Starting phenix.real_space_refine (version: dev) on Tue Apr 5 18:41:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/04_2022/6cxc_7774_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/04_2022/6cxc_7774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/04_2022/6cxc_7774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/04_2022/6cxc_7774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/04_2022/6cxc_7774_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/04_2022/6cxc_7774_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "X ARG 38": "NH1" <-> "NH2" Residue "X ARG 96": "NH1" <-> "NH2" Residue "Y ARG 132": "NH1" <-> "NH2" Residue "Y ARG 144": "NH1" <-> "NH2" Residue "Y ARG 152": "NH1" <-> "NH2" Residue "Y ARG 168": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 179": "NH1" <-> "NH2" Residue "Y ARG 222": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "J ARG 132": "NH1" <-> "NH2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 175": "NH1" <-> "NH2" Residue "J ARG 179": "NH1" <-> "NH2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "K ARG 132": "NH1" <-> "NH2" Residue "K ARG 144": "NH1" <-> "NH2" Residue "K ARG 152": "NH1" <-> "NH2" Residue "K ARG 168": "NH1" <-> "NH2" Residue "K ARG 175": "NH1" <-> "NH2" Residue "K ARG 179": "NH1" <-> "NH2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "B PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "F ARG 507": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 15196 Number of models: 1 Model: "" Number of chains: 18 Chain: "X" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Y" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 847 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 103, 'PCIS': 1} Chain: "G" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "J" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 847 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 103, 'PCIS': 1} Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 847 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 103, 'PCIS': 1} Chain: "A" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 580 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "B" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2765 Classifications: {'peptide': 358} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 345, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2733 Classifications: {'peptide': 352} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 339, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 580 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "F" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2726 Classifications: {'peptide': 351} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 338, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.76, per 1000 atoms: 0.58 Number of scatterers: 15196 At special positions: 0 Unit cell: (153.061, 139.261, 190.699, 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 84 16.00 O 2989 8.00 N 2541 7.00 C 9582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS X 20 " - pdb=" SG CYS X 94 " distance=2.04 Simple disulfide: pdb=" SG CYS G 20 " - pdb=" SG CYS G 94 " distance=2.04 Simple disulfide: pdb=" SG CYS I 20 " - pdb=" SG CYS I 94 " distance=2.04 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.04 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS D 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 322 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 358 " - pdb=" SG CYS D 367 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 393 " distance=2.03 Simple disulfide: pdb=" SG CYS D 416 " - pdb=" SG CYS D 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS F 439 " distance=2.03 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS F 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 322 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 367 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 393 " distance=2.03 Simple disulfide: pdb=" SG CYS F 416 " - pdb=" SG CYS F 422 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 70 " " NAG C 601 " - " ASN C 70 " " NAG E 601 " - " ASN E 70 " Time building additional restraints: 6.16 Conformation dependent library (CDL) restraints added in 2.4 seconds 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 34 sheets defined 27.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'X' and resid 85 through 89 Processing helix chain 'Y' and resid 164 through 166 No H-bonds generated for 'chain 'Y' and resid 164 through 166' Processing helix chain 'Y' and resid 193 through 197 removed outlier: 3.682A pdb=" N LEU Y 197 " --> pdb=" O SER Y 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 Processing helix chain 'J' and resid 164 through 166 No H-bonds generated for 'chain 'J' and resid 164 through 166' Processing helix chain 'J' and resid 193 through 197 removed outlier: 3.681A pdb=" N LEU J 197 " --> pdb=" O SER J 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 89 Processing helix chain 'K' and resid 164 through 166 No H-bonds generated for 'chain 'K' and resid 164 through 166' Processing helix chain 'K' and resid 193 through 197 removed outlier: 3.682A pdb=" N LEU K 197 " --> pdb=" O SER K 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.694A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 156 through 202 removed outlier: 3.752A pdb=" N GLY B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU B 163 " --> pdb=" O HIS B 159 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 4.416A pdb=" N ASN B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 209 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 5.002A pdb=" N GLU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 240 removed outlier: 3.815A pdb=" N ILE B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.534A pdb=" N LEU B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 4.090A pdb=" N LEU B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.695A pdb=" N VAL B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.533A pdb=" N VAL B 379 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 501 removed outlier: 3.627A pdb=" N ASN B 500 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 4.446A pdb=" N PHE B 505 " --> pdb=" O GLN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 514 Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.732A pdb=" N TYR C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 176 removed outlier: 3.720A pdb=" N SER D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 202 removed outlier: 3.942A pdb=" N SER D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 removed outlier: 4.054A pdb=" N ASN D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 removed outlier: 4.243A pdb=" N GLU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.692A pdb=" N ILE D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.571A pdb=" N LEU D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 removed outlier: 4.080A pdb=" N LEU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.633A pdb=" N VAL D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.571A pdb=" N VAL D 379 " --> pdb=" O PRO D 376 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D 380 " --> pdb=" O SER D 377 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN D 383 " --> pdb=" O ASN D 380 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 384 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 510 removed outlier: 3.902A pdb=" N ASN D 500 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 503 " --> pdb=" O ILE D 499 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 505 " --> pdb=" O GLN D 501 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 509 " --> pdb=" O PHE D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 514 Processing helix chain 'E' and resid 82 through 94 removed outlier: 3.731A pdb=" N TYR E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 92 " --> pdb=" O ASN E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'F' and resid 158 through 202 removed outlier: 3.723A pdb=" N GLY F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU F 163 " --> pdb=" O HIS F 159 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN F 183 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 185 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 190 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS F 201 " --> pdb=" O ASN F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 214 removed outlier: 4.037A pdb=" N ASN F 208 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS F 209 " --> pdb=" O PRO F 205 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 210 " --> pdb=" O ILE F 206 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS F 212 " --> pdb=" O ASN F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 227 removed outlier: 4.238A pdb=" N GLU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN F 227 " --> pdb=" O PHE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 240 removed outlier: 3.518A pdb=" N LEU F 231 " --> pdb=" O ASN F 227 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE F 237 " --> pdb=" O ILE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 removed outlier: 3.661A pdb=" N LEU F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET F 264 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 277 removed outlier: 4.109A pdb=" N LEU F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.631A pdb=" N VAL F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG F 282 " --> pdb=" O VAL F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.572A pdb=" N VAL F 379 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN F 380 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN F 383 " --> pdb=" O ASN F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 510 removed outlier: 3.889A pdb=" N ASN F 500 " --> pdb=" O ASN F 496 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 503 " --> pdb=" O ILE F 499 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE F 505 " --> pdb=" O GLN F 501 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER F 509 " --> pdb=" O PHE F 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 2 through 4 removed outlier: 3.687A pdb=" N CYS X 20 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA X 67 " --> pdb=" O GLN X 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 8 through 10 Processing sheet with id=AA3, first strand: chain 'X' and resid 42 through 49 removed outlier: 6.643A pdb=" N TRP X 34 " --> pdb=" O ILE X 46 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG X 48 " --> pdb=" O MET X 32 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET X 32 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL X 35 " --> pdb=" O PHE X 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN X 37 " --> pdb=" O VAL X 91 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL X 91 " --> pdb=" O GLN X 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 119 through 120 removed outlier: 3.611A pdb=" N CYS Y 137 " --> pdb=" O PHE Y 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 167 through 168 removed outlier: 6.546A pdb=" N TRP Y 149 " --> pdb=" O LEU Y 161 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR Y 163 " --> pdb=" O VAL Y 147 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL Y 147 " --> pdb=" O TYR Y 163 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER Y 148 " --> pdb=" O LEU Y 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE Y 201 " --> pdb=" O TYR Y 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 2 through 4 removed outlier: 3.686A pdb=" N CYS G 20 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 67 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 8 through 10 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 49 removed outlier: 6.643A pdb=" N TRP G 34 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG G 48 " --> pdb=" O MET G 32 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET G 32 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL G 35 " --> pdb=" O PHE G 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN G 37 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G 91 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 119 through 120 removed outlier: 3.612A pdb=" N CYS J 137 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 167 through 168 removed outlier: 6.545A pdb=" N TRP J 149 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR J 163 " --> pdb=" O VAL J 147 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL J 147 " --> pdb=" O TYR J 163 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER J 148 " --> pdb=" O LEU J 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE J 201 " --> pdb=" O TYR J 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 2 through 4 removed outlier: 3.687A pdb=" N CYS I 20 " --> pdb=" O ALA I 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA I 67 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 8 through 10 Processing sheet with id=AB4, first strand: chain 'I' and resid 42 through 49 removed outlier: 6.644A pdb=" N TRP I 34 " --> pdb=" O ILE I 46 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG I 48 " --> pdb=" O MET I 32 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET I 32 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL I 35 " --> pdb=" O PHE I 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN I 37 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL I 91 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 119 through 120 removed outlier: 3.611A pdb=" N CYS K 137 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 167 through 168 removed outlier: 6.545A pdb=" N TRP K 149 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N TYR K 163 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL K 147 " --> pdb=" O TYR K 163 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER K 148 " --> pdb=" O LEU K 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE K 201 " --> pdb=" O TYR K 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.720A pdb=" N VAL A 40 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 41 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 315 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 243 through 244 removed outlier: 5.469A pdb=" N SER B 287 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN B 302 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N MET B 289 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL B 300 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 297 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 59 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLY B 307 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG A 49 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 367 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 243 through 244 removed outlier: 5.469A pdb=" N SER B 287 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN B 302 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N MET B 289 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL B 300 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 297 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 59 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLY B 307 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG A 49 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL D 469 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AC2, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.907A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 430 through 434 removed outlier: 7.153A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 449 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 466 through 467 removed outlier: 6.595A pdb=" N LEU B 467 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA E 47 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE F 309 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ARG E 49 " --> pdb=" O GLY F 307 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLY F 307 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 59 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 297 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA F 298 " --> pdb=" O SER F 290 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 466 through 467 removed outlier: 6.595A pdb=" N LEU B 467 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS F 367 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 31 through 33 removed outlier: 3.730A pdb=" N VAL C 40 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 41 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS D 315 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 243 through 244 removed outlier: 3.597A pdb=" N SER D 287 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER D 287 " --> pdb=" O GLN D 302 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN D 302 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N MET D 289 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL D 300 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 297 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 59 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY D 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG C 49 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 47 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS D 367 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 243 through 244 removed outlier: 3.597A pdb=" N SER D 287 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER D 287 " --> pdb=" O GLN D 302 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN D 302 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N MET D 289 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL D 300 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 297 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 59 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY D 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG C 49 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 47 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 341 through 345 removed outlier: 3.519A pdb=" N TRP D 341 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 404 through 407 removed outlier: 3.758A pdb=" N SER D 404 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS D 416 " --> pdb=" O GLY D 438 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 430 through 434 removed outlier: 7.159A pdb=" N ALA D 424 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR D 434 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS D 422 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR D 449 " --> pdb=" O SER D 425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.742A pdb=" N VAL E 40 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR E 33 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER E 41 " --> pdb=" O LYS F 315 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS F 315 " --> pdb=" O SER E 41 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 341 through 345 removed outlier: 3.592A pdb=" N TRP F 341 " --> pdb=" O PHE F 352 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 404 through 407 removed outlier: 3.704A pdb=" N SER F 404 " --> pdb=" O SER F 415 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS F 416 " --> pdb=" O GLY F 438 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 430 through 434 removed outlier: 7.146A pdb=" N ALA F 424 " --> pdb=" O ILE F 432 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR F 434 " --> pdb=" O CYS F 422 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N CYS F 422 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR F 449 " --> pdb=" O SER F 425 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 6.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4819 1.34 - 1.46: 3582 1.46 - 1.59: 6936 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 15451 Sorted by residual: bond pdb=" C ASP D 310 " pdb=" N THR D 311 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.59e-02 3.96e+03 4.05e+00 bond pdb=" CB GLU D 236 " pdb=" CG GLU D 236 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" CG1 ILE D 233 " pdb=" CD1 ILE D 233 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.35e+00 bond pdb=" CB GLU B 236 " pdb=" CG GLU B 236 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CB GLU F 236 " pdb=" CG GLU F 236 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.19e+00 ... (remaining 15446 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.01: 218 105.01 - 112.27: 7985 112.27 - 119.54: 5146 119.54 - 126.81: 7419 126.81 - 134.07: 149 Bond angle restraints: 20917 Sorted by residual: angle pdb=" C ALA B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta sigma weight residual 120.77 128.68 -7.91 1.31e+00 5.83e-01 3.65e+01 angle pdb=" N ASP B 401 " pdb=" CA ASP B 401 " pdb=" C ASP B 401 " ideal model delta sigma weight residual 107.93 115.36 -7.43 1.65e+00 3.67e-01 2.03e+01 angle pdb=" N THR B 267 " pdb=" CA THR B 267 " pdb=" C THR B 267 " ideal model delta sigma weight residual 110.43 116.07 -5.64 1.31e+00 5.83e-01 1.85e+01 angle pdb=" N LYS F 399 " pdb=" CA LYS F 399 " pdb=" C LYS F 399 " ideal model delta sigma weight residual 113.18 107.60 5.58 1.33e+00 5.65e-01 1.76e+01 angle pdb=" N LYS D 399 " pdb=" CA LYS D 399 " pdb=" C LYS D 399 " ideal model delta sigma weight residual 113.18 107.61 5.57 1.33e+00 5.65e-01 1.75e+01 ... (remaining 20912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.67: 9049 20.67 - 41.34: 299 41.34 - 62.01: 45 62.01 - 82.68: 9 82.68 - 103.34: 2 Dihedral angle restraints: 9404 sinusoidal: 3739 harmonic: 5665 Sorted by residual: dihedral pdb=" CA ASP B 401 " pdb=" C ASP B 401 " pdb=" N VAL B 402 " pdb=" CA VAL B 402 " ideal model delta harmonic sigma weight residual 180.00 138.46 41.54 0 5.00e+00 4.00e-02 6.90e+01 dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 393 " pdb=" CB CYS B 393 " ideal model delta sinusoidal sigma weight residual -86.00 -148.95 62.95 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -139.14 53.14 1 1.00e+01 1.00e-02 3.84e+01 ... (remaining 9401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 2439 0.153 - 0.306: 12 0.306 - 0.459: 0 0.459 - 0.612: 0 0.612 - 0.764: 3 Chirality restraints: 2454 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 70 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 70 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 70 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 2451 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 401 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ASP B 401 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP B 401 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 402 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 264 " -0.035 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO B 265 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 264 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO D 265 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.029 5.00e-02 4.00e+02 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1551 2.74 - 3.28: 14514 3.28 - 3.82: 25191 3.82 - 4.36: 28952 4.36 - 4.90: 48518 Nonbonded interactions: 118726 Sorted by model distance: nonbonded pdb=" O VAL D 482 " pdb=" OH TYR F 198 " model vdw 2.198 2.440 nonbonded pdb=" O ILE B 499 " pdb=" OG SER B 502 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR B 198 " pdb=" O VAL F 482 " model vdw 2.249 2.440 nonbonded pdb=" O VAL B 482 " pdb=" OH TYR D 198 " model vdw 2.253 2.440 nonbonded pdb=" O VAL F 187 " pdb=" OG SER F 190 " model vdw 2.259 2.440 ... (remaining 118721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 97 or resid 601)) selection = chain 'C' selection = (chain 'E' and (resid 26 through 97 or resid 601)) } ncs_group { reference = (chain 'B' and (resid 155 through 514 or resid 800)) selection = (chain 'D' and (resid 155 through 322 or resid 333 through 514 or resid 800)) selection = (chain 'F' and (resid 155 through 322 or resid 333 through 514 or resid 800)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9582 2.51 5 N 2541 2.21 5 O 2989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.050 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.140 Process input model: 42.050 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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 : 0.006 0.060 15451 Z= 0.414 Angle : 1.024 12.686 20917 Z= 0.588 Chirality : 0.060 0.764 2454 Planarity : 0.006 0.054 2631 Dihedral : 10.947 103.344 5681 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.06 (0.15), residues: 1915 helix: -3.46 (0.15), residues: 418 sheet: -2.14 (0.20), residues: 469 loop : -2.62 (0.17), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 649 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 650 average time/residue: 0.3229 time to fit residues: 286.7754 Evaluate side-chains 303 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 0.0870 chunk 171 optimal weight: 6.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 80 GLN Y 141 GLN Y 169 HIS ** Y 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 205 HIS J 167 ASN J 169 HIS ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS A 67 ASN A 98 GLN B 159 HIS ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 371 ASN B 496 ASN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN D 496 ASN F 159 HIS ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 ASN F 268 ASN F 496 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 15451 Z= 0.209 Angle : 0.728 10.981 20917 Z= 0.379 Chirality : 0.049 0.573 2454 Planarity : 0.005 0.042 2631 Dihedral : 7.062 103.584 2098 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.17), residues: 1915 helix: -2.34 (0.19), residues: 459 sheet: -1.65 (0.22), residues: 484 loop : -2.25 (0.17), residues: 972 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 372 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 23 residues processed: 407 average time/residue: 0.2797 time to fit residues: 165.0080 Evaluate side-chains 307 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1331 time to fit residues: 8.3574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 81 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN B 501 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN D 500 ASN D 501 GLN E 81 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN F 501 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 15451 Z= 0.279 Angle : 0.730 10.891 20917 Z= 0.380 Chirality : 0.048 0.523 2454 Planarity : 0.005 0.076 2631 Dihedral : 6.908 103.794 2098 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.17), residues: 1915 helix: -1.58 (0.22), residues: 461 sheet: -1.18 (0.23), residues: 473 loop : -2.29 (0.17), residues: 981 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 304 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 31 residues processed: 341 average time/residue: 0.2556 time to fit residues: 129.9834 Evaluate side-chains 295 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 264 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1438 time to fit residues: 10.6097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN ** F 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 15451 Z= 0.469 Angle : 0.905 11.748 20917 Z= 0.477 Chirality : 0.052 0.525 2454 Planarity : 0.006 0.075 2631 Dihedral : 7.715 105.764 2098 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 32.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 4.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.08 (0.17), residues: 1915 helix: -1.58 (0.22), residues: 457 sheet: -1.56 (0.23), residues: 506 loop : -2.55 (0.17), residues: 952 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 248 time to evaluate : 1.809 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 outliers start: 71 outliers final: 44 residues processed: 295 average time/residue: 0.2561 time to fit residues: 113.1664 Evaluate side-chains 263 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 1.971 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1390 time to fit residues: 13.7856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 163 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN B 183 ASN B 371 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN ** F 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 15451 Z= 0.200 Angle : 0.722 11.413 20917 Z= 0.363 Chirality : 0.048 0.524 2454 Planarity : 0.004 0.045 2631 Dihedral : 6.803 105.725 2098 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.18), residues: 1915 helix: -1.32 (0.22), residues: 468 sheet: -1.23 (0.22), residues: 505 loop : -2.22 (0.18), residues: 942 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 280 time to evaluate : 2.097 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 outliers start: 24 outliers final: 8 residues processed: 296 average time/residue: 0.2594 time to fit residues: 114.3070 Evaluate side-chains 252 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 244 time to evaluate : 2.060 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1227 time to fit residues: 4.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 122 GLN ** Y 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 ASN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 15451 Z= 0.184 Angle : 0.691 13.627 20917 Z= 0.346 Chirality : 0.047 0.505 2454 Planarity : 0.004 0.044 2631 Dihedral : 6.397 104.657 2098 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.18), residues: 1915 helix: -0.88 (0.23), residues: 459 sheet: -1.26 (0.22), residues: 531 loop : -1.96 (0.19), residues: 925 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 285 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 303 average time/residue: 0.2655 time to fit residues: 119.9751 Evaluate side-chains 262 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 246 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1367 time to fit residues: 6.5951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15451 Z= 0.175 Angle : 0.694 11.599 20917 Z= 0.345 Chirality : 0.047 0.499 2454 Planarity : 0.004 0.057 2631 Dihedral : 6.194 104.290 2098 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.18), residues: 1915 helix: -0.91 (0.23), residues: 462 sheet: -1.29 (0.22), residues: 522 loop : -1.79 (0.19), residues: 931 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 284 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 292 average time/residue: 0.2608 time to fit residues: 113.7318 Evaluate side-chains 257 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1503 time to fit residues: 3.9207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 30.0000 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 ASN ** F 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.7112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 15451 Z= 0.450 Angle : 0.888 11.917 20917 Z= 0.461 Chirality : 0.051 0.521 2454 Planarity : 0.005 0.068 2631 Dihedral : 7.247 105.829 2098 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 32.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.18), residues: 1915 helix: -1.29 (0.22), residues: 461 sheet: -1.42 (0.23), residues: 504 loop : -2.18 (0.18), residues: 950 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 2.101 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 outliers start: 38 outliers final: 19 residues processed: 255 average time/residue: 0.2425 time to fit residues: 95.6995 Evaluate side-chains 238 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1357 time to fit residues: 7.3259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 160 optimal weight: 0.4980 chunk 111 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15451 Z= 0.183 Angle : 0.739 13.409 20917 Z= 0.362 Chirality : 0.048 0.516 2454 Planarity : 0.004 0.049 2631 Dihedral : 6.436 105.627 2098 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.18), residues: 1915 helix: -0.94 (0.23), residues: 455 sheet: -1.36 (0.23), residues: 486 loop : -1.92 (0.19), residues: 974 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 261 time to evaluate : 2.241 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 outliers start: 14 outliers final: 6 residues processed: 270 average time/residue: 0.2616 time to fit residues: 106.4679 Evaluate side-chains 241 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 1.909 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1422 time to fit residues: 4.2524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** F 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 15451 Z= 0.258 Angle : 0.754 12.515 20917 Z= 0.379 Chirality : 0.048 0.499 2454 Planarity : 0.005 0.133 2631 Dihedral : 6.589 105.231 2098 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.18), residues: 1915 helix: -0.98 (0.23), residues: 461 sheet: -1.34 (0.22), residues: 503 loop : -1.99 (0.19), residues: 951 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 243 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 248 average time/residue: 0.2670 time to fit residues: 99.2811 Evaluate side-chains 238 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 2.134 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1458 time to fit residues: 3.4394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 22 optimal weight: 0.0570 chunk 41 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 2.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 501 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 = 0.3764 r_free = 0.3764 target = 0.070291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.060991 restraints weight = 98059.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.062287 restraints weight = 57084.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.063129 restraints weight = 38218.409| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.7367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 15451 Z= 0.218 Angle : 0.739 13.601 20917 Z= 0.367 Chirality : 0.047 0.492 2454 Planarity : 0.005 0.128 2631 Dihedral : 6.451 105.440 2098 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.18), residues: 1915 helix: -0.86 (0.24), residues: 455 sheet: -1.34 (0.23), residues: 485 loop : -1.97 (0.19), residues: 975 =============================================================================== Job complete usr+sys time: 3102.90 seconds wall clock time: 58 minutes 17.26 seconds (3497.26 seconds total)