Starting phenix.real_space_refine on Tue Jul 23 16:01:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2c_30954/07_2024/7e2c_30954_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2c_30954/07_2024/7e2c_30954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2c_30954/07_2024/7e2c_30954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2c_30954/07_2024/7e2c_30954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2c_30954/07_2024/7e2c_30954_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2c_30954/07_2024/7e2c_30954_neut.cif" } resolution = 4.18 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 14589 2.51 5 N 3997 2.21 5 O 4348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 139": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G ARG 277": "NH1" <-> "NH2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "I ARG 793": "NH1" <-> "NH2" Residue "I GLU 803": "OE1" <-> "OE2" Residue "I ARG 816": "NH1" <-> "NH2" Residue "I GLU 833": "OE1" <-> "OE2" Residue "I GLU 864": "OE1" <-> "OE2" Residue "J GLU 459": "OE1" <-> "OE2" Residue "J ARG 487": "NH1" <-> "NH2" Residue "J ARG 535": "NH1" <-> "NH2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "J ARG 600": "NH1" <-> "NH2" Residue "J PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 779": "NH1" <-> "NH2" Residue "J ARG 820": "NH1" <-> "NH2" Residue "J ARG 821": "NH1" <-> "NH2" Residue "J GLU 996": "OE1" <-> "OE2" Residue "J ARG 1027": "NH1" <-> "NH2" Residue "J GLU 1029": "OE1" <-> "OE2" Residue "J GLU 1112": "OE1" <-> "OE2" Residue "J PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1179": "OE1" <-> "OE2" Residue "J TYR 1233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 547": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23020 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1206 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "B" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1458 Classifications: {'peptide': 195} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 38} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 4, 'GLU:plan': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1482 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "D" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1234 Classifications: {'peptide': 151} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1295 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1470 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "G" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1612 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1172 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 4258 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 660} Link IDs: {'PTRANS': 17, 'TRANS': 781} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 2381 Unresolved non-hydrogen angles: 3030 Unresolved non-hydrogen dihedrals: 1971 Unresolved non-hydrogen chiralities: 227 Planarities with less than four sites: {'GLN:plan1': 29, 'ARG:plan': 25, 'TYR:plan': 24, 'ASN:plan1': 43, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 43, 'GLU:plan': 62, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1266 Chain: "J" Number of atoms: 6265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6265 Classifications: {'peptide': 873} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 37, 'TRANS': 835} Chain breaks: 5 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 936 Unresolved non-hydrogen angles: 1195 Unresolved non-hydrogen dihedrals: 774 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 20, 'PHE:plan': 9, 'GLU:plan': 11, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 448 Chain: "K" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1568 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 602 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 8, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 213 Time building chain proxies: 14.24, per 1000 atoms: 0.62 Number of scatterers: 23020 At special positions: 0 Unit cell: (193.107, 258.567, 146.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 4348 8.00 N 3997 7.00 C 14589 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: 9.68 Conformation dependent library (CDL) restraints added in 4.7 seconds 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6340 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 35 sheets defined 30.7% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.959A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 121 removed outlier: 3.930A pdb=" N CYS A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'B' and resid 41 through 61 removed outlier: 3.868A pdb=" N TYR B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 101 through 110 removed outlier: 3.658A pdb=" N HIS B 106 " --> pdb=" O HIS B 102 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 4.046A pdb=" N ARG B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.826A pdb=" N ILE B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.991A pdb=" N MET B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 211' Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 230 removed outlier: 4.017A pdb=" N GLY B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 222 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 21 removed outlier: 4.846A pdb=" N GLY C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 45 removed outlier: 3.601A pdb=" N PHE C 30 " --> pdb=" O ASN C 26 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 75 removed outlier: 3.824A pdb=" N ASN C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP C 54 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 97 removed outlier: 3.895A pdb=" N GLU C 88 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 removed outlier: 3.594A pdb=" N CYS C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 removed outlier: 4.106A pdb=" N LYS D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 109 Processing helix chain 'D' and resid 142 through 154 removed outlier: 3.726A pdb=" N ILE D 146 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 47 removed outlier: 3.803A pdb=" N TYR E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 190 removed outlier: 3.652A pdb=" N ALA E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 removed outlier: 3.766A pdb=" N LYS E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 18 removed outlier: 3.903A pdb=" N GLU F 15 " --> pdb=" O LYS F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 45 removed outlier: 4.054A pdb=" N PHE F 30 " --> pdb=" O ASN F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.953A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE F 68 " --> pdb=" O GLY F 64 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 99 removed outlier: 4.451A pdb=" N LYS F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 136 removed outlier: 3.817A pdb=" N MET F 135 " --> pdb=" O MET F 132 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS F 136 " --> pdb=" O ASP F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 154 removed outlier: 3.689A pdb=" N LYS F 149 " --> pdb=" O CYS F 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 77 Processing helix chain 'G' and resid 79 through 107 removed outlier: 3.747A pdb=" N PHE G 83 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY G 91 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE G 96 " --> pdb=" O HIS G 92 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 187 removed outlier: 3.578A pdb=" N HIS G 184 " --> pdb=" O LEU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 Processing helix chain 'G' and resid 227 through 229 No H-bonds generated for 'chain 'G' and resid 227 through 229' Processing helix chain 'G' and resid 230 through 242 removed outlier: 3.782A pdb=" N CYS G 234 " --> pdb=" O GLU G 230 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY G 235 " --> pdb=" O TYR G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 279 removed outlier: 3.536A pdb=" N LEU G 275 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 removed outlier: 4.410A pdb=" N TRP H 53 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 146 removed outlier: 3.525A pdb=" N TYR H 134 " --> pdb=" O MET H 130 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU H 136 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU H 139 " --> pdb=" O GLN H 135 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 169 removed outlier: 4.006A pdb=" N ARG H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 269 removed outlier: 3.666A pdb=" N SER I 259 " --> pdb=" O SER I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 289 removed outlier: 3.896A pdb=" N PHE I 282 " --> pdb=" O HIS I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 314 Processing helix chain 'I' and resid 322 through 333 Processing helix chain 'I' and resid 334 through 337 Processing helix chain 'I' and resid 348 through 367 Processing helix chain 'I' and resid 399 through 409 Processing helix chain 'I' and resid 409 through 417 removed outlier: 3.938A pdb=" N SER I 415 " --> pdb=" O LYS I 411 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU I 416 " --> pdb=" O GLU I 412 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE I 417 " --> pdb=" O ILE I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 418 through 421 removed outlier: 3.803A pdb=" N GLU I 421 " --> pdb=" O ASN I 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 418 through 421' Processing helix chain 'I' and resid 456 through 460 removed outlier: 3.632A pdb=" N TYR I 459 " --> pdb=" O TYR I 456 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR I 460 " --> pdb=" O GLU I 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 456 through 460' Processing helix chain 'I' and resid 467 through 472 Processing helix chain 'I' and resid 476 through 481 removed outlier: 4.516A pdb=" N HIS I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 526 removed outlier: 4.414A pdb=" N LYS I 523 " --> pdb=" O GLU I 519 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS I 524 " --> pdb=" O ILE I 520 " (cutoff:3.500A) Processing helix chain 'I' and resid 862 through 866 Processing helix chain 'I' and resid 867 through 869 No H-bonds generated for 'chain 'I' and resid 867 through 869' Processing helix chain 'I' and resid 886 through 888 No H-bonds generated for 'chain 'I' and resid 886 through 888' Processing helix chain 'I' and resid 889 through 894 Processing helix chain 'I' and resid 896 through 900 removed outlier: 3.635A pdb=" N LYS I 899 " --> pdb=" O GLU I 896 " (cutoff:3.500A) Processing helix chain 'I' and resid 921 through 924 removed outlier: 4.056A pdb=" N ASN I 924 " --> pdb=" O ILE I 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 921 through 924' Processing helix chain 'I' and resid 925 through 930 removed outlier: 4.215A pdb=" N LYS I 929 " --> pdb=" O LYS I 925 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE I 930 " --> pdb=" O THR I 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 925 through 930' Processing helix chain 'I' and resid 933 through 938 Processing helix chain 'I' and resid 939 through 947 Processing helix chain 'J' and resid 267 through 286 Processing helix chain 'J' and resid 310 through 328 Processing helix chain 'J' and resid 381 through 395 removed outlier: 3.816A pdb=" N MET J 385 " --> pdb=" O SER J 381 " (cutoff:3.500A) Proline residue: J 388 - end of helix Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 426 through 441 Proline residue: J 436 - end of helix Processing helix chain 'J' and resid 459 through 475 removed outlier: 4.402A pdb=" N LEU J 465 " --> pdb=" O SER J 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 478 No H-bonds generated for 'chain 'J' and resid 476 through 478' Processing helix chain 'J' and resid 506 through 524 removed outlier: 3.612A pdb=" N GLN J 510 " --> pdb=" O GLN J 506 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR J 521 " --> pdb=" O MET J 517 " (cutoff:3.500A) Processing helix chain 'J' and resid 526 through 544 removed outlier: 3.751A pdb=" N GLN J 530 " --> pdb=" O TYR J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 553 through 563 Processing helix chain 'J' and resid 584 through 603 Processing helix chain 'J' and resid 604 through 619 Processing helix chain 'J' and resid 636 through 641 Processing helix chain 'J' and resid 897 through 905 Proline residue: J 903 - end of helix Processing helix chain 'J' and resid 920 through 924 removed outlier: 3.631A pdb=" N LEU J 924 " --> pdb=" O LEU J 921 " (cutoff:3.500A) Processing helix chain 'J' and resid 954 through 958 removed outlier: 4.271A pdb=" N PHE J 957 " --> pdb=" O ALA J 954 " (cutoff:3.500A) Processing helix chain 'J' and resid 1016 through 1026 Processing helix chain 'J' and resid 1112 through 1129 removed outlier: 3.683A pdb=" N ARG J1118 " --> pdb=" O THR J1114 " (cutoff:3.500A) Processing helix chain 'J' and resid 1158 through 1163 removed outlier: 3.756A pdb=" N TYR J1162 " --> pdb=" O HIS J1158 " (cutoff:3.500A) Processing helix chain 'J' and resid 1197 through 1201 removed outlier: 3.558A pdb=" N CYS J1200 " --> pdb=" O THR J1197 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG J1201 " --> pdb=" O SER J1198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1197 through 1201' Processing helix chain 'K' and resid 237 through 249 removed outlier: 4.939A pdb=" N LEU K 243 " --> pdb=" O ALA K 239 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR K 244 " --> pdb=" O SER K 240 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE K 247 " --> pdb=" O LEU K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 500 removed outlier: 3.716A pdb=" N LEU K 489 " --> pdb=" O ASN K 485 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA K 497 " --> pdb=" O TYR K 493 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY K 499 " --> pdb=" O LYS K 495 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE K 500 " --> pdb=" O ILE K 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 4.563A pdb=" N ILE A 86 " --> pdb=" O MET A 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 77 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AA3, first strand: chain 'B' and resid 177 through 179 removed outlier: 3.721A pdb=" N THR B 183 " --> pdb=" O ASN B 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.571A pdb=" N SER B 259 " --> pdb=" O CYS B 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 106 removed outlier: 3.678A pdb=" N LEU C 117 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 176 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 9 removed outlier: 3.954A pdb=" N SER D 5 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG D 68 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU E 4 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASN E 20 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE E 6 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN E 18 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL E 8 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 24 through 25 Processing sheet with id=AA8, first strand: chain 'F' and resid 161 through 165 removed outlier: 6.986A pdb=" N GLU F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 209 through 213 Processing sheet with id=AB1, first strand: chain 'H' and resid 14 through 20 removed outlier: 3.528A pdb=" N ILE H 8 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET H 113 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR H 101 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP H 93 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA H 102 " --> pdb=" O LYS H 91 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS H 91 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE H 104 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU H 89 " --> pdb=" O ILE H 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 563 through 565 removed outlier: 3.805A pdb=" N MET I 580 " --> pdb=" O SER I 621 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU I 582 " --> pdb=" O GLU I 619 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 674 through 677 Processing sheet with id=AB4, first strand: chain 'I' and resid 742 through 745 Processing sheet with id=AB5, first strand: chain 'I' and resid 769 through 772 removed outlier: 3.714A pdb=" N ILE I 781 " --> pdb=" O LYS I 778 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 769 through 772 removed outlier: 4.012A pdb=" N PHE I 782 " --> pdb=" O ILE I 841 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 819 through 820 removed outlier: 4.943A pdb=" N LEU I 799 " --> pdb=" O ASN I 860 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN I 860 " --> pdb=" O LEU I 799 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER I 801 " --> pdb=" O ARG I 858 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN I 854 " --> pdb=" O SER I 805 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 983 through 984 removed outlier: 8.266A pdb=" N GLU I 983 " --> pdb=" O VAL I1078 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 987 through 992 Processing sheet with id=AC1, first strand: chain 'J' and resid 753 through 757 removed outlier: 3.659A pdb=" N SER J 804 " --> pdb=" O ILE J 754 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU J 756 " --> pdb=" O LYS J 802 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LYS J 802 " --> pdb=" O GLU J 756 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 860 through 861 removed outlier: 3.570A pdb=" N ASN J 861 " --> pdb=" O THR J 990 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'J' and resid 967 through 970 Processing sheet with id=AC4, first strand: chain 'J' and resid 995 through 996 Processing sheet with id=AC5, first strand: chain 'J' and resid 995 through 996 Processing sheet with id=AC6, first strand: chain 'J' and resid 1055 through 1057 removed outlier: 3.634A pdb=" N ASN J1134 " --> pdb=" O ASN J1055 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 1172 through 1177 Processing sheet with id=AC8, first strand: chain 'J' and resid 1181 through 1182 removed outlier: 3.502A pdb=" N VAL J1182 " --> pdb=" O SER J1287 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 1208 through 1209 Processing sheet with id=AD1, first strand: chain 'J' and resid 1231 through 1232 Processing sheet with id=AD2, first strand: chain 'K' and resid 217 through 221 Processing sheet with id=AD3, first strand: chain 'K' and resid 283 through 284 Processing sheet with id=AD4, first strand: chain 'K' and resid 267 through 268 removed outlier: 4.317A pdb=" N LYS K 306 " --> pdb=" O LEU K 268 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 310 through 311 Processing sheet with id=AD6, first strand: chain 'K' and resid 411 through 414 Processing sheet with id=AD7, first strand: chain 'K' and resid 420 through 421 removed outlier: 5.909A pdb=" N LYS K 420 " --> pdb=" O VAL K 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'K' and resid 444 through 446 767 hydrogen bonds defined for protein. 2157 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.84 Time building geometry restraints manager: 10.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6858 1.34 - 1.46: 4929 1.46 - 1.58: 11447 1.58 - 1.70: 1 1.70 - 1.83: 134 Bond restraints: 23369 Sorted by residual: bond pdb=" N PHE G 215 " pdb=" CA PHE G 215 " ideal model delta sigma weight residual 1.463 1.421 0.042 9.30e-03 1.16e+04 2.04e+01 bond pdb=" N PHE H 29 " pdb=" CA PHE H 29 " ideal model delta sigma weight residual 1.457 1.488 -0.032 9.10e-03 1.21e+04 1.23e+01 bond pdb=" N ILE H 40 " pdb=" CA ILE H 40 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.73e+00 bond pdb=" C PHE J 485 " pdb=" N PRO J 486 " ideal model delta sigma weight residual 1.330 1.366 -0.036 1.23e-02 6.61e+03 8.61e+00 bond pdb=" N VAL J 955 " pdb=" CA VAL J 955 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 8.17e+00 ... (remaining 23364 not shown) Histogram of bond angle deviations from ideal: 89.82 - 100.03: 25 100.03 - 110.23: 5103 110.23 - 120.43: 17305 120.43 - 130.63: 9305 130.63 - 140.83: 85 Bond angle restraints: 31823 Sorted by residual: angle pdb=" N PRO I 346 " pdb=" CA PRO I 346 " pdb=" CB PRO I 346 " ideal model delta sigma weight residual 102.28 110.18 -7.90 7.50e-01 1.78e+00 1.11e+02 angle pdb=" N PRO I 976 " pdb=" CA PRO I 976 " pdb=" CB PRO I 976 " ideal model delta sigma weight residual 103.25 112.79 -9.54 1.05e+00 9.07e-01 8.26e+01 angle pdb=" N PRO I1076 " pdb=" CA PRO I1076 " pdb=" CB PRO I1076 " ideal model delta sigma weight residual 103.25 112.05 -8.80 1.05e+00 9.07e-01 7.02e+01 angle pdb=" N PRO H 26 " pdb=" CA PRO H 26 " pdb=" CB PRO H 26 " ideal model delta sigma weight residual 103.25 111.90 -8.65 1.05e+00 9.07e-01 6.79e+01 angle pdb=" N PRO K 325 " pdb=" CA PRO K 325 " pdb=" CB PRO K 325 " ideal model delta sigma weight residual 103.25 111.80 -8.55 1.05e+00 9.07e-01 6.63e+01 ... (remaining 31818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 12415 17.00 - 34.00: 1319 34.00 - 51.00: 207 51.00 - 68.00: 53 68.00 - 85.00: 18 Dihedral angle restraints: 14012 sinusoidal: 4312 harmonic: 9700 Sorted by residual: dihedral pdb=" CA SER A 132 " pdb=" C SER A 132 " pdb=" N ILE A 133 " pdb=" CA ILE A 133 " ideal model delta harmonic sigma weight residual 180.00 150.08 29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ARG I1051 " pdb=" C ARG I1051 " pdb=" N CYS I1052 " pdb=" CA CYS I1052 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLU J 563 " pdb=" C GLU J 563 " pdb=" N LEU J 564 " pdb=" CA LEU J 564 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 14009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3370 0.120 - 0.240: 363 0.240 - 0.360: 48 0.360 - 0.480: 14 0.480 - 0.600: 4 Chirality restraints: 3799 Sorted by residual: chirality pdb=" CB VAL F 155 " pdb=" CA VAL F 155 " pdb=" CG1 VAL F 155 " pdb=" CG2 VAL F 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" CB ILE E 172 " pdb=" CA ILE E 172 " pdb=" CG1 ILE E 172 " pdb=" CG2 ILE E 172 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CB ILE E 70 " pdb=" CA ILE E 70 " pdb=" CG1 ILE E 70 " pdb=" CG2 ILE E 70 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.14e+00 ... (remaining 3796 not shown) Planarity restraints: 4159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 67 " 0.077 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO E 68 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO E 68 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 68 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 633 " -0.021 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C LYS J 633 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS J 633 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU J 634 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 635 " 0.018 2.00e-02 2.50e+03 2.87e-02 1.64e+01 pdb=" CG TYR J 635 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR J 635 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR J 635 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR J 635 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR J 635 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR J 635 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR J 635 " 0.011 2.00e-02 2.50e+03 ... (remaining 4156 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 10 2.32 - 2.96: 10749 2.96 - 3.61: 34379 3.61 - 4.25: 47829 4.25 - 4.90: 77204 Nonbonded interactions: 170171 Sorted by model distance: nonbonded pdb=" CG2 ILE A 79 " pdb=" OE1 GLN A 81 " model vdw 1.675 3.460 nonbonded pdb=" CE LYS A 35 " pdb=" CB ASP I 377 " model vdw 1.831 3.840 nonbonded pdb=" O ASN I 379 " pdb=" O TYR I 380 " model vdw 2.021 3.040 nonbonded pdb=" NZ LYS A 35 " pdb=" CA ASP I 377 " model vdw 2.212 3.550 nonbonded pdb=" OH TYR H 4 " pdb=" OD1 ASN H 37 " model vdw 2.249 2.440 ... (remaining 170166 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 'C' and resid 8 through 189) selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.440 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: 0.170 Extract box with map and model: 0.860 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 65.410 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 23369 Z= 0.568 Angle : 1.501 22.918 31823 Z= 0.837 Chirality : 0.083 0.600 3799 Planarity : 0.008 0.117 4159 Dihedral : 15.124 85.001 7672 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 1.08 % Allowed : 15.30 % Favored : 83.62 % Rotamer: Outliers : 0.94 % Allowed : 1.99 % Favored : 97.07 % Cbeta Deviations : 0.09 % 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: -5.41 (0.11), residues: 3235 helix: -3.32 (0.11), residues: 967 sheet: -2.88 (0.21), residues: 520 loop : -4.12 (0.11), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP I1024 HIS 0.013 0.002 HIS H 172 PHE 0.058 0.004 PHE I 784 TYR 0.052 0.004 TYR K 447 ARG 0.021 0.001 ARG J 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 418 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.8931 (t) cc_final: 0.8506 (t) REVERT: A 88 ILE cc_start: 0.7376 (mm) cc_final: 0.6894 (mm) REVERT: A 93 LYS cc_start: 0.5155 (OUTLIER) cc_final: 0.4725 (tppp) REVERT: A 131 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8431 (tmtt) REVERT: B 151 MET cc_start: 0.7226 (pmm) cc_final: 0.6638 (pmm) REVERT: B 181 ARG cc_start: 0.7520 (mpt180) cc_final: 0.7303 (mtm-85) REVERT: C 59 MET cc_start: 0.7154 (ttt) cc_final: 0.6316 (ttm) REVERT: C 135 MET cc_start: 0.2034 (tpt) cc_final: 0.1646 (tpp) REVERT: C 154 MET cc_start: 0.6290 (mmp) cc_final: 0.6080 (mmt) REVERT: D 36 GLN cc_start: 0.6679 (mp-120) cc_final: 0.6395 (mm110) REVERT: E 21 PHE cc_start: 0.8175 (m-80) cc_final: 0.7827 (m-80) REVERT: E 174 ILE cc_start: 0.7503 (tt) cc_final: 0.7086 (mm) REVERT: F 27 THR cc_start: 0.7553 (p) cc_final: 0.7276 (t) REVERT: F 62 ASN cc_start: 0.8560 (t0) cc_final: 0.7840 (t0) REVERT: F 188 ILE cc_start: 0.7672 (mm) cc_final: 0.7029 (tt) REVERT: G 69 MET cc_start: 0.8643 (ttp) cc_final: 0.8417 (ttm) REVERT: G 212 VAL cc_start: 0.8213 (t) cc_final: 0.7963 (t) REVERT: G 230 GLU cc_start: 0.7797 (pm20) cc_final: 0.7596 (pm20) REVERT: G 236 ILE cc_start: 0.8786 (tp) cc_final: 0.8542 (tp) REVERT: G 238 LYS cc_start: 0.8115 (ttpp) cc_final: 0.7863 (tttp) REVERT: H 16 TYR cc_start: 0.7627 (t80) cc_final: 0.7170 (t80) REVERT: H 17 GLU cc_start: 0.6428 (pm20) cc_final: 0.5767 (tt0) REVERT: J 787 ILE cc_start: 0.5917 (mp) cc_final: 0.5650 (mp) REVERT: J 902 LYS cc_start: 0.8196 (tptp) cc_final: 0.7926 (tppt) REVERT: J 1226 ARG cc_start: 0.7881 (mpp80) cc_final: 0.7519 (mtm180) REVERT: K 496 ILE cc_start: 0.9032 (mt) cc_final: 0.8825 (mm) outliers start: 18 outliers final: 9 residues processed: 434 average time/residue: 0.3435 time to fit residues: 230.2714 Evaluate side-chains 262 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 252 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 84 optimal weight: 0.0060 chunk 166 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 296 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 ASN C 20 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN G 243 ASN G 253 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN ** J 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1174 GLN J1272 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23369 Z= 0.222 Angle : 0.727 12.845 31823 Z= 0.391 Chirality : 0.047 0.247 3799 Planarity : 0.005 0.082 4159 Dihedral : 6.882 28.462 3449 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.30 % Favored : 87.42 % Rotamer: Outliers : 0.26 % Allowed : 8.52 % Favored : 91.22 % 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: -4.56 (0.13), residues: 3235 helix: -1.95 (0.14), residues: 1016 sheet: -2.59 (0.22), residues: 514 loop : -4.00 (0.12), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I1024 HIS 0.005 0.001 HIS J 621 PHE 0.031 0.002 PHE A 109 TYR 0.022 0.002 TYR J 648 ARG 0.004 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 342 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7976 (mm) cc_final: 0.7611 (mm) REVERT: A 131 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8329 (tmtt) REVERT: B 151 MET cc_start: 0.7342 (pmm) cc_final: 0.6414 (pmm) REVERT: C 11 LYS cc_start: 0.8688 (tmtt) cc_final: 0.8149 (mmmt) REVERT: D 4 TYR cc_start: 0.7960 (m-10) cc_final: 0.7749 (m-10) REVERT: D 36 GLN cc_start: 0.6626 (mp-120) cc_final: 0.6393 (mm-40) REVERT: E 191 MET cc_start: 0.7300 (mmm) cc_final: 0.6885 (mmm) REVERT: F 62 ASN cc_start: 0.8370 (t0) cc_final: 0.7735 (t0) REVERT: F 188 ILE cc_start: 0.7874 (mm) cc_final: 0.7154 (tt) REVERT: G 236 ILE cc_start: 0.8768 (tp) cc_final: 0.8516 (tp) REVERT: H 17 GLU cc_start: 0.6009 (pm20) cc_final: 0.5643 (tt0) REVERT: H 146 MET cc_start: 0.7488 (mmt) cc_final: 0.6865 (mmt) REVERT: I 838 CYS cc_start: 0.8098 (p) cc_final: 0.7615 (m) REVERT: J 745 ILE cc_start: 0.7301 (tt) cc_final: 0.7079 (tt) REVERT: J 1272 ASN cc_start: 0.7344 (OUTLIER) cc_final: 0.6412 (t0) REVERT: K 496 ILE cc_start: 0.8997 (mt) cc_final: 0.8710 (mm) outliers start: 5 outliers final: 0 residues processed: 345 average time/residue: 0.3631 time to fit residues: 196.3424 Evaluate side-chains 252 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 246 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 296 optimal weight: 0.0470 chunk 320 optimal weight: 0.7980 chunk 264 optimal weight: 0.0010 chunk 294 optimal weight: 0.8980 chunk 101 optimal weight: 0.0370 chunk 237 optimal weight: 1.9990 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 50 ASN C 62 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23369 Z= 0.178 Angle : 0.662 11.552 31823 Z= 0.350 Chirality : 0.046 0.199 3799 Planarity : 0.004 0.063 4159 Dihedral : 5.859 23.852 3449 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.53 % Favored : 88.25 % Rotamer: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % 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: -3.99 (0.13), residues: 3235 helix: -1.17 (0.15), residues: 1011 sheet: -2.23 (0.22), residues: 491 loop : -3.87 (0.12), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 7 HIS 0.006 0.001 HIS H 42 PHE 0.029 0.002 PHE B 184 TYR 0.014 0.001 TYR E 183 ARG 0.012 0.001 ARG J 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 358 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.2306 (tpp) cc_final: 0.2037 (tpp) REVERT: A 88 ILE cc_start: 0.8048 (mm) cc_final: 0.7821 (mm) REVERT: A 131 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8285 (tmtt) REVERT: C 11 LYS cc_start: 0.8547 (tmtt) cc_final: 0.8179 (mmmt) REVERT: C 59 MET cc_start: 0.6787 (ttt) cc_final: 0.6083 (ttm) REVERT: C 154 MET cc_start: 0.6394 (mmt) cc_final: 0.5568 (mmt) REVERT: D 4 TYR cc_start: 0.7951 (m-10) cc_final: 0.7680 (m-10) REVERT: D 135 GLN cc_start: 0.6464 (mp10) cc_final: 0.6233 (mp10) REVERT: E 191 MET cc_start: 0.7333 (mmm) cc_final: 0.6849 (mmm) REVERT: F 13 MET cc_start: 0.8578 (ppp) cc_final: 0.7699 (ppp) REVERT: F 188 ILE cc_start: 0.7776 (mm) cc_final: 0.7122 (tt) REVERT: G 62 MET cc_start: 0.7512 (tmm) cc_final: 0.7302 (tmm) REVERT: G 169 MET cc_start: 0.5511 (mpp) cc_final: 0.5144 (mpp) REVERT: G 204 GLU cc_start: 0.7749 (pt0) cc_final: 0.7534 (pt0) REVERT: I 838 CYS cc_start: 0.8194 (p) cc_final: 0.7922 (p) REVERT: J 1212 ASP cc_start: 0.8185 (m-30) cc_final: 0.7980 (m-30) REVERT: J 1226 ARG cc_start: 0.7776 (mpp80) cc_final: 0.7513 (mtm180) REVERT: J 1272 ASN cc_start: 0.7706 (p0) cc_final: 0.7094 (t0) outliers start: 2 outliers final: 0 residues processed: 360 average time/residue: 0.3289 time to fit residues: 186.0842 Evaluate side-chains 253 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 0.7980 chunk 222 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 297 optimal weight: 10.0000 chunk 315 optimal weight: 0.0020 chunk 155 optimal weight: 2.9990 chunk 282 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 HIS ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN J 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23369 Z= 0.208 Angle : 0.667 13.870 31823 Z= 0.352 Chirality : 0.047 0.310 3799 Planarity : 0.004 0.062 4159 Dihedral : 5.645 24.526 3449 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.99 % Favored : 87.79 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % 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: -3.68 (0.14), residues: 3235 helix: -0.68 (0.16), residues: 1002 sheet: -2.10 (0.22), residues: 501 loop : -3.83 (0.13), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP J 584 HIS 0.005 0.001 HIS K 490 PHE 0.020 0.002 PHE A 109 TYR 0.019 0.002 TYR A 46 ARG 0.004 0.000 ARG J 655 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.8196 (mm) cc_final: 0.7983 (mm) REVERT: A 90 PHE cc_start: 0.7823 (m-80) cc_final: 0.7366 (m-10) REVERT: A 131 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8246 (tmtt) REVERT: B 151 MET cc_start: 0.7278 (pmm) cc_final: 0.6305 (pmm) REVERT: C 11 LYS cc_start: 0.8485 (tmtt) cc_final: 0.8144 (mmmt) REVERT: C 154 MET cc_start: 0.6492 (mmt) cc_final: 0.5799 (mmt) REVERT: D 4 TYR cc_start: 0.7970 (m-10) cc_final: 0.7570 (m-10) REVERT: E 191 MET cc_start: 0.7518 (mmm) cc_final: 0.6693 (mmm) REVERT: F 13 MET cc_start: 0.8583 (ppp) cc_final: 0.6609 (mpp) REVERT: F 188 ILE cc_start: 0.7766 (mm) cc_final: 0.7132 (tt) REVERT: G 204 GLU cc_start: 0.7748 (pt0) cc_final: 0.7468 (pt0) REVERT: H 146 MET cc_start: 0.7618 (mmt) cc_final: 0.7001 (mmt) REVERT: I 799 LEU cc_start: 0.8570 (tt) cc_final: 0.7880 (mp) REVERT: I 838 CYS cc_start: 0.8341 (p) cc_final: 0.8062 (p) REVERT: J 1212 ASP cc_start: 0.8306 (m-30) cc_final: 0.8069 (m-30) REVERT: J 1272 ASN cc_start: 0.7614 (p0) cc_final: 0.7009 (t0) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.3087 time to fit residues: 164.5097 Evaluate side-chains 248 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 262 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 268 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 160 optimal weight: 0.0170 chunk 282 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23369 Z= 0.213 Angle : 0.661 12.950 31823 Z= 0.346 Chirality : 0.047 0.196 3799 Planarity : 0.004 0.057 4159 Dihedral : 5.489 23.526 3449 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.30 % Favored : 87.48 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: -3.48 (0.14), residues: 3235 helix: -0.40 (0.17), residues: 1007 sheet: -2.02 (0.23), residues: 480 loop : -3.77 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 584 HIS 0.005 0.001 HIS K 490 PHE 0.017 0.002 PHE C 115 TYR 0.019 0.002 TYR J 619 ARG 0.018 0.001 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8111 (tmtt) REVERT: B 159 PHE cc_start: 0.6584 (m-10) cc_final: 0.6374 (m-80) REVERT: B 207 GLU cc_start: 0.7000 (mp0) cc_final: 0.6511 (mm-30) REVERT: B 216 GLU cc_start: 0.7412 (tt0) cc_final: 0.7170 (tp30) REVERT: B 260 PHE cc_start: 0.8731 (m-80) cc_final: 0.8514 (m-10) REVERT: C 11 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8132 (mmmt) REVERT: C 154 MET cc_start: 0.6521 (mmt) cc_final: 0.5875 (mmt) REVERT: E 120 ARG cc_start: 0.7806 (tpp80) cc_final: 0.7523 (tpp80) REVERT: E 191 MET cc_start: 0.7538 (mmm) cc_final: 0.6534 (mmm) REVERT: F 188 ILE cc_start: 0.7746 (mm) cc_final: 0.7168 (tt) REVERT: G 62 MET cc_start: 0.7646 (tmm) cc_final: 0.7397 (tmm) REVERT: I 799 LEU cc_start: 0.8634 (tt) cc_final: 0.7929 (mp) REVERT: I 838 CYS cc_start: 0.8429 (p) cc_final: 0.8189 (p) REVERT: I 1024 TRP cc_start: 0.6577 (p-90) cc_final: 0.6087 (p-90) REVERT: J 563 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7952 (tm-30) REVERT: J 1212 ASP cc_start: 0.8322 (m-30) cc_final: 0.8110 (m-30) REVERT: J 1272 ASN cc_start: 0.7727 (p0) cc_final: 0.7087 (t0) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3164 time to fit residues: 170.8113 Evaluate side-chains 244 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 0.9990 chunk 283 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 315 optimal weight: 0.0270 chunk 261 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN J1205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23369 Z= 0.203 Angle : 0.653 12.483 31823 Z= 0.345 Chirality : 0.047 0.235 3799 Planarity : 0.004 0.061 4159 Dihedral : 5.379 22.949 3449 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.55 % Favored : 87.23 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -3.32 (0.14), residues: 3235 helix: -0.22 (0.17), residues: 998 sheet: -1.92 (0.23), residues: 478 loop : -3.69 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 584 HIS 0.006 0.001 HIS H 42 PHE 0.021 0.002 PHE J 757 TYR 0.022 0.002 TYR J 635 ARG 0.008 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7911 (m-80) cc_final: 0.7627 (m-10) REVERT: A 131 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8128 (tmtt) REVERT: B 151 MET cc_start: 0.7143 (pmm) cc_final: 0.6303 (pmm) REVERT: C 11 LYS cc_start: 0.8398 (tmtt) cc_final: 0.8006 (mmmt) REVERT: C 154 MET cc_start: 0.6588 (mmt) cc_final: 0.5916 (mmt) REVERT: D 4 TYR cc_start: 0.7951 (m-10) cc_final: 0.7496 (m-10) REVERT: E 120 ARG cc_start: 0.7760 (tpp80) cc_final: 0.7538 (tpp80) REVERT: F 13 MET cc_start: 0.8750 (ppp) cc_final: 0.8075 (ppp) REVERT: F 188 ILE cc_start: 0.7672 (mm) cc_final: 0.7126 (tt) REVERT: G 68 GLU cc_start: 0.6423 (tp30) cc_final: 0.5901 (tm-30) REVERT: G 272 ARG cc_start: 0.7538 (tpp80) cc_final: 0.7310 (tpp80) REVERT: G 276 ASP cc_start: 0.8738 (m-30) cc_final: 0.8519 (m-30) REVERT: I 799 LEU cc_start: 0.8621 (tt) cc_final: 0.8033 (mp) REVERT: I 1024 TRP cc_start: 0.6644 (p-90) cc_final: 0.6210 (p-90) REVERT: J 745 ILE cc_start: 0.7574 (tt) cc_final: 0.7372 (tt) REVERT: J 1212 ASP cc_start: 0.8291 (m-30) cc_final: 0.8058 (m-30) REVERT: J 1272 ASN cc_start: 0.7695 (p0) cc_final: 0.7083 (t0) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.3250 time to fit residues: 170.6930 Evaluate side-chains 252 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 179 optimal weight: 3.9990 chunk 230 optimal weight: 0.4980 chunk 178 optimal weight: 9.9990 chunk 265 optimal weight: 0.0970 chunk 176 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23369 Z= 0.258 Angle : 0.690 14.489 31823 Z= 0.364 Chirality : 0.047 0.257 3799 Planarity : 0.004 0.066 4159 Dihedral : 5.550 23.260 3449 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.34 % Favored : 85.44 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: -3.33 (0.14), residues: 3235 helix: -0.20 (0.17), residues: 999 sheet: -1.97 (0.23), residues: 489 loop : -3.70 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I1024 HIS 0.005 0.001 HIS H 42 PHE 0.021 0.002 PHE J1121 TYR 0.019 0.002 TYR J 607 ARG 0.005 0.000 ARG J 655 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7918 (m-80) cc_final: 0.7592 (m-10) REVERT: A 131 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8076 (tmtt) REVERT: B 150 GLU cc_start: 0.6520 (mp0) cc_final: 0.6231 (mm-30) REVERT: B 151 MET cc_start: 0.7222 (pmm) cc_final: 0.6243 (pmm) REVERT: C 11 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7941 (mmtm) REVERT: C 59 MET cc_start: 0.7012 (ttt) cc_final: 0.6491 (ttm) REVERT: C 154 MET cc_start: 0.6768 (mmt) cc_final: 0.6183 (mmt) REVERT: D 4 TYR cc_start: 0.8001 (m-10) cc_final: 0.7506 (m-10) REVERT: E 120 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7723 (tpp80) REVERT: F 175 GLU cc_start: 0.7172 (pt0) cc_final: 0.6931 (pt0) REVERT: F 188 ILE cc_start: 0.7822 (mm) cc_final: 0.7206 (tt) REVERT: G 62 MET cc_start: 0.7903 (tmm) cc_final: 0.7655 (tmm) REVERT: G 238 LYS cc_start: 0.8311 (ttpp) cc_final: 0.7961 (tttt) REVERT: G 272 ARG cc_start: 0.7506 (tpp80) cc_final: 0.7257 (tpp80) REVERT: H 130 MET cc_start: 0.8400 (ptm) cc_final: 0.8135 (ppp) REVERT: I 787 LEU cc_start: 0.9037 (tp) cc_final: 0.8805 (tp) REVERT: I 799 LEU cc_start: 0.8661 (tt) cc_final: 0.7955 (mp) REVERT: I 838 CYS cc_start: 0.8367 (p) cc_final: 0.8108 (p) REVERT: J 1212 ASP cc_start: 0.8366 (m-30) cc_final: 0.8141 (m-30) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.3457 time to fit residues: 178.4007 Evaluate side-chains 248 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 199 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN ** J 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23369 Z= 0.210 Angle : 0.663 13.839 31823 Z= 0.348 Chirality : 0.047 0.233 3799 Planarity : 0.004 0.055 4159 Dihedral : 5.408 23.421 3449 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.46 % Favored : 87.33 % Rotamer: Outliers : 0.05 % Allowed : 1.46 % Favored : 98.48 % 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: -3.21 (0.14), residues: 3235 helix: -0.09 (0.17), residues: 1009 sheet: -1.84 (0.23), residues: 473 loop : -3.67 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I1024 HIS 0.005 0.001 HIS H 42 PHE 0.022 0.002 PHE J 757 TYR 0.017 0.002 TYR B 191 ARG 0.011 0.000 ARG J 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 326 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7874 (m-80) cc_final: 0.7586 (m-10) REVERT: A 131 LYS cc_start: 0.8505 (mmmm) cc_final: 0.8024 (tmtt) REVERT: C 11 LYS cc_start: 0.8076 (tmtt) cc_final: 0.7765 (mmtm) REVERT: C 34 TYR cc_start: 0.6923 (t80) cc_final: 0.6624 (t80) REVERT: C 154 MET cc_start: 0.6734 (mmt) cc_final: 0.6078 (mmt) REVERT: D 4 TYR cc_start: 0.8032 (m-10) cc_final: 0.7582 (m-10) REVERT: E 120 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7648 (tpp80) REVERT: F 13 MET cc_start: 0.8645 (ppp) cc_final: 0.6326 (mpp) REVERT: G 62 MET cc_start: 0.7874 (tmm) cc_final: 0.7629 (tmm) REVERT: G 68 GLU cc_start: 0.6050 (tp30) cc_final: 0.5323 (tp30) REVERT: G 238 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7909 (tttm) REVERT: H 130 MET cc_start: 0.8361 (ptm) cc_final: 0.8054 (ppp) REVERT: I 799 LEU cc_start: 0.8742 (tt) cc_final: 0.8096 (mp) REVERT: I 838 CYS cc_start: 0.8356 (p) cc_final: 0.8093 (p) REVERT: J 470 LYS cc_start: 0.8093 (tmmt) cc_final: 0.7699 (ttpt) REVERT: J 745 ILE cc_start: 0.7253 (tt) cc_final: 0.7023 (tt) REVERT: J 1212 ASP cc_start: 0.8322 (m-30) cc_final: 0.8085 (m-30) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.3260 time to fit residues: 168.3141 Evaluate side-chains 246 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 0.7980 chunk 301 optimal weight: 20.0000 chunk 274 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 229 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 566 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23369 Z= 0.215 Angle : 0.677 13.765 31823 Z= 0.353 Chirality : 0.047 0.241 3799 Planarity : 0.004 0.062 4159 Dihedral : 5.357 23.001 3449 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.72 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -3.14 (0.14), residues: 3235 helix: -0.06 (0.17), residues: 1007 sheet: -1.84 (0.23), residues: 481 loop : -3.60 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I1024 HIS 0.006 0.001 HIS H 42 PHE 0.024 0.002 PHE I 784 TYR 0.023 0.002 TYR J1261 ARG 0.007 0.000 ARG J 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7956 (m-80) cc_final: 0.7653 (m-10) REVERT: A 131 LYS cc_start: 0.8389 (mmmm) cc_final: 0.7894 (tmtt) REVERT: B 122 ARG cc_start: 0.6084 (mmt180) cc_final: 0.5829 (mmt180) REVERT: C 11 LYS cc_start: 0.8147 (tmtt) cc_final: 0.7869 (mmtm) REVERT: C 34 TYR cc_start: 0.6952 (t80) cc_final: 0.6553 (t80) REVERT: C 154 MET cc_start: 0.6740 (mmt) cc_final: 0.6211 (mmt) REVERT: D 4 TYR cc_start: 0.8022 (m-10) cc_final: 0.7450 (m-80) REVERT: E 120 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7693 (tpp80) REVERT: F 13 MET cc_start: 0.8488 (ppp) cc_final: 0.6805 (mmt) REVERT: G 62 MET cc_start: 0.7772 (tmm) cc_final: 0.7533 (tmm) REVERT: G 276 ASP cc_start: 0.8725 (m-30) cc_final: 0.8522 (m-30) REVERT: H 16 TYR cc_start: 0.7297 (t80) cc_final: 0.7057 (t80) REVERT: H 139 GLU cc_start: 0.8236 (mp0) cc_final: 0.7805 (mp0) REVERT: I 787 LEU cc_start: 0.9056 (tp) cc_final: 0.8828 (tp) REVERT: I 799 LEU cc_start: 0.8709 (tt) cc_final: 0.8019 (mp) REVERT: I 838 CYS cc_start: 0.8327 (p) cc_final: 0.8028 (p) REVERT: J 597 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7837 (mppt) REVERT: J 745 ILE cc_start: 0.7243 (tt) cc_final: 0.6994 (tt) REVERT: J 1212 ASP cc_start: 0.8320 (m-30) cc_final: 0.8088 (m-30) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.3038 time to fit residues: 152.0352 Evaluate side-chains 241 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 324 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 551 HIS J 628 GLN ** J 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23369 Z= 0.360 Angle : 0.804 13.737 31823 Z= 0.425 Chirality : 0.051 0.258 3799 Planarity : 0.005 0.071 4159 Dihedral : 6.098 28.683 3449 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.32 % Favored : 83.46 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -3.47 (0.14), residues: 3235 helix: -0.40 (0.16), residues: 997 sheet: -1.99 (0.24), residues: 464 loop : -3.73 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP I1024 HIS 0.007 0.002 HIS J 621 PHE 0.027 0.003 PHE J1121 TYR 0.026 0.003 TYR J 635 ARG 0.008 0.001 ARG J 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7972 (m-80) cc_final: 0.7549 (m-10) REVERT: A 131 LYS cc_start: 0.8607 (mmmm) cc_final: 0.7924 (tmtt) REVERT: B 151 MET cc_start: 0.6976 (pmm) cc_final: 0.5702 (pmm) REVERT: B 175 ASN cc_start: 0.7063 (m-40) cc_final: 0.6810 (m-40) REVERT: C 154 MET cc_start: 0.6839 (mmt) cc_final: 0.6184 (mmt) REVERT: D 4 TYR cc_start: 0.7951 (m-10) cc_final: 0.7617 (m-10) REVERT: E 120 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7894 (tpp80) REVERT: F 70 ASP cc_start: 0.8061 (t70) cc_final: 0.7860 (t0) REVERT: F 175 GLU cc_start: 0.7329 (pt0) cc_final: 0.7071 (pt0) REVERT: H 16 TYR cc_start: 0.7444 (t80) cc_final: 0.7127 (t80) REVERT: H 130 MET cc_start: 0.8367 (ptm) cc_final: 0.8126 (ppp) REVERT: H 139 GLU cc_start: 0.8300 (mp0) cc_final: 0.7749 (mp0) REVERT: I 787 LEU cc_start: 0.9002 (tp) cc_final: 0.8763 (tp) REVERT: I 799 LEU cc_start: 0.8802 (tt) cc_final: 0.7964 (mp) REVERT: I 838 CYS cc_start: 0.8389 (p) cc_final: 0.8173 (p) REVERT: J 745 ILE cc_start: 0.7425 (tt) cc_final: 0.7204 (tt) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3178 time to fit residues: 146.1200 Evaluate side-chains 222 residues out of total 3056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 158 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 275 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 259 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 chunk 265 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.100193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.094721 restraints weight = 109613.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.094349 restraints weight = 157860.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.094696 restraints weight = 146276.955| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 105 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23369 Z= 0.215 Angle : 0.693 13.808 31823 Z= 0.362 Chirality : 0.048 0.228 3799 Planarity : 0.004 0.057 4159 Dihedral : 5.596 25.698 3449 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.92 % Favored : 86.86 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -3.24 (0.14), residues: 3235 helix: -0.17 (0.17), residues: 1000 sheet: -1.85 (0.23), residues: 480 loop : -3.63 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I1024 HIS 0.005 0.001 HIS H 42 PHE 0.028 0.002 PHE A 109 TYR 0.020 0.002 TYR J1261 ARG 0.007 0.000 ARG G 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4686.18 seconds wall clock time: 84 minutes 21.85 seconds (5061.85 seconds total)