Starting phenix.real_space_refine (version: dev) on Sat May 14 21:22:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/05_2022/6zbb_11149_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/05_2022/6zbb_11149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/05_2022/6zbb_11149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/05_2022/6zbb_11149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/05_2022/6zbb_11149_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/05_2022/6zbb_11149_trim_updated.pdb" } resolution = 3.61 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 stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "P PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 20936 Number of models: 1 Model: "" Number of chains: 20 Chain: "8" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 696 Classifications: {'peptide': 41} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "K" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3557 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "b" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1791 Classifications: {'peptide': 112} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "d" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 893 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 45, 'PCIS': 1} Chain: "e" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 975 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 596 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 84 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "b" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 161 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "f" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 11.14, per 1000 atoms: 0.53 Number of scatterers: 20936 At special positions: 0 Unit cell: (110.04, 125.76, 121.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 8 15.00 O 1836 8.00 N 1617 7.00 C 6974 6.00 H 10446 1.00 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: 17.69 Conformation dependent library (CDL) restraints added in 2.0 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain '8' and resid 2 through 4 No H-bonds generated for 'chain '8' and resid 2 through 4' Processing helix chain '8' and resid 6 through 20 removed outlier: 4.532A pdb=" N LEU 8 10 " --> pdb=" O SER 8 7 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU 8 14 " --> pdb=" O THR 8 11 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER 8 15 " --> pdb=" O MET 8 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU 8 18 " --> pdb=" O SER 8 15 " (cutoff:3.500A) Processing helix chain '8' and resid 23 through 30 removed outlier: 3.568A pdb=" N SER 8 29 " --> pdb=" O GLN 8 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 38 removed outlier: 4.043A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY K 20 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 72 removed outlier: 3.934A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 38 removed outlier: 4.355A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY L 20 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 72 removed outlier: 3.892A pdb=" N LEU L 52 " --> pdb=" O SER L 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 37 removed outlier: 5.097A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE M 9 " --> pdb=" O ALA M 5 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 72 removed outlier: 4.271A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 37 removed outlier: 4.148A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA N 19 " --> pdb=" O THR N 15 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLY N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.833A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 38 removed outlier: 3.782A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 73 removed outlier: 4.268A pdb=" N VAL O 67 " --> pdb=" O PHE O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 38 removed outlier: 4.539A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA P 19 " --> pdb=" O THR P 15 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 72 removed outlier: 3.737A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 38 removed outlier: 4.359A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.619A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 38 removed outlier: 3.902A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 72 removed outlier: 3.762A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 9 No H-bonds generated for 'chain 'a' and resid 7 through 9' Processing helix chain 'a' and resid 19 through 30 removed outlier: 4.268A pdb=" N VAL a 24 " --> pdb=" O THR a 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE a 26 " --> pdb=" O ILE a 23 " (cutoff:3.500A) Proline residue: a 27 - end of helix Processing helix chain 'a' and resid 41 through 57 removed outlier: 4.072A pdb=" N GLN a 46 " --> pdb=" O PHE a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 86 removed outlier: 5.305A pdb=" N TRP a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR a 69 " --> pdb=" O GLY a 65 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N MET a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU a 84 " --> pdb=" O GLY a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 96 No H-bonds generated for 'chain 'a' and resid 94 through 96' Processing helix chain 'a' and resid 98 through 128 Proline residue: a 107 - end of helix removed outlier: 7.486A pdb=" N LYS a 122 " --> pdb=" O ARG a 118 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA a 123 " --> pdb=" O ASN a 119 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE a 128 " --> pdb=" O SER a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 135 through 150 Proline residue: a 139 - end of helix removed outlier: 4.891A pdb=" N ILE a 143 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR a 146 " --> pdb=" O ILE a 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 152 through 183 removed outlier: 3.656A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY a 167 " --> pdb=" O ASN a 163 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS a 172 " --> pdb=" O HIS a 168 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER a 183 " --> pdb=" O LEU a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 225 removed outlier: 3.787A pdb=" N MET a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 15 No H-bonds generated for 'chain 'b' and resid 13 through 15' Processing helix chain 'b' and resid 19 through 29 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 33 through 47 Processing helix chain 'b' and resid 55 through 111 removed outlier: 5.905A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 115 through 122 removed outlier: 3.677A pdb=" N LYS d 120 " --> pdb=" O LYS d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 132 through 138 removed outlier: 3.877A pdb=" N GLU d 137 " --> pdb=" O GLU d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 142 No H-bonds generated for 'chain 'd' and resid 140 through 142' Processing helix chain 'd' and resid 146 through 148 No H-bonds generated for 'chain 'd' and resid 146 through 148' Processing helix chain 'e' and resid 8 through 56 Proline residue: e 34 - end of helix Processing helix chain 'f' and resid 11 through 13 No H-bonds generated for 'chain 'f' and resid 11 through 13' Processing helix chain 'f' and resid 17 through 25 Proline residue: f 20 - end of helix Processing helix chain 'f' and resid 30 through 48 removed outlier: 3.856A pdb=" N ALA f 36 " --> pdb=" O GLY f 32 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG f 39 " --> pdb=" O GLY f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 56 through 74 removed outlier: 3.654A pdb=" N SER f 60 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N MET f 61 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU f 63 " --> pdb=" O SER f 60 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL f 67 " --> pdb=" O ALA f 64 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU f 69 " --> pdb=" O TYR f 66 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG f 73 " --> pdb=" O ASN f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 81 No H-bonds generated for 'chain 'f' and resid 79 through 81' Processing helix chain 'g' and resid 22 through 36 removed outlier: 3.701A pdb=" N ALA g 27 " --> pdb=" O LYS g 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR g 32 " --> pdb=" O THR g 28 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 61 Proline residue: g 46 - end of helix removed outlier: 3.571A pdb=" N LYS g 60 " --> pdb=" O ASN g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 66 Processing helix chain 'g' and resid 69 through 93 removed outlier: 3.568A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 18 removed outlier: 4.364A pdb=" N ILE j 11 " --> pdb=" O LYS j 7 " (cutoff:3.500A) Proline residue: j 12 - end of helix Proline residue: j 15 - end of helix Processing helix chain 'j' and resid 24 through 47 Processing helix chain 'k' and resid 14 through 17 No H-bonds generated for 'chain 'k' and resid 14 through 17' Processing helix chain 'k' and resid 24 through 45 741 hydrogen bonds defined for protein. 2082 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: 7.08 Time building geometry restraints manager: 18.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10436 1.03 - 1.23: 121 1.23 - 1.43: 4165 1.43 - 1.62: 6307 1.62 - 1.82: 114 Bond restraints: 21143 Sorted by residual: bond pdb=" CB7 CDL a 301 " pdb=" OB8 CDL a 301 " ideal model delta sigma weight residual 1.334 1.406 -0.072 1.10e-02 8.26e+03 4.25e+01 bond pdb=" CB7 CDL b 301 " pdb=" OB8 CDL b 301 " ideal model delta sigma weight residual 1.334 1.405 -0.071 1.10e-02 8.26e+03 4.19e+01 bond pdb=" CB7 CDL b 302 " pdb=" OB8 CDL b 302 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.10e-02 8.26e+03 4.03e+01 bond pdb=" CA7 CDL b 302 " pdb=" OA8 CDL b 302 " ideal model delta sigma weight residual 1.334 1.398 -0.064 1.10e-02 8.26e+03 3.38e+01 bond pdb=" CA7 CDL a 301 " pdb=" OA8 CDL a 301 " ideal model delta sigma weight residual 1.334 1.397 -0.063 1.10e-02 8.26e+03 3.26e+01 ... (remaining 21138 not shown) Histogram of bond angle deviations from ideal: 95.06 - 102.85: 66 102.85 - 110.64: 22416 110.64 - 118.43: 6398 118.43 - 126.21: 9059 126.21 - 134.00: 141 Bond angle restraints: 38080 Sorted by residual: angle pdb=" C51 CDL b 302 " pdb=" CB5 CDL b 302 " pdb=" OB6 CDL b 302 " ideal model delta sigma weight residual 111.33 121.07 -9.74 1.32e+00 5.72e-01 5.43e+01 angle pdb=" C11 CDL b 302 " pdb=" CA5 CDL b 302 " pdb=" OA6 CDL b 302 " ideal model delta sigma weight residual 111.33 120.68 -9.35 1.32e+00 5.72e-01 5.00e+01 angle pdb=" C11 CDL a 301 " pdb=" CA5 CDL a 301 " pdb=" OA6 CDL a 301 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.59e+01 angle pdb=" C11 CDL b 301 " pdb=" CA5 CDL b 301 " pdb=" OA6 CDL b 301 " ideal model delta sigma weight residual 111.33 119.92 -8.59 1.32e+00 5.72e-01 4.22e+01 angle pdb=" C51 CDL a 301 " pdb=" CB5 CDL a 301 " pdb=" OB6 CDL a 301 " ideal model delta sigma weight residual 111.33 119.88 -8.55 1.32e+00 5.72e-01 4.18e+01 ... (remaining 38075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 7458 17.68 - 35.37: 770 35.37 - 53.05: 198 53.05 - 70.73: 44 70.73 - 88.42: 15 Dihedral angle restraints: 8485 sinusoidal: 3947 harmonic: 4538 Sorted by residual: dihedral pdb=" CA LEU M 62 " pdb=" C LEU M 62 " pdb=" N PHE M 63 " pdb=" CA PHE M 63 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LYS b 48 " pdb=" C LYS b 48 " pdb=" N GLU b 49 " pdb=" CA GLU b 49 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE M 29 " pdb=" C PHE M 29 " pdb=" N GLY M 30 " pdb=" CA GLY M 30 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 8482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1074 0.034 - 0.069: 426 0.069 - 0.103: 111 0.103 - 0.137: 33 0.137 - 0.172: 7 Chirality restraints: 1651 Sorted by residual: chirality pdb=" CB ILE R 9 " pdb=" CA ILE R 9 " pdb=" CG1 ILE R 9 " pdb=" CG2 ILE R 9 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PRO a 89 " pdb=" N PRO a 89 " pdb=" C PRO a 89 " pdb=" CB PRO a 89 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA LEU M 62 " pdb=" N LEU M 62 " pdb=" C LEU M 62 " pdb=" CB LEU M 62 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1648 not shown) Planarity restraints: 2980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 101 " -0.067 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C8 LHG f 101 " 0.020 2.00e-02 2.50e+03 pdb=" O7 LHG f 101 " 0.021 2.00e-02 2.50e+03 pdb=" O9 LHG f 101 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG f 101 " -0.057 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C24 LHG f 101 " 0.017 2.00e-02 2.50e+03 pdb=" O10 LHG f 101 " 0.021 2.00e-02 2.50e+03 pdb=" O8 LHG f 101 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 102 " 0.054 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" C8 LHG f 102 " -0.016 2.00e-02 2.50e+03 pdb=" O7 LHG f 102 " -0.017 2.00e-02 2.50e+03 pdb=" O9 LHG f 102 " -0.022 2.00e-02 2.50e+03 ... (remaining 2977 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 467 2.08 - 2.71: 35942 2.71 - 3.34: 64003 3.34 - 3.97: 75675 3.97 - 4.60: 121689 Nonbonded interactions: 297776 Sorted by model distance: nonbonded pdb="HH22 ARG a 36 " pdb=" O PRO b 3 " model vdw 1.453 1.850 nonbonded pdb=" O GLY k 13 " pdb=" H TYR k 17 " model vdw 1.490 1.850 nonbonded pdb=" O ILE R 2 " pdb=" H ALA R 6 " model vdw 1.491 1.850 nonbonded pdb=" OD1 ASN 8 32 " pdb=" H PHE 8 33 " model vdw 1.527 1.850 nonbonded pdb=" H THR d 131 " pdb=" OD2 ASP d 134 " model vdw 1.528 1.850 ... (remaining 297771 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 'K' selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = chain 'P' selection = (chain 'Q' and resid 1 through 74) selection = (chain 'R' and resid 1 through 74) } 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 55 5.16 5 C 6974 2.51 5 N 1617 2.21 5 O 1836 1.98 5 H 10446 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.350 Extract box with map and model: 27.380 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.170 Process input model: 69.760 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.008 0.083 10697 Z= 0.480 Angle : 1.026 12.413 14408 Z= 0.511 Chirality : 0.041 0.172 1651 Planarity : 0.004 0.041 1726 Dihedral : 16.651 88.133 3885 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.21 (0.24), residues: 1270 helix: 0.37 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -1.79 (0.40), residues: 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.4355 time to fit residues: 161.9686 Evaluate side-chains 203 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 10697 Z= 0.283 Angle : 0.644 7.270 14408 Z= 0.336 Chirality : 0.039 0.152 1651 Planarity : 0.004 0.059 1726 Dihedral : 12.966 59.912 1654 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.11 (0.24), residues: 1270 helix: 0.39 (0.16), residues: 1016 sheet: None (None), residues: 0 loop : -1.63 (0.42), residues: 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 231 average time/residue: 0.4212 time to fit residues: 146.3652 Evaluate side-chains 213 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 1.687 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2507 time to fit residues: 8.4031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 112 optimal weight: 0.0070 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 10697 Z= 0.218 Angle : 0.597 6.215 14408 Z= 0.309 Chirality : 0.037 0.141 1651 Planarity : 0.004 0.057 1726 Dihedral : 11.983 58.942 1654 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.18 (0.24), residues: 1270 helix: 0.58 (0.17), residues: 1018 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 237 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 237 average time/residue: 0.4074 time to fit residues: 141.9782 Evaluate side-chains 208 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2298 time to fit residues: 3.5321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 45 GLN a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 10697 Z= 0.213 Angle : 0.592 6.959 14408 Z= 0.305 Chirality : 0.037 0.142 1651 Planarity : 0.004 0.057 1726 Dihedral : 11.393 59.983 1654 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1270 helix: 0.66 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -1.14 (0.42), residues: 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 229 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 234 average time/residue: 0.4246 time to fit residues: 146.6299 Evaluate side-chains 216 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 208 time to evaluate : 1.556 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2418 time to fit residues: 5.2598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 108 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.124 10697 Z= 0.191 Angle : 0.581 7.130 14408 Z= 0.296 Chirality : 0.036 0.171 1651 Planarity : 0.003 0.052 1726 Dihedral : 10.676 59.924 1654 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1270 helix: 0.81 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -1.16 (0.41), residues: 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 234 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 237 average time/residue: 0.4285 time to fit residues: 151.5988 Evaluate side-chains 218 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.777 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2273 time to fit residues: 3.7345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 44 GLN a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.410 10697 Z= 0.315 Angle : 0.642 24.789 14408 Z= 0.325 Chirality : 0.037 0.142 1651 Planarity : 0.004 0.091 1726 Dihedral : 10.262 59.040 1654 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.72 (0.24), residues: 1270 helix: 0.90 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -1.02 (0.42), residues: 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 221 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 228 average time/residue: 0.4159 time to fit residues: 140.5048 Evaluate side-chains 220 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 208 time to evaluate : 1.656 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2511 time to fit residues: 7.1636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 101 optimal weight: 0.0970 chunk 67 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 10697 Z= 0.184 Angle : 0.580 9.692 14408 Z= 0.299 Chirality : 0.036 0.182 1651 Planarity : 0.004 0.087 1726 Dihedral : 9.820 59.651 1654 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.92 (0.24), residues: 1270 helix: 1.01 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -0.83 (0.42), residues: 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 232 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 234 average time/residue: 0.4139 time to fit residues: 142.9582 Evaluate side-chains 215 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 1.617 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2148 time to fit residues: 2.7087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.122 10697 Z= 0.630 Angle : 1.039 97.488 14408 Z= 0.433 Chirality : 0.037 0.245 1651 Planarity : 0.004 0.097 1726 Dihedral : 9.663 59.879 1654 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.13 % 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: 0.96 (0.24), residues: 1270 helix: 1.04 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -0.83 (0.42), residues: 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 219 average time/residue: 0.4182 time to fit residues: 134.9533 Evaluate side-chains 218 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 210 time to evaluate : 1.642 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2541 time to fit residues: 5.4216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 106 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.089 10697 Z= 0.615 Angle : 1.035 97.300 14408 Z= 0.428 Chirality : 0.037 0.286 1651 Planarity : 0.004 0.094 1726 Dihedral : 9.392 59.874 1654 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1270 helix: 1.08 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -0.64 (0.43), residues: 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 226 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 228 average time/residue: 0.4224 time to fit residues: 142.3650 Evaluate side-chains 228 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 221 time to evaluate : 1.757 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2248 time to fit residues: 4.9823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 25 GLN ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.534 10697 Z= 0.411 Angle : 0.722 29.027 14408 Z= 0.389 Chirality : 0.037 0.155 1651 Planarity : 0.004 0.072 1726 Dihedral : 9.318 59.982 1654 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.30 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1270 helix: 1.08 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -0.68 (0.43), residues: 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 227 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 228 average time/residue: 0.4187 time to fit residues: 141.2252 Evaluate side-chains 218 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2576 time to fit residues: 3.7223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.086647 restraints weight = 73117.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.089704 restraints weight = 31633.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.091492 restraints weight = 19700.477| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.252 10697 Z= 0.237 Angle : 0.639 20.015 14408 Z= 0.337 Chirality : 0.037 0.153 1651 Planarity : 0.003 0.046 1726 Dihedral : 9.081 59.520 1654 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1270 helix: 1.10 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.56 (0.44), residues: 238 =============================================================================== Job complete usr+sys time: 4628.92 seconds wall clock time: 83 minutes 2.41 seconds (4982.41 seconds total)