24136 Z= 0.343 Chirality : 0.040 0.200 2636 Planarity : 0.005 0.069 2690 Dihedral : 22.004 165.745 3208 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.35 % Favored : 95.37 % Rotamer Outliers : 0.57 % 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: 1.07 (0.23), residues: 548 sheet: 0.41 (0.28), residues: 330 loop : -1.14 (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 232 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 227 average time/residue: 0.2970 time to fit residues: 102.1369 Evaluate side-chains 222 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 218 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1657 time to fit residues: 3.5644 ------------------------------------------------------------------------------- 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: 0.7980 chunk 125 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 150 optimal weight: 0.0670 chunk 15 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 160 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 HIS ** C 766 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17466 Z= 0.179 Angle : 0.676 11.318 24136 Z= 0.346 Chirality : 0.040 0.224 2636 Planarity : 0.005 0.069 2690 Dihedral : 21.865 166.943 3208 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.29 % Favored : 95.43 % Rotamer Outliers : 0.57 % 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: -0.18 (0.19), residues: 1794 helix: 1.13 (0.23), residues: 548 sheet: 0.49 (0.28), residues: 330 loop : -1.15 (0.19), residues: 916 ********************** 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 253 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 244 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 247 average time/residue: 0.3010 time to fit residues: 112.6965 Evaluate side-chains 225 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 218 time to evaluate : 1.928 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1722 time to fit residues: 4.7184 ------------------------------------------------------------------------------- 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: 10.0000 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 chunk 155 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 ASN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 HIS ** C 874 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097927 restraints weight = 32957.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.100703 restraints weight = 17736.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102531 restraints weight = 12065.323| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17466 Z= 0.213 Angle : 0.696 15.232 24136 Z= 0.353 Chirality : 0.041 0.253 2636 Planarity : 0.005 0.069 2690 Dihedral : 21.828 167.189 3208 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.35 % Favored : 95.37 % 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: -0.14 (0.19), residues: 1794 helix: 1.17 (0.23), residues: 546 sheet: 0.45 (0.28), residues: 330 loop : -1.09 (0.19), residues: 918 =============================================================================== Job complete usr+sys time: 3161.52 seconds wall clock time: 58 minutes 14.60 seconds (3494.60 seconds total)