Starting phenix.real_space_refine on Tue Apr 9 12:47:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2024/7cge_30355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2024/7cge_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_2024/7cge_30355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2024/7cge_30355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2024/7cge_30355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cge_30355/04_2024/7cge_30355_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 8.32, per 1000 atoms: 0.51 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: 6.34 Conformation dependent library (CDL) restraints added in 3.0 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: 2.82 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: 4.28 Time building geometry restraints manager: 6.88 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 - 33.15: 9694 33.15 - 66.29: 364 66.29 - 99.44: 60 99.44 - 132.58: 40 132.58 - 165.73: 12 Dihedral angle restraints: 10170 sinusoidal: 4216 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 10167 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: 2.040 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: 8.200 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 43.040 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.590 ------------------------------------------------------------------------------- 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 : 20.890 165.728 6346 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 % Allowed : 6.06 % Favored : 92.99 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 9 HIS 0.009 0.002 HIS D 241 PHE 0.028 0.003 PHE G 118 TYR 0.035 0.003 TYR B 261 ARG 0.009 0.001 ARG A 111 *********************** 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 : 1.887 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7862 (mtm-85) REVERT: A 134 MET cc_start: 0.9257 (mmt) cc_final: 0.9048 (mmm) REVERT: A 197 MET cc_start: 0.8645 (mmm) cc_final: 0.8414 (tpt) REVERT: B 13 ASP cc_start: 0.7032 (t70) cc_final: 0.6469 (t0) REVERT: B 130 GLU cc_start: 0.8159 (tp30) cc_final: 0.7923 (tp30) REVERT: C 21 ASP cc_start: 0.8047 (t70) cc_final: 0.7570 (t70) REVERT: C 22 GLN cc_start: 0.8718 (pp30) cc_final: 0.8404 (pp30) REVERT: C 23 ASP cc_start: 0.8515 (p0) cc_final: 0.8042 (p0) REVERT: D 18 ARG cc_start: 0.8115 (ptm160) cc_final: 0.7862 (mtm-85) REVERT: D 39 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8789 (tppt) REVERT: D 134 MET cc_start: 0.9271 (mmt) cc_final: 0.9034 (mmm) REVERT: D 197 MET cc_start: 0.8660 (mmm) cc_final: 0.8430 (tpt) REVERT: E 13 ASP cc_start: 0.7137 (t70) cc_final: 0.6537 (t0) REVERT: E 40 MET cc_start: 0.8519 (mtm) cc_final: 0.8314 (mtm) REVERT: E 130 GLU cc_start: 0.8272 (tp30) cc_final: 0.8030 (tp30) REVERT: E 180 MET cc_start: 0.8935 (mtt) cc_final: 0.8722 (mtm) REVERT: F 14 LEU cc_start: 0.8457 (tp) cc_final: 0.8255 (tm) REVERT: F 21 ASP cc_start: 0.8002 (t70) cc_final: 0.7558 (t70) REVERT: F 22 GLN cc_start: 0.8728 (pp30) cc_final: 0.8422 (pp30) REVERT: F 23 ASP cc_start: 0.8647 (p0) cc_final: 0.8167 (p0) REVERT: G 5 LYS cc_start: 0.8496 (tppt) cc_final: 0.8278 (tmmm) REVERT: G 88 GLN cc_start: 0.7923 (tp40) cc_final: 0.7174 (pm20) REVERT: G 92 HIS cc_start: 0.7626 (t70) cc_final: 0.7313 (t-170) REVERT: I 85 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7730 (mm-30) REVERT: J 5 LYS cc_start: 0.8506 (tppt) cc_final: 0.8273 (tmmm) REVERT: J 67 ARG cc_start: 0.6422 (mmt180) cc_final: 0.5813 (mmm-85) REVERT: J 89 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7860 (mpp-170) REVERT: J 92 HIS cc_start: 0.7846 (t70) cc_final: 0.7394 (t70) REVERT: L 85 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7787 (mm-30) outliers start: 16 outliers final: 3 residues processed: 342 average time/residue: 1.6770 time to fit residues: 623.4810 Evaluate side-chains 272 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 269 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 83 THR 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: 0.7980 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.0060 chunk 159 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 overall best weight: 0.4714 ------------------------------------------------------------------------------- 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 57 GLN ** 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 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 226 HIS F 89 ASN G 88 GLN H 135 GLN 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: 0.8318 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16668 Z= 0.173 Angle : 0.674 8.447 22518 Z= 0.340 Chirality : 0.042 0.186 2668 Planarity : 0.005 0.056 2796 Dihedral : 21.615 162.883 2796 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.29 % Favored : 90.42 % Rotamer: Outliers : 2.79 % Allowed : 15.56 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.15), residues: 2056 helix: -1.93 (0.14), residues: 854 sheet: -1.63 (0.33), residues: 238 loop : -2.93 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 9 HIS 0.003 0.001 HIS D 11 PHE 0.015 0.001 PHE G 118 TYR 0.013 0.001 TYR E 261 ARG 0.008 0.000 ARG F 97 *********************** 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: 47 poor density : 312 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7735 (ttm170) REVERT: A 197 MET cc_start: 0.8593 (mmm) cc_final: 0.8393 (tpt) REVERT: B 139 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8574 (mmmt) REVERT: C 75 GLN cc_start: 0.7195 (pt0) cc_final: 0.6785 (mt0) REVERT: D 15 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8314 (ptmm) REVERT: D 39 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8716 (ttpt) REVERT: F 22 GLN cc_start: 0.8681 (pp30) cc_final: 0.8231 (pp30) REVERT: F 49 ARG cc_start: 0.7935 (pmt170) cc_final: 0.7659 (pmt170) REVERT: G 88 GLN cc_start: 0.7640 (tp-100) cc_final: 0.6991 (pm20) REVERT: G 92 HIS cc_start: 0.7545 (t70) cc_final: 0.7128 (t70) REVERT: G 93 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6903 (mp) REVERT: I 85 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7304 (mm-30) REVERT: J 83 THR cc_start: 0.5782 (OUTLIER) cc_final: 0.5499 (t) REVERT: J 89 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7680 (mmp80) REVERT: J 92 HIS cc_start: 0.7672 (t70) cc_final: 0.7182 (t70) REVERT: L 47 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: L 85 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7447 (mm-30) REVERT: L 143 LEU cc_start: 0.8064 (pp) cc_final: 0.7596 (mt) outliers start: 47 outliers final: 12 residues processed: 332 average time/residue: 1.6704 time to fit residues: 603.2588 Evaluate side-chains 288 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 271 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 MET Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 47 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 0.0070 chunk 148 optimal weight: 7.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 175 GLN B 214 HIS E 57 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN E 214 HIS H 110 GLN K 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16668 Z= 0.279 Angle : 0.691 9.213 22518 Z= 0.346 Chirality : 0.044 0.205 2668 Planarity : 0.005 0.056 2796 Dihedral : 20.484 163.693 2793 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.36 % Favored : 89.45 % Rotamer: Outliers : 4.69 % Allowed : 16.33 % Favored : 78.98 % 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: -2.24 (0.18), residues: 2056 helix: -0.27 (0.17), residues: 858 sheet: -1.69 (0.32), residues: 256 loop : -2.63 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 9 HIS 0.003 0.001 HIS H 92 PHE 0.019 0.002 PHE G 13 TYR 0.026 0.002 TYR E 261 ARG 0.006 0.001 ARG F 97 *********************** 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 355 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 276 time to evaluate : 1.689 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7709 (ttm170) REVERT: A 197 MET cc_start: 0.8618 (mmm) cc_final: 0.8361 (tpt) REVERT: C 49 ARG cc_start: 0.8170 (pmt170) cc_final: 0.7678 (pmt170) REVERT: E 58 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7219 (pp) REVERT: F 22 GLN cc_start: 0.8710 (pp30) cc_final: 0.8356 (pp30) REVERT: G 88 GLN cc_start: 0.7519 (tp-100) cc_final: 0.6813 (pm20) REVERT: G 93 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7055 (mp) REVERT: G 139 SER cc_start: 0.7971 (p) cc_final: 0.7468 (m) REVERT: H 27 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8253 (tttm) REVERT: I 47 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: I 109 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: J 89 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7632 (mmp80) REVERT: K 27 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8219 (tttm) REVERT: L 47 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: L 143 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7770 (mt) outliers start: 79 outliers final: 22 residues processed: 317 average time/residue: 1.7181 time to fit residues: 589.3751 Evaluate side-chains 288 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 259 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 141 MET Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 0.0570 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 175 GLN E 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16668 Z= 0.191 Angle : 0.619 7.435 22518 Z= 0.310 Chirality : 0.042 0.169 2668 Planarity : 0.004 0.053 2796 Dihedral : 19.400 163.394 2792 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.58 % Favored : 90.22 % Rotamer: Outliers : 4.16 % Allowed : 18.35 % Favored : 77.49 % 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: -1.64 (0.18), residues: 2056 helix: 0.48 (0.19), residues: 850 sheet: -1.42 (0.32), residues: 262 loop : -2.53 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 186 HIS 0.003 0.001 HIS B 203 PHE 0.010 0.001 PHE G 13 TYR 0.016 0.001 TYR E 261 ARG 0.006 0.000 ARG A 18 *********************** 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 336 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 266 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8337 (tp) REVERT: A 18 ARG cc_start: 0.8351 (mtp85) cc_final: 0.8141 (mtp85) REVERT: A 38 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7691 (ttm170) REVERT: A 197 MET cc_start: 0.8618 (mmm) cc_final: 0.8340 (tpt) REVERT: B 26 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7997 (t0) REVERT: B 58 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6627 (pt) REVERT: C 21 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7495 (t70) REVERT: C 22 GLN cc_start: 0.8797 (pp30) cc_final: 0.8446 (pp30) REVERT: C 68 GLN cc_start: 0.8165 (pp30) cc_final: 0.7598 (pp30) REVERT: C 93 ASP cc_start: 0.8220 (p0) cc_final: 0.7858 (p0) REVERT: D 18 ARG cc_start: 0.8234 (mtp85) cc_final: 0.8000 (mtp85) REVERT: E 26 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8008 (t0) REVERT: E 58 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6596 (pt) REVERT: F 21 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7556 (t70) REVERT: F 22 GLN cc_start: 0.8752 (pp30) cc_final: 0.8347 (pp30) REVERT: G 88 GLN cc_start: 0.7462 (tp-100) cc_final: 0.6771 (pm20) REVERT: G 93 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7139 (mp) REVERT: G 139 SER cc_start: 0.8005 (p) cc_final: 0.7505 (m) REVERT: I 47 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: I 109 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: J 89 ARG cc_start: 0.8018 (ttp-110) cc_final: 0.7590 (mmp80) REVERT: L 47 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: L 143 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7788 (mt) outliers start: 70 outliers final: 25 residues processed: 309 average time/residue: 1.6710 time to fit residues: 560.7617 Evaluate side-chains 299 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 261 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 141 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.0020 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 175 GLN C 89 ASN E 175 GLN H 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16668 Z= 0.260 Angle : 0.656 10.282 22518 Z= 0.327 Chirality : 0.044 0.232 2668 Planarity : 0.005 0.053 2796 Dihedral : 18.986 162.063 2792 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.97 % Favored : 89.83 % Rotamer: Outliers : 4.22 % Allowed : 19.36 % Favored : 76.43 % 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: -1.40 (0.19), residues: 2056 helix: 0.70 (0.19), residues: 860 sheet: -1.56 (0.32), residues: 256 loop : -2.37 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 186 HIS 0.003 0.001 HIS H 92 PHE 0.014 0.001 PHE G 13 TYR 0.024 0.002 TYR E 261 ARG 0.009 0.001 ARG A 233 *********************** 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 338 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 267 time to evaluate : 1.754 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7683 (ttm170) REVERT: A 197 MET cc_start: 0.8651 (mmm) cc_final: 0.8425 (tpt) REVERT: A 233 ARG cc_start: 0.7361 (ttm110) cc_final: 0.7160 (ttm-80) REVERT: C 21 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7549 (t70) REVERT: C 22 GLN cc_start: 0.8881 (pp30) cc_final: 0.8468 (pp30) REVERT: C 49 ARG cc_start: 0.8193 (pmt170) cc_final: 0.7807 (pmt170) REVERT: C 68 GLN cc_start: 0.8236 (pp30) cc_final: 0.7696 (pp30) REVERT: C 93 ASP cc_start: 0.8221 (p0) cc_final: 0.7823 (p0) REVERT: D 233 ARG cc_start: 0.7366 (ttm110) cc_final: 0.7161 (ttm-80) REVERT: E 58 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.6826 (pt) REVERT: F 21 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7491 (t70) REVERT: F 22 GLN cc_start: 0.8816 (pp30) cc_final: 0.8426 (pp30) REVERT: G 88 GLN cc_start: 0.7444 (tp-100) cc_final: 0.6743 (pm20) REVERT: G 93 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7102 (mp) REVERT: G 139 SER cc_start: 0.8019 (p) cc_final: 0.7508 (m) REVERT: I 47 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: I 109 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: J 89 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7650 (mpp-170) REVERT: L 47 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: L 143 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7820 (mt) outliers start: 71 outliers final: 37 residues processed: 310 average time/residue: 1.6942 time to fit residues: 569.2262 Evaluate side-chains 310 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 264 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 141 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.3980 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN H 110 GLN K 110 GLN K 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2896 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= 0.167 Angle : 0.603 9.302 22518 Z= 0.300 Chirality : 0.041 0.185 2668 Planarity : 0.004 0.056 2796 Dihedral : 18.097 172.920 2792 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.19 % Favored : 90.61 % Rotamer: Outliers : 4.45 % Allowed : 19.77 % Favored : 75.77 % 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: -1.08 (0.19), residues: 2056 helix: 1.06 (0.19), residues: 860 sheet: -1.27 (0.32), residues: 262 loop : -2.34 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 186 HIS 0.002 0.001 HIS E 122 PHE 0.009 0.001 PHE J 13 TYR 0.014 0.001 TYR E 261 ARG 0.007 0.000 ARG D 233 *********************** 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 338 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 263 time to evaluate : 1.910 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8289 (tp) REVERT: A 197 MET cc_start: 0.8603 (mmm) cc_final: 0.8381 (tpt) REVERT: B 48 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8554 (m) REVERT: B 58 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6309 (pt) REVERT: C 22 GLN cc_start: 0.8862 (pp30) cc_final: 0.8624 (pp30) REVERT: C 49 ARG cc_start: 0.8154 (pmt170) cc_final: 0.7709 (pmt170) REVERT: C 68 GLN cc_start: 0.8603 (pp30) cc_final: 0.8229 (pp30) REVERT: C 93 ASP cc_start: 0.8127 (p0) cc_final: 0.7669 (p0) REVERT: D 14 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8293 (tp) REVERT: E 25 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: E 26 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8059 (t0) REVERT: E 48 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8551 (m) REVERT: E 58 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6297 (pt) REVERT: F 21 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7482 (t70) REVERT: F 22 GLN cc_start: 0.8827 (pp30) cc_final: 0.8479 (pp30) REVERT: G 67 ARG cc_start: 0.5726 (mmt180) cc_final: 0.5484 (mmm160) REVERT: G 89 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7601 (mpt180) REVERT: G 92 HIS cc_start: 0.7776 (t70) cc_final: 0.7155 (t70) REVERT: G 93 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7105 (mp) REVERT: G 139 SER cc_start: 0.7992 (p) cc_final: 0.7489 (m) REVERT: G 141 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.6016 (ptp) REVERT: G 151 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7170 (pp) REVERT: I 37 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7531 (tp30) REVERT: I 47 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: I 109 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: J 42 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7755 (mp) REVERT: J 89 ARG cc_start: 0.7943 (ttp-110) cc_final: 0.7662 (mpp-170) REVERT: L 47 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: L 143 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7767 (mt) outliers start: 75 outliers final: 28 residues processed: 313 average time/residue: 1.6258 time to fit residues: 553.4773 Evaluate side-chains 304 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 259 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 MET Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 119 optimal weight: 0.4980 chunk 90 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 175 GLN H 110 GLN K 110 GLN K 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16668 Z= 0.161 Angle : 0.603 8.818 22518 Z= 0.299 Chirality : 0.041 0.230 2668 Planarity : 0.004 0.056 2796 Dihedral : 16.861 154.067 2792 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.44 % Favored : 90.42 % Rotamer: Outliers : 3.92 % Allowed : 20.61 % Favored : 75.48 % 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: -0.83 (0.19), residues: 2056 helix: 1.30 (0.19), residues: 866 sheet: -1.09 (0.34), residues: 246 loop : -2.27 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.002 0.001 HIS B 203 PHE 0.010 0.001 PHE G 13 TYR 0.015 0.001 TYR B 261 ARG 0.009 0.000 ARG A 233 *********************** 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 328 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 262 time to evaluate : 1.749 Fit side-chains REVERT: A 18 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7794 (mmm160) REVERT: A 197 MET cc_start: 0.8602 (mmm) cc_final: 0.8381 (tpt) REVERT: A 233 ARG cc_start: 0.7246 (ttm110) cc_final: 0.7041 (ttm-80) REVERT: B 26 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8178 (t0) REVERT: B 48 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8522 (m) REVERT: B 58 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6067 (pt) REVERT: C 22 GLN cc_start: 0.8879 (pp30) cc_final: 0.8653 (pp30) REVERT: C 68 GLN cc_start: 0.8575 (pp30) cc_final: 0.8244 (pp30) REVERT: C 93 ASP cc_start: 0.8115 (p0) cc_final: 0.7643 (p0) REVERT: D 14 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8248 (tp) REVERT: D 18 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7725 (mmm160) REVERT: D 233 ARG cc_start: 0.7262 (ttm110) cc_final: 0.7053 (ttm-80) REVERT: D 256 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8696 (mt) REVERT: E 25 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7192 (m-30) REVERT: E 26 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8129 (t0) REVERT: E 48 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8524 (m) REVERT: E 58 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6354 (pt) REVERT: G 5 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7712 (ttpt) REVERT: G 87 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6870 (mm-30) REVERT: G 88 GLN cc_start: 0.6878 (tp-100) cc_final: 0.6552 (pm20) REVERT: G 92 HIS cc_start: 0.7812 (t70) cc_final: 0.7136 (t70) REVERT: G 93 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7094 (mp) REVERT: G 139 SER cc_start: 0.8070 (p) cc_final: 0.7575 (m) REVERT: I 47 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: J 5 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7708 (ttpt) REVERT: J 87 GLU cc_start: 0.7458 (tp30) cc_final: 0.7190 (tp30) REVERT: J 89 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7653 (mpp-170) REVERT: L 47 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: L 143 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7602 (mt) outliers start: 66 outliers final: 26 residues processed: 307 average time/residue: 1.7037 time to fit residues: 567.8276 Evaluate side-chains 299 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 258 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.8980 chunk 78 optimal weight: 0.0020 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.0070 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.0570 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 0.0370 overall best weight: 0.2002 ------------------------------------------------------------------------------- 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 E 62 HIS H 110 GLN K 110 GLN K 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16668 Z= 0.140 Angle : 0.583 9.999 22518 Z= 0.288 Chirality : 0.041 0.219 2668 Planarity : 0.004 0.057 2796 Dihedral : 15.112 142.732 2792 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.32 % Favored : 91.63 % Rotamer: Outliers : 2.67 % Allowed : 22.27 % Favored : 75.06 % 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: -0.52 (0.20), residues: 2056 helix: 1.65 (0.19), residues: 864 sheet: -0.96 (0.33), residues: 262 loop : -2.20 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 216 HIS 0.002 0.001 HIS L 92 PHE 0.009 0.001 PHE A 219 TYR 0.015 0.001 TYR K 111 ARG 0.021 0.001 ARG H 67 *********************** 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 331 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 286 time to evaluate : 1.865 Fit side-chains REVERT: A 18 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7792 (mmm160) REVERT: B 58 ILE cc_start: 0.6594 (OUTLIER) cc_final: 0.6018 (pp) REVERT: C 21 ASP cc_start: 0.8008 (t70) cc_final: 0.7662 (t70) REVERT: C 22 GLN cc_start: 0.8892 (pp30) cc_final: 0.8481 (pp30) REVERT: C 23 ASP cc_start: 0.8254 (p0) cc_final: 0.7822 (p0) REVERT: C 68 GLN cc_start: 0.8739 (pp30) cc_final: 0.8497 (pp30) REVERT: D 18 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7762 (mmm160) REVERT: D 256 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8661 (mt) REVERT: E 58 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.6027 (pp) REVERT: F 82 TYR cc_start: 0.7898 (m-80) cc_final: 0.7662 (m-80) REVERT: G 5 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7563 (ttpt) REVERT: G 85 GLU cc_start: 0.6225 (tt0) cc_final: 0.5818 (tm-30) REVERT: G 87 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6758 (mm-30) REVERT: G 88 GLN cc_start: 0.6699 (tp-100) cc_final: 0.6493 (pm20) REVERT: G 92 HIS cc_start: 0.7733 (t70) cc_final: 0.7066 (t70) REVERT: G 93 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.7003 (mp) REVERT: G 139 SER cc_start: 0.8157 (p) cc_final: 0.7701 (m) REVERT: H 67 ARG cc_start: 0.6989 (mtp-110) cc_final: 0.6543 (mtm180) REVERT: I 109 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: J 5 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7562 (ttpt) REVERT: J 89 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7621 (mmp80) REVERT: L 143 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7554 (mt) outliers start: 45 outliers final: 16 residues processed: 317 average time/residue: 1.6797 time to fit residues: 577.5625 Evaluate side-chains 284 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0470 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 173 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 115 GLN C 78 ASN D 220 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS E 115 GLN E 175 GLN H 110 GLN K 110 GLN K 149 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16668 Z= 0.197 Angle : 0.620 9.137 22518 Z= 0.307 Chirality : 0.042 0.255 2668 Planarity : 0.004 0.056 2796 Dihedral : 15.052 142.300 2792 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.75 % Favored : 91.10 % Rotamer: Outliers : 2.38 % Allowed : 22.98 % Favored : 74.64 % 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: -0.51 (0.19), residues: 2056 helix: 1.66 (0.19), residues: 862 sheet: -0.91 (0.33), residues: 266 loop : -2.20 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 29 HIS 0.003 0.001 HIS E 62 PHE 0.013 0.001 PHE G 13 TYR 0.018 0.001 TYR B 261 ARG 0.012 0.000 ARG H 67 *********************** 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 303 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 263 time to evaluate : 1.873 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7624 (mmm160) REVERT: B 58 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6276 (pp) REVERT: D 18 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7824 (mmm160) REVERT: D 256 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8666 (mt) REVERT: E 58 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6290 (pp) REVERT: G 87 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6811 (mm-30) REVERT: G 88 GLN cc_start: 0.6760 (tp-100) cc_final: 0.6541 (pm20) REVERT: G 92 HIS cc_start: 0.7971 (t70) cc_final: 0.7343 (t70) REVERT: G 93 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7090 (mp) REVERT: G 139 SER cc_start: 0.8111 (p) cc_final: 0.7661 (m) REVERT: I 47 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: I 109 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7547 (tp30) REVERT: I 144 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: J 5 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7672 (ttpt) REVERT: J 89 ARG cc_start: 0.8002 (ttp-110) cc_final: 0.7656 (mmp80) REVERT: L 47 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7311 (m-30) REVERT: L 143 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7562 (mt) outliers start: 40 outliers final: 16 residues processed: 290 average time/residue: 1.7665 time to fit residues: 553.4534 Evaluate side-chains 284 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 258 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 149 GLN Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 187 optimal weight: 0.2980 chunk 161 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 115 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS H 110 GLN K 110 GLN K 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16668 Z= 0.192 Angle : 0.623 10.097 22518 Z= 0.309 Chirality : 0.042 0.227 2668 Planarity : 0.004 0.057 2796 Dihedral : 14.917 141.754 2792 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.05 % Favored : 90.81 % Rotamer: Outliers : 2.02 % Allowed : 23.40 % Favored : 74.58 % 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: -0.46 (0.20), residues: 2056 helix: 1.69 (0.19), residues: 860 sheet: -0.92 (0.33), residues: 262 loop : -2.13 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 29 HIS 0.004 0.001 HIS B 62 PHE 0.011 0.001 PHE G 13 TYR 0.018 0.001 TYR B 261 ARG 0.007 0.000 ARG H 67 ********************** 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 290 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 1.905 Fit side-chains REVERT: A 18 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7717 (mmm-85) REVERT: B 58 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6273 (pp) REVERT: C 21 ASP cc_start: 0.7999 (t70) cc_final: 0.7675 (t70) REVERT: C 22 GLN cc_start: 0.8958 (pp30) cc_final: 0.8726 (pp30) REVERT: C 23 ASP cc_start: 0.8366 (p0) cc_final: 0.7981 (p0) REVERT: D 18 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7760 (mmm-85) REVERT: D 256 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8673 (mt) REVERT: E 58 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6256 (pp) REVERT: F 93 ASP cc_start: 0.8088 (p0) cc_final: 0.7640 (p0) REVERT: G 87 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6871 (mm-30) REVERT: G 92 HIS cc_start: 0.7958 (t70) cc_final: 0.7286 (t70) REVERT: G 93 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7196 (mp) REVERT: G 139 SER cc_start: 0.8082 (p) cc_final: 0.7652 (m) REVERT: H 42 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6815 (mp) REVERT: I 109 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7547 (tp30) REVERT: I 144 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: J 5 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7663 (ttpt) REVERT: J 89 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7656 (mmp80) REVERT: L 47 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: L 143 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7569 (mt) outliers start: 34 outliers final: 18 residues processed: 281 average time/residue: 1.7957 time to fit residues: 546.2798 Evaluate side-chains 280 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 149 GLN Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 142 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS H 110 GLN K 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101283 restraints weight = 22184.239| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.88 r_work: 0.3048 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 16668 Z= 0.210 Angle : 0.815 59.187 22518 Z= 0.445 Chirality : 0.043 0.496 2668 Planarity : 0.004 0.057 2796 Dihedral : 14.912 141.733 2792 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.39 % Favored : 90.47 % Rotamer: Outliers : 2.20 % Allowed : 23.28 % Favored : 74.52 % Cbeta Deviations : 0.05 % 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: -0.45 (0.20), residues: 2056 helix: 1.70 (0.19), residues: 860 sheet: -0.92 (0.33), residues: 262 loop : -2.13 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 29 HIS 0.003 0.001 HIS B 62 PHE 0.011 0.001 PHE G 13 TYR 0.017 0.001 TYR B 261 ARG 0.004 0.000 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8156.51 seconds wall clock time: 145 minutes 39.84 seconds (8739.84 seconds total)