Starting phenix.real_space_refine (version: 1.19rc7) on Sun Dec 6 17:31:53 2020 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xra_22293/12_2020/6xra_22293_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xra_22293/12_2020/6xra_22293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xra_22293/12_2020/6xra_22293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xra_22293/12_2020/6xra_22293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xra_22293/12_2020/6xra_22293_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xra_22293/12_2020/6xra_22293_neut.pdb" } resolution = 3.0 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= 0.001 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 8808 Number of models: 1 Model: "" Number of chains: 21 Chain: "C" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2688 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 2 Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2688 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 2 Chain: "B" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2688 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'NAG': 3, 'MAN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'NAG': 3, 'MAN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'NAG': 3, 'MAN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.21, per 1000 atoms: 0.59 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' } Number of scatterers: 8808 At special positions: 0 Unit cell: (73.425, 74.25, 229.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1887 8.00 N 1416 7.00 C 5469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.09 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.09 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.09 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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 Links applied ALPHA1-3 " MAN E 3 " - " MAN E 4 " " MAN F 3 " - " MAN F 4 " " MAN J 3 " - " MAN J 4 " " MAN K 3 " - " MAN K 4 " " MAN O 3 " - " MAN O 4 " " MAN P 3 " - " MAN P 4 " ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " " NAG G 2 " - " MAN G 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG Q 2 " - " MAN Q 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1401 " - " ASN A 709 " " NAG A1402 " - " ASN A 717 " " NAG B1401 " - " ASN B 709 " " NAG B1402 " - " ASN B 717 " " NAG C1401 " - " ASN C 709 " " NAG C1402 " - " ASN C 717 " " NAG D 1 " - " ASN C1074 " " NAG F 1 " - " ASN C1134 " " NAG G 1 " - " ASN C1158 " " NAG H 1 " - " ASN C1194 " " NAG I 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN A1158 " " NAG M 1 " - " ASN A1194 " " NAG N 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B1158 " " NAG R 1 " - " ASN B1194 " Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 52.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.738A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.638A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 1034 removed outlier: 3.524A pdb=" N ASN C 953 " --> pdb=" O GLN C 949 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1154 Processing helix chain 'C' and resid 1168 through 1172 Processing helix chain 'C' and resid 1181 through 1193 Processing helix chain 'C' and resid 1194 through 1197 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.738A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.638A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 1034 removed outlier: 3.524A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1154 Processing helix chain 'A' and resid 1168 through 1172 Processing helix chain 'A' and resid 1181 through 1193 Processing helix chain 'A' and resid 1194 through 1197 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.738A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.638A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 1034 removed outlier: 3.524A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1154 Processing helix chain 'B' and resid 1168 through 1172 Processing helix chain 'B' and resid 1181 through 1193 Processing helix chain 'B' and resid 1194 through 1197 Processing sheet with id=AA1, first strand: chain 'C' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AA4, first strand: chain 'C' and resid 1129 through 1134 removed outlier: 6.202A pdb=" N VAL C1129 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR B 724 " --> pdb=" O VAL C1129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C1131 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE B 726 " --> pdb=" O GLY C1131 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C1133 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1129 through 1134 removed outlier: 6.202A pdb=" N VAL C1129 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR B 724 " --> pdb=" O VAL C1129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C1131 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE B 726 " --> pdb=" O GLY C1131 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C1133 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AA9, first strand: chain 'B' and resid 1081 through 1083 539 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1909 1.33 - 1.45: 2080 1.45 - 1.58: 4891 1.58 - 1.70: 6 1.70 - 1.83: 48 Bond restraints: 8934 Sorted by residual: bond pdb=" CA CYS B1043 " pdb=" C CYS B1043 " ideal model delta sigma weight residual 1.530 1.584 -0.054 1.17e-02 7.31e+03 2.14e+01 bond pdb=" CA CYS C1043 " pdb=" C CYS C1043 " ideal model delta sigma weight residual 1.530 1.584 -0.054 1.17e-02 7.31e+03 2.12e+01 bond pdb=" CA CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sigma weight residual 1.532 1.600 -0.068 1.48e-02 4.57e+03 2.12e+01 bond pdb=" CA CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sigma weight residual 1.532 1.600 -0.068 1.48e-02 4.57e+03 2.10e+01 bond pdb=" CA CYS A1043 " pdb=" C CYS A1043 " ideal model delta sigma weight residual 1.530 1.584 -0.054 1.17e-02 7.31e+03 2.09e+01 ... (remaining 8929 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.08: 237 106.08 - 113.18: 4680 113.18 - 120.28: 3945 120.28 - 127.38: 3234 127.38 - 134.47: 36 Bond angle restraints: 12132 Sorted by residual: angle pdb=" N PHE A1042 " pdb=" CA PHE A1042 " pdb=" C PHE A1042 " ideal model delta sigma weight residual 110.20 99.11 11.09 1.58e+00 4.01e-01 4.92e+01 angle pdb=" N PHE C1042 " pdb=" CA PHE C1042 " pdb=" C PHE C1042 " ideal model delta sigma weight residual 110.20 99.12 11.08 1.58e+00 4.01e-01 4.92e+01 angle pdb=" N PHE B1042 " pdb=" CA PHE B1042 " pdb=" C PHE B1042 " ideal model delta sigma weight residual 110.20 99.14 11.06 1.58e+00 4.01e-01 4.90e+01 angle pdb=" N CYS B1126 " pdb=" CA CYS B1126 " pdb=" C CYS B1126 " ideal model delta sigma weight residual 112.24 120.60 -8.36 1.28e+00 6.10e-01 4.27e+01 angle pdb=" N CYS C1126 " pdb=" CA CYS C1126 " pdb=" C CYS C1126 " ideal model delta sigma weight residual 112.24 120.59 -8.35 1.28e+00 6.10e-01 4.25e+01 ... (remaining 12127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.32: 4903 19.32 - 38.64: 359 38.64 - 57.96: 99 57.96 - 77.29: 18 77.29 - 96.61: 21 Dihedral angle restraints: 5400 sinusoidal: 2355 harmonic: 3045 Sorted by residual: dihedral pdb=" N ASN B 709 " pdb=" C ASN B 709 " pdb=" CA ASN B 709 " pdb=" CB ASN B 709 " ideal model delta harmonic sigma weight residual 122.80 141.15 -18.35 0 2.50e+00 1.60e-01 5.39e+01 dihedral pdb=" N ASN C 709 " pdb=" C ASN C 709 " pdb=" CA ASN C 709 " pdb=" CB ASN C 709 " ideal model delta harmonic sigma weight residual 122.80 141.15 -18.35 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" N ASN A 709 " pdb=" C ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta harmonic sigma weight residual 122.80 141.12 -18.32 0 2.50e+00 1.60e-01 5.37e+01 ... (remaining 5397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 1459 0.170 - 0.339: 116 0.339 - 0.509: 12 0.509 - 0.678: 6 0.678 - 0.848: 3 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA ASN B 709 " pdb=" N ASN B 709 " pdb=" C ASN B 709 " pdb=" CB ASN B 709 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" CA ASN C 709 " pdb=" N ASN C 709 " pdb=" C ASN C 709 " pdb=" CB ASN C 709 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CA ASN A 709 " pdb=" N ASN A 709 " pdb=" C ASN A 709 " pdb=" CB ASN A 709 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 1593 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1194 " 0.179 2.00e-02 2.50e+03 1.86e-01 4.30e+02 pdb=" CG ASN A1194 " -0.105 2.00e-02 2.50e+03 pdb=" OD1 ASN A1194 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1194 " -0.285 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1194 " 0.179 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" CG ASN C1194 " -0.105 2.00e-02 2.50e+03 pdb=" OD1 ASN C1194 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C1194 " -0.285 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1194 " 0.169 2.00e-02 2.50e+03 1.79e-01 4.02e+02 pdb=" CG ASN B1194 " -0.103 2.00e-02 2.50e+03 pdb=" OD1 ASN B1194 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B1194 " -0.277 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.212 2.00e-02 2.50e+03 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 300 2.73 - 3.27: 8900 3.27 - 3.82: 13861 3.82 - 4.36: 17872 4.36 - 4.90: 28530 Nonbonded interactions: 69463 Sorted by model distance: nonbonded pdb=" OD1 ASN C1173 " pdb=" C1 NAG C1417 " model vdw 2.189 3.470 nonbonded pdb=" OD1 ASN B1173 " pdb=" C1 NAG B1417 " model vdw 2.259 3.470 nonbonded pdb=" OD1 ASN A1173 " pdb=" C1 NAG A1417 " model vdw 2.291 3.470 nonbonded pdb=" ND2 ASN C1173 " pdb=" C1 NAG C1417 " model vdw 2.296 3.550 nonbonded pdb=" CB ASN B 709 " pdb=" O THR B1077 " model vdw 2.305 3.440 ... (remaining 69458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 8808 8808 False True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5469 2.51 5 N 1416 2.21 5 O 1887 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 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: 4.840 Set model interpretation parameters: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 25.110 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.040 Process input model: 30.320 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.050 Internal consistency checks: 0.000 Total: 71.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.012 0.068 8934 Angle : 1.882 11.891 12132 Chirality : 0.110 0.848 1596 Planarity : 0.012 0.069 1488 Dihedral : 16.522 96.608 3384 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 2.61 % Cbeta Deviations : 1.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.22), residues: 1026 helix: -1.86 (0.18), residues: 480 sheet: 0.69 (0.55), residues: 84 loop : -1.96 (0.26), residues: 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.002 Fit side-chains outliers start: 24 outliers final: 6 residues processed: 164 average time/residue: 0.8690 time to fit residues: 144.1672 Evaluate side-chains 82 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 6 poor density : 76 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.3833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.0570 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 703 ASN C 751 ASN C 925 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 751 ASN A 925 ASN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN A1101 HIS A1106 GLN B 703 ASN B 751 ASN B 925 ASN B1064 HIS B1098 ASN B1101 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.037 8934 Angle : 0.666 7.009 12132 Chirality : 0.056 0.618 1596 Planarity : 0.005 0.043 1488 Dihedral : 10.022 93.418 1509 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1026 helix: 0.60 (0.21), residues: 498 sheet: -0.21 (0.42), residues: 153 loop : -0.98 (0.32), residues: 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 6 poor density : 120 time to evaluate : 1.006 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 126 average time/residue: 1.0149 time to fit residues: 129.4958 Evaluate side-chains 60 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS C1106 GLN C1108 ASN C1135 ASN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1135 ASN B1083 HIS B1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.050 8934 Angle : 0.644 5.589 12132 Chirality : 0.053 0.546 1596 Planarity : 0.005 0.041 1488 Dihedral : 9.859 93.312 1509 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1026 helix: 1.33 (0.21), residues: 492 sheet: -0.30 (0.45), residues: 126 loop : -1.06 (0.30), residues: 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.970 Fit side-chains outliers start: 1 outliers final: 2 residues processed: 98 average time/residue: 1.1250 time to fit residues: 111.8286 Evaluate side-chains 61 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.2335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 98 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 764 ASN ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.042 8934 Angle : 0.579 6.357 12132 Chirality : 0.050 0.515 1596 Planarity : 0.004 0.042 1488 Dihedral : 9.627 92.243 1509 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1026 helix: 1.67 (0.22), residues: 495 sheet: -0.20 (0.45), residues: 126 loop : -1.11 (0.30), residues: 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.961 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 1.2222 time to fit residues: 116.5046 Evaluate side-chains 47 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 762 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.041 8934 Angle : 0.623 5.453 12132 Chirality : 0.050 0.498 1596 Planarity : 0.005 0.044 1488 Dihedral : 9.639 92.960 1509 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1026 helix: 1.54 (0.22), residues: 495 sheet: -0.26 (0.44), residues: 126 loop : -1.13 (0.30), residues: 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.989 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 1.1498 time to fit residues: 108.6108 Evaluate side-chains 45 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.047 8934 Angle : 0.678 5.773 12132 Chirality : 0.052 0.487 1596 Planarity : 0.005 0.045 1488 Dihedral : 9.778 94.136 1509 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1026 helix: 1.22 (0.22), residues: 495 sheet: -0.72 (0.43), residues: 126 loop : -1.29 (0.30), residues: 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 1.3020 time to fit residues: 118.9019 Evaluate side-chains 43 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.0470 chunk 29 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.033 8934 Angle : 0.574 5.426 12132 Chirality : 0.048 0.452 1596 Planarity : 0.004 0.042 1488 Dihedral : 9.533 92.199 1509 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1026 helix: 1.66 (0.23), residues: 498 sheet: -0.64 (0.40), residues: 144 loop : -1.41 (0.30), residues: 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.958 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 1.3039 time to fit residues: 118.9776 Evaluate side-chains 51 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0070 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.036 8934 Angle : 0.604 5.367 12132 Chirality : 0.049 0.449 1596 Planarity : 0.004 0.041 1488 Dihedral : 9.552 92.468 1509 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1026 helix: 1.58 (0.22), residues: 495 sheet: -0.63 (0.40), residues: 144 loop : -1.25 (0.31), residues: 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.929 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 1.2988 time to fit residues: 118.4435 Evaluate side-chains 43 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.036 8934 Angle : 0.611 6.324 12132 Chirality : 0.049 0.440 1596 Planarity : 0.004 0.042 1488 Dihedral : 9.547 92.223 1509 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1026 helix: 1.59 (0.22), residues: 495 sheet: -0.54 (0.40), residues: 144 loop : -1.27 (0.31), residues: 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 1.2539 time to fit residues: 118.3142 Evaluate side-chains 50 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.035 8934 Angle : 0.600 5.331 12132 Chirality : 0.049 0.433 1596 Planarity : 0.004 0.041 1488 Dihedral : 9.514 91.909 1509 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1026 helix: 1.63 (0.22), residues: 495 sheet: -0.50 (0.41), residues: 144 loop : -1.25 (0.31), residues: 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield and 0 Emsley and 1026 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.947 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.2274 time to fit residues: 114.5794 Evaluate side-chains 47 residues out of total 921 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.177887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.143221 restraints weight = 11805.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.147076 restraints weight = 6445.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.149472 restraints weight = 4465.104| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.037 8934 ANGLE : 0.617 6.139 12132 CHIRALITY : 0.049 0.438 1596 PLANARITY : 0.004 0.042 1488 DIHEDRAL : 9.549 92.329 1509 MIN NONBONDED DISTANCE : 2.199 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 10.87 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.48 % FAVORED : 95.52 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: 0.34 (0.26), RESIDUES: 1026 HELIX: 1.56 (0.22), RESIDUES: 495 SHEET: -0.49 (0.41), RESIDUES: 144 LOOP : -1.26 (0.31), RESIDUES: 387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.037 8934 Angle : 0.617 6.139 12132 Chirality : 0.049 0.438 1596 Planarity : 0.004 0.042 1488 Dihedral : 9.549 92.329 1509 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1026 helix: 1.56 (0.22), residues: 495 sheet: -0.49 (0.41), residues: 144 loop : -1.26 (0.31), residues: 387 =============================================================================== Job complete usr+sys time: 2881.44 seconds wall clock time: 52 minutes 21.49 seconds (3141.49 seconds total)