Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 02:51:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2023/7cge_30355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2023/7cge_30355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2023/7cge_30355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2023/7cge_30355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2023/7cge_30355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2023/7cge_30355_updated.pdb" } resolution = 2.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 68 5.16 5 C 10624 2.51 5 N 2654 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K GLU 37": "OE1" <-> "OE2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K GLU 85": "OE1" <-> "OE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ARG 55": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16406 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "C" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "F" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "G" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "K" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "L" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 306 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 204 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.53, per 1000 atoms: 0.52 Number of scatterers: 16406 At special positions: 0 Unit cell: (106.526, 114.135, 141.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 12 15.00 O 3048 8.00 N 2654 7.00 C 10624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.81 Conformation dependent library (CDL) restraints added in 2.3 seconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 20 sheets defined 36.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.740A pdb=" N LEU A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 removed outlier: 3.597A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 80 removed outlier: 4.802A pdb=" N LEU A 57 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 58 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 59 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL A 61 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 64 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 65 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 66 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 67 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 70 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 71 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY A 74 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 76 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 77 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 removed outlier: 3.543A pdb=" N LEU A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY A 88 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 91 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 92 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 94 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 96 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 125 removed outlier: 3.526A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.530A pdb=" N GLU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 144 through 174 Proline residue: A 156 - end of helix removed outlier: 3.503A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.602A pdb=" N MET A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 222 removed outlier: 3.500A pdb=" N LEU A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 257 removed outlier: 3.828A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.510A pdb=" N ILE B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 54' Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.658A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 122 through 131 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.735A pdb=" N PHE B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'D' and resid 6 through 31 removed outlier: 3.741A pdb=" N LEU D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 removed outlier: 3.597A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 4.802A pdb=" N LEU D 57 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 58 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 59 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 60 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 61 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 62 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 64 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 65 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 67 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 70 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY D 71 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 73 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY D 74 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR D 75 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 76 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 77 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 79 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.543A pdb=" N LEU D 87 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY D 88 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA D 92 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 94 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 96 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 125 removed outlier: 3.525A pdb=" N ALA D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.530A pdb=" N GLU D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 144 through 174 Proline residue: D 156 - end of helix removed outlier: 3.503A pdb=" N VAL D 160 " --> pdb=" O PRO D 156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 removed outlier: 3.602A pdb=" N MET D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 222 removed outlier: 3.501A pdb=" N LEU D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 257 removed outlier: 3.828A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.510A pdb=" N ILE E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 50 through 54' Processing helix chain 'E' and resid 77 through 83 removed outlier: 3.659A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 122 through 131 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 177 through 192 Processing helix chain 'E' and resid 205 through 208 No H-bonds generated for 'chain 'E' and resid 205 through 208' Processing helix chain 'E' and resid 238 through 245 removed outlier: 3.735A pdb=" N PHE E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 52 through 67 Processing helix chain 'F' and resid 81 through 87 Processing helix chain 'G' and resid 5 through 26 Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'H' and resid 7 through 27 Processing helix chain 'H' and resid 145 through 150 Processing helix chain 'I' and resid 6 through 25 removed outlier: 3.571A pdb=" N LEU I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA I 17 " --> pdb=" O PHE I 13 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 151 Processing helix chain 'J' and resid 5 through 26 Processing helix chain 'J' and resid 144 through 148 Processing helix chain 'K' and resid 7 through 27 Processing helix chain 'K' and resid 145 through 150 Processing helix chain 'L' and resid 6 through 25 removed outlier: 3.559A pdb=" N LEU L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 151 removed outlier: 3.501A pdb=" N GLY L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.698A pdb=" N VAL B 31 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B 10 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 29 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 16 through 18 Processing sheet with id= C, first strand: chain 'B' and resid 225 through 227 removed outlier: 3.528A pdb=" N ALA B 225 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 214 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS B 198 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B 39 " --> pdb=" O CYS B 198 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 200 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY B 41 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER B 202 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 5 through 9 Processing sheet with id= E, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.700A pdb=" N VAL E 31 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP E 10 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU E 29 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 16 through 18 Processing sheet with id= G, first strand: chain 'E' and resid 225 through 227 removed outlier: 3.528A pdb=" N ALA E 225 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS E 214 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS E 198 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 39 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL E 200 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY E 41 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER E 202 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 5 through 9 Processing sheet with id= I, first strand: chain 'G' and resid 39 through 46 removed outlier: 8.417A pdb=" N VAL G 65 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL G 58 " --> pdb=" O VAL G 65 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 81 through 87 removed outlier: 6.137A pdb=" N ASP H 132 " --> pdb=" O TYR H 43 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR H 45 " --> pdb=" O ASP H 132 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE H 134 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 98 through 102 Processing sheet with id= L, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.328A pdb=" N ILE H 60 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL H 64 " --> pdb=" O ILE H 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 39 through 45 removed outlier: 8.570A pdb=" N VAL I 65 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 98 through 102 removed outlier: 3.716A pdb=" N SER I 98 " --> pdb=" O ASN I 115 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN I 115 " --> pdb=" O SER I 98 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 132 through 134 removed outlier: 4.645A pdb=" N THR J 45 " --> pdb=" O ILE J 134 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU J 42 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR J 83 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA J 69 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL J 58 " --> pdb=" O VAL J 65 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 39 through 45 Processing sheet with id= Q, first strand: chain 'K' and resid 98 through 102 Processing sheet with id= R, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.227A pdb=" N ILE K 60 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 39 through 45 removed outlier: 4.966A pdb=" N ASP L 70 " --> pdb=" O THR L 83 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL L 68 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU L 87 " --> pdb=" O GLY L 66 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY L 66 " --> pdb=" O GLU L 87 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 98 through 102 removed outlier: 3.674A pdb=" N SER L 98 " --> pdb=" O ASN L 115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN L 115 " --> pdb=" O SER L 98 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1611 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: 4.26 Time building geometry restraints manager: 6.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2643 1.31 - 1.43: 4026 1.43 - 1.56: 9824 1.56 - 1.68: 51 1.68 - 1.81: 124 Bond restraints: 16668 Sorted by residual: bond pdb=" C1 PGW A 301 " pdb=" O01 PGW A 301 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 PGW D 302 " pdb=" O01 PGW D 302 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C19 PGW A 301 " pdb=" O03 PGW A 301 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C19 PGW D 302 " pdb=" O03 PGW D 302 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 PGW A 302 " pdb=" O01 PGW A 302 " ideal model delta sigma weight residual 1.332 1.418 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 16663 not shown) Histogram of bond angle deviations from ideal: 80.28 - 91.04: 12 91.04 - 101.81: 69 101.81 - 112.57: 9233 112.57 - 123.34: 12440 123.34 - 134.10: 764 Bond angle restraints: 22518 Sorted by residual: angle pdb=" C19 PGW D 304 " pdb=" C20 PGW D 304 " pdb=" C21 PGW D 304 " ideal model delta sigma weight residual 114.60 80.28 34.32 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C19 PGW A 303 " pdb=" C20 PGW A 303 " pdb=" C21 PGW A 303 " ideal model delta sigma weight residual 114.60 80.32 34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C19 PGW A 304 " pdb=" C20 PGW A 304 " pdb=" C21 PGW A 304 " ideal model delta sigma weight residual 114.60 81.26 33.34 3.00e+00 1.11e-01 1.24e+02 angle pdb=" C19 PGW A 306 " pdb=" C20 PGW A 306 " pdb=" C21 PGW A 306 " ideal model delta sigma weight residual 114.60 81.29 33.31 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C19 PGW J 201 " pdb=" C20 PGW J 201 " pdb=" C21 PGW J 201 " ideal model delta sigma weight residual 114.60 81.35 33.25 3.00e+00 1.11e-01 1.23e+02 ... (remaining 22513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.63: 9476 28.63 - 57.25: 446 57.25 - 85.88: 40 85.88 - 114.50: 26 114.50 - 143.13: 26 Dihedral angle restraints: 10014 sinusoidal: 4060 harmonic: 5954 Sorted by residual: dihedral pdb=" CA ASP J 136 " pdb=" C ASP J 136 " pdb=" N THR J 137 " pdb=" CA THR J 137 " ideal model delta harmonic sigma weight residual 180.00 150.20 29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LYS J 129 " pdb=" C LYS J 129 " pdb=" N ASP J 130 " pdb=" CA ASP J 130 " ideal model delta harmonic sigma weight residual -180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA SER B 146 " pdb=" C SER B 146 " pdb=" N GLY B 147 " pdb=" CA GLY B 147 " ideal model delta harmonic sigma weight residual 180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 10011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2250 0.077 - 0.154: 379 0.154 - 0.230: 30 0.230 - 0.307: 5 0.307 - 0.384: 4 Chirality restraints: 2668 Sorted by residual: chirality pdb=" CB ILE E 223 " pdb=" CA ILE E 223 " pdb=" CG1 ILE E 223 " pdb=" CG2 ILE E 223 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB ILE B 223 " pdb=" CA ILE B 223 " pdb=" CG1 ILE B 223 " pdb=" CG2 ILE B 223 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB THR E 114 " pdb=" CA THR E 114 " pdb=" OG1 THR E 114 " pdb=" CG2 THR E 114 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2665 not shown) Planarity restraints: 2796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 120 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO I 121 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO I 121 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 121 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 155 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO D 156 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 155 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO A 156 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.038 5.00e-02 4.00e+02 ... (remaining 2793 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1753 2.74 - 3.28: 14706 3.28 - 3.82: 25030 3.82 - 4.36: 30974 4.36 - 4.90: 53620 Nonbonded interactions: 126083 Sorted by model distance: nonbonded pdb=" O LEU E 110 " pdb=" OG1 THR E 114 " model vdw 2.198 2.440 nonbonded pdb=" O LEU B 110 " pdb=" OG1 THR B 114 " model vdw 2.199 2.440 nonbonded pdb=" CE1 PHE G 46 " pdb=" CG2 THR G 137 " model vdw 2.225 3.760 nonbonded pdb=" CD1 PHE G 46 " pdb=" CG2 THR G 137 " model vdw 2.234 3.760 nonbonded pdb=" O PRO J 94 " pdb=" OG SER J 97 " model vdw 2.284 2.440 ... (remaining 126078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 259 or resid 301 through 304)) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'G' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'H' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'I' selection = (chain 'J' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'K' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.010 Extract box with map and model: 8.630 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 40.570 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.011 0.090 16668 Z= 0.689 Angle : 1.494 34.319 22518 Z= 0.674 Chirality : 0.059 0.384 2668 Planarity : 0.007 0.075 2796 Dihedral : 18.718 143.126 6190 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.19 % Favored : 88.23 % Rotamer Outliers : 0.95 % 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: -5.74 (0.13), residues: 2056 helix: -4.53 (0.06), residues: 878 sheet: -2.34 (0.29), residues: 290 loop : -3.39 (0.16), residues: 888 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 332 time to evaluate : 2.012 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 342 average time/residue: 1.6231 time to fit residues: 603.4783 Evaluate side-chains 263 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 260 time to evaluate : 1.993 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1504 time to fit residues: 2.8829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 104 optimal weight: 0.0370 chunk 82 optimal weight: 0.0670 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 50 ASN A 73 GLN A 190 GLN B 7 ASN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 175 GLN B 191 ASN B 226 HIS C 89 ASN D 29 ASN D 50 ASN D 73 GLN D 190 GLN E 7 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 191 ASN E 226 HIS F 89 ASN G 92 HIS H 135 GLN J 92 HIS J 110 GLN J 135 GLN L 110 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 16668 Z= 0.167 Angle : 0.659 8.231 22518 Z= 0.337 Chirality : 0.041 0.176 2668 Planarity : 0.005 0.056 2796 Dihedral : 18.090 134.915 2636 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.34 % Favored : 90.42 % Rotamer Outliers : 2.91 % 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: -3.49 (0.16), residues: 2056 helix: -1.84 (0.14), residues: 854 sheet: -1.61 (0.33), residues: 238 loop : -2.94 (0.17), residues: 964 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 310 time to evaluate : 2.022 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 11 residues processed: 332 average time/residue: 1.6180 time to fit residues: 585.3509 Evaluate side-chains 278 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 267 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 2 residues processed: 10 average time/residue: 0.7088 time to fit residues: 11.0764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 0.0770 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 214 HIS C 75 GLN C 89 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN E 214 HIS H 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 16668 Z= 0.266 Angle : 0.688 9.190 22518 Z= 0.345 Chirality : 0.043 0.223 2668 Planarity : 0.005 0.057 2796 Dihedral : 16.962 137.659 2636 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.21 % Favored : 89.59 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.18), residues: 2056 helix: -0.22 (0.18), residues: 856 sheet: -1.70 (0.32), residues: 256 loop : -2.64 (0.18), residues: 944 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 275 time to evaluate : 1.985 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 22 residues processed: 313 average time/residue: 1.6807 time to fit residues: 572.7785 Evaluate side-chains 282 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 260 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 12 residues processed: 11 average time/residue: 0.5197 time to fit residues: 9.9205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN G 92 HIS K 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 16668 Z= 0.158 Angle : 0.601 8.668 22518 Z= 0.301 Chirality : 0.041 0.169 2668 Planarity : 0.004 0.058 2796 Dihedral : 15.582 153.731 2636 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.00 % Favored : 90.81 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.18), residues: 2056 helix: 0.55 (0.19), residues: 856 sheet: -1.38 (0.33), residues: 246 loop : -2.59 (0.18), residues: 954 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 281 time to evaluate : 1.767 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 14 residues processed: 326 average time/residue: 1.6036 time to fit residues: 569.7523 Evaluate side-chains 285 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 271 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.4194 time to fit residues: 4.6002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 168 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 62 HIS B 175 GLN E 62 HIS E 175 GLN H 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 16668 Z= 0.298 Angle : 0.675 7.707 22518 Z= 0.337 Chirality : 0.044 0.249 2668 Planarity : 0.005 0.055 2796 Dihedral : 15.435 158.026 2636 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.12 % Favored : 89.69 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2056 helix: 0.69 (0.19), residues: 858 sheet: -1.55 (0.32), residues: 260 loop : -2.49 (0.18), residues: 938 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 287 time to evaluate : 1.717 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 31 residues processed: 331 average time/residue: 1.5968 time to fit residues: 574.7680 Evaluate side-chains 308 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 277 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 8 average time/residue: 0.6285 time to fit residues: 8.5741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 115 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 175 GLN C 75 GLN E 62 HIS E 175 GLN H 110 GLN K 110 GLN K 149 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16668 Z= 0.168 Angle : 0.611 9.620 22518 Z= 0.305 Chirality : 0.041 0.176 2668 Planarity : 0.004 0.056 2796 Dihedral : 14.717 168.379 2636 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.19 % Favored : 90.61 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.19), residues: 2056 helix: 1.09 (0.19), residues: 858 sheet: -1.25 (0.32), residues: 266 loop : -2.48 (0.19), residues: 932 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 268 time to evaluate : 1.977 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 30 residues processed: 316 average time/residue: 1.6245 time to fit residues: 559.9623 Evaluate side-chains 297 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 6 average time/residue: 0.8232 time to fit residues: 8.3027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 0.0670 chunk 90 optimal weight: 0.0070 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS C 75 GLN E 62 HIS E 175 GLN H 110 GLN K 110 GLN K 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16668 Z= 0.198 Angle : 0.625 8.907 22518 Z= 0.313 Chirality : 0.042 0.240 2668 Planarity : 0.004 0.056 2796 Dihedral : 13.893 115.584 2636 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.53 % Favored : 90.32 % Rotamer Outliers : 3.27 % 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: -0.97 (0.19), residues: 2056 helix: 1.19 (0.19), residues: 866 sheet: -1.09 (0.33), residues: 262 loop : -2.39 (0.19), residues: 928 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 270 time to evaluate : 2.024 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 28 residues processed: 313 average time/residue: 1.6033 time to fit residues: 546.5586 Evaluate side-chains 288 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 260 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.2000 time to fit residues: 3.6010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 97 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN B 62 HIS C 78 ASN E 62 HIS E 175 GLN H 110 GLN H 149 GLN K 110 GLN K 149 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 16668 Z= 0.163 Angle : 0.600 8.447 22518 Z= 0.301 Chirality : 0.041 0.230 2668 Planarity : 0.004 0.057 2796 Dihedral : 12.883 99.200 2636 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.46 % Favored : 91.39 % Rotamer Outliers : 2.49 % 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: -0.69 (0.19), residues: 2056 helix: 1.44 (0.19), residues: 866 sheet: -1.08 (0.34), residues: 242 loop : -2.21 (0.19), residues: 948 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 273 time to evaluate : 2.022 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 27 residues processed: 309 average time/residue: 1.6058 time to fit residues: 539.8996 Evaluate side-chains 294 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 267 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 26 residues processed: 2 average time/residue: 0.2314 time to fit residues: 3.1725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 173 optimal weight: 0.4980 chunk 182 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN D 220 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS H 110 GLN H 149 GLN K 110 GLN K 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16668 Z= 0.183 Angle : 0.617 9.571 22518 Z= 0.309 Chirality : 0.042 0.252 2668 Planarity : 0.004 0.055 2796 Dihedral : 12.551 91.493 2636 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.10 % Favored : 90.76 % Rotamer Outliers : 2.73 % 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: -0.59 (0.19), residues: 2056 helix: 1.48 (0.19), residues: 868 sheet: -0.99 (0.34), residues: 242 loop : -2.12 (0.20), residues: 946 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 268 time to evaluate : 1.875 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 26 residues processed: 304 average time/residue: 1.6809 time to fit residues: 559.5672 Evaluate side-chains 290 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 3 average time/residue: 0.2049 time to fit residues: 3.5537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 134 optimal weight: 0.0980 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 0.0030 chunk 128 optimal weight: 2.9990 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 175 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS E 115 GLN H 110 GLN K 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16668 Z= 0.263 Angle : 0.664 9.181 22518 Z= 0.332 Chirality : 0.044 0.234 2668 Planarity : 0.005 0.056 2796 Dihedral : 12.688 103.473 2636 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.97 % Favored : 89.88 % Rotamer Outliers : 2.14 % 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: -0.70 (0.19), residues: 2056 helix: 1.28 (0.19), residues: 876 sheet: -0.89 (0.33), residues: 266 loop : -2.16 (0.20), residues: 914 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 264 time to evaluate : 1.973 Fit side-chains outliers start: 36 outliers final: 26 residues processed: 295 average time/residue: 1.6318 time to fit residues: 523.8281 Evaluate side-chains 290 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 0 time to fit residues: 2.5083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0060 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN C 75 GLN C 78 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS E 115 GLN F 78 ASN H 110 GLN K 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.100798 restraints weight = 22197.971| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.88 r_work: 0.3039 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16668 Z= 0.166 Angle : 0.618 9.577 22518 Z= 0.310 Chirality : 0.041 0.226 2668 Planarity : 0.004 0.058 2796 Dihedral : 11.945 94.046 2636 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.24 % Favored : 90.61 % Rotamer Outliers : 2.26 % 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: -0.53 (0.20), residues: 2056 helix: 1.53 (0.19), residues: 868 sheet: -0.82 (0.33), residues: 266 loop : -2.15 (0.20), residues: 922 =============================================================================== Job complete usr+sys time: 7901.28 seconds wall clock time: 139 minutes 31.97 seconds (8371.97 seconds total)