Starting phenix.real_space_refine on Fri Sep 27 07:11:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/09_2024/6cxc_7774_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/09_2024/6cxc_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_7774/09_2024/6cxc_7774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/09_2024/6cxc_7774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/09_2024/6cxc_7774_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/09_2024/6cxc_7774_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} 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: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} 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: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} 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: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 345} 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: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 339} 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: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 338} 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.15, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 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: 3.75 Conformation dependent library (CDL) restraints added in 2.1 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: 2.22 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: 4.88 Time building geometry restraints manager: 4.37 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=" C1 NAG B 800 " pdb=" O5 NAG B 800 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+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=" C1 NAG F 800 " pdb=" O5 NAG F 800 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+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 ... (remaining 15446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 20267 2.54 - 5.07: 591 5.07 - 7.61: 49 7.61 - 10.15: 7 10.15 - 12.69: 3 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 - 21.29: 9122 21.29 - 42.58: 316 42.58 - 63.86: 40 63.86 - 85.15: 8 85.15 - 106.44: 8 Dihedral angle restraints: 9494 sinusoidal: 3829 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 9491 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 3.040 nonbonded pdb=" O ILE B 499 " pdb=" OG SER B 502 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 198 " pdb=" O VAL F 482 " model vdw 2.249 3.040 nonbonded pdb=" O VAL B 482 " pdb=" OH TYR D 198 " model vdw 2.253 3.040 nonbonded pdb=" O VAL F 187 " pdb=" OG SER F 190 " model vdw 2.259 3.040 ... (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 Time spend for trying shortcut: 0.00 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 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: 0.790 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 36.060 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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= 0.418 Angle : 1.028 12.686 20917 Z= 0.588 Chirality : 0.060 0.764 2454 Planarity : 0.006 0.054 2631 Dihedral : 11.599 106.438 5771 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 % Allowed : 4.94 % Favored : 94.77 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP Y 206 HIS 0.006 0.002 HIS Y 169 PHE 0.018 0.003 PHE G 103 TYR 0.032 0.003 TYR F 250 ARG 0.012 0.002 ARG B 282 *********************** 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 : 1.831 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 REVERT: Y 200 TYR cc_start: 0.7843 (m-80) cc_final: 0.6648 (m-10) REVERT: Y 216 THR cc_start: 0.6778 (m) cc_final: 0.6169 (m) REVERT: Y 218 LEU cc_start: 0.8141 (mp) cc_final: 0.7925 (mp) REVERT: J 200 TYR cc_start: 0.7868 (m-80) cc_final: 0.6118 (m-80) REVERT: J 202 CYS cc_start: 0.5799 (t) cc_final: 0.5483 (t) REVERT: J 216 THR cc_start: 0.6877 (m) cc_final: 0.6611 (m) REVERT: J 218 LEU cc_start: 0.8271 (mp) cc_final: 0.7490 (mp) REVERT: I 19 SER cc_start: 0.7740 (m) cc_final: 0.7479 (p) REVERT: K 200 TYR cc_start: 0.8298 (m-80) cc_final: 0.7070 (m-10) REVERT: K 218 LEU cc_start: 0.8489 (mp) cc_final: 0.8077 (mp) REVERT: A 33 TYR cc_start: 0.6997 (m-80) cc_final: 0.6736 (m-80) REVERT: B 171 LEU cc_start: 0.8833 (tt) cc_final: 0.8623 (tt) REVERT: B 410 LEU cc_start: 0.7513 (pt) cc_final: 0.6702 (pt) REVERT: C 45 LEU cc_start: 0.8319 (pt) cc_final: 0.7887 (pt) REVERT: C 85 LYS cc_start: 0.8846 (tmmt) cc_final: 0.8181 (tttt) REVERT: D 505 PHE cc_start: 0.8304 (m-80) cc_final: 0.8069 (m-80) REVERT: E 85 LYS cc_start: 0.8943 (tmmt) cc_final: 0.8146 (ttpp) REVERT: E 88 ASN cc_start: 0.7669 (m110) cc_final: 0.7396 (m110) REVERT: F 171 LEU cc_start: 0.8836 (tt) cc_final: 0.8499 (tt) REVERT: F 280 ILE cc_start: 0.8224 (mm) cc_final: 0.7773 (mm) outliers start: 5 outliers final: 0 residues processed: 650 average time/residue: 0.3280 time to fit residues: 290.7728 Evaluate side-chains 306 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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: 0.9980 chunk 143 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 80 GLN X 99 ASN 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 205 HIS ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS K 205 HIS A 67 ASN A 98 GLN B 159 HIS B 268 ASN B 496 ASN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 ASN F 159 HIS ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 ASN F 268 ASN F 494 GLN F 496 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15451 Z= 0.207 Angle : 0.748 11.376 20917 Z= 0.388 Chirality : 0.048 0.484 2454 Planarity : 0.005 0.043 2631 Dihedral : 7.811 71.235 2188 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.99 % Allowed : 17.36 % Favored : 79.66 % 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: -3.22 (0.17), residues: 1915 helix: -2.34 (0.19), residues: 457 sheet: -1.68 (0.22), residues: 490 loop : -2.24 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 149 HIS 0.004 0.001 HIS J 205 PHE 0.022 0.002 PHE B 505 TYR 0.026 0.002 TYR B 391 ARG 0.010 0.001 ARG I 96 *********************** 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 428 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 376 time to evaluate : 1.720 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: Y 200 TYR cc_start: 0.6978 (m-80) cc_final: 0.6046 (m-80) REVERT: Y 205 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7451 (t70) REVERT: J 144 ARG cc_start: 0.6811 (mpt90) cc_final: 0.6412 (mmt180) REVERT: I 25 TYR cc_start: 0.6539 (t80) cc_final: 0.6315 (t80) REVERT: K 200 TYR cc_start: 0.7183 (m-80) cc_final: 0.6331 (m-80) REVERT: K 205 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7658 (t70) REVERT: B 280 ILE cc_start: 0.7928 (mm) cc_final: 0.7727 (mt) REVERT: B 400 THR cc_start: 0.6915 (OUTLIER) cc_final: 0.6622 (p) REVERT: C 82 GLU cc_start: 0.6806 (tp30) cc_final: 0.6286 (tp30) REVERT: E 82 GLU cc_start: 0.6970 (tp30) cc_final: 0.6385 (tp30) REVERT: F 280 ILE cc_start: 0.8420 (mm) cc_final: 0.8130 (mt) REVERT: F 289 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6415 (ttp) REVERT: F 486 ASP cc_start: 0.6604 (p0) cc_final: 0.6277 (p0) outliers start: 52 outliers final: 17 residues processed: 410 average time/residue: 0.2812 time to fit residues: 165.3855 Evaluate side-chains 306 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 285 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 99 ASN Y 122 GLN Y 205 HIS K 141 GLN K 167 ASN K 205 HIS A 67 ASN A 81 GLN B 183 ASN B 462 GLN B 501 GLN D 284 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN F 183 ASN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5087 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= 0.270 Angle : 0.746 12.019 20917 Z= 0.386 Chirality : 0.048 0.477 2454 Planarity : 0.005 0.063 2631 Dihedral : 6.882 56.929 2188 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.74 % Allowed : 19.14 % Favored : 77.13 % 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: -2.83 (0.17), residues: 1915 helix: -1.69 (0.22), residues: 461 sheet: -1.17 (0.24), residues: 452 loop : -2.32 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 34 HIS 0.008 0.001 HIS J 205 PHE 0.015 0.002 PHE G 103 TYR 0.018 0.002 TYR B 391 ARG 0.004 0.001 ARG G 96 *********************** 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 365 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 300 time to evaluate : 1.757 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: Y 185 PHE cc_start: 0.6107 (m-80) cc_final: 0.5815 (m-10) REVERT: Y 200 TYR cc_start: 0.7320 (m-80) cc_final: 0.6530 (m-80) REVERT: Y 205 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.7159 (t70) REVERT: G 49 LEU cc_start: 0.6736 (tp) cc_final: 0.6475 (tp) REVERT: J 162 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8590 (tp) REVERT: I 68 LEU cc_start: 0.8169 (tp) cc_final: 0.7929 (tp) REVERT: K 153 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.6914 (mtmm) REVERT: K 200 TYR cc_start: 0.7635 (m-80) cc_final: 0.6972 (m-80) REVERT: B 289 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6482 (ptt) REVERT: B 400 THR cc_start: 0.6800 (OUTLIER) cc_final: 0.6459 (p) REVERT: E 30 GLU cc_start: 0.8000 (pt0) cc_final: 0.7672 (tt0) REVERT: F 250 TYR cc_start: 0.6897 (m-10) cc_final: 0.6543 (m-10) REVERT: F 391 TYR cc_start: 0.4693 (t80) cc_final: 0.4423 (t80) outliers start: 65 outliers final: 42 residues processed: 345 average time/residue: 0.2573 time to fit residues: 130.8094 Evaluate side-chains 309 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 262 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 167 ASN Y 205 HIS J 167 ASN J 205 HIS K 205 HIS A 67 ASN B 202 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15451 Z= 0.254 Angle : 0.737 12.249 20917 Z= 0.376 Chirality : 0.047 0.466 2454 Planarity : 0.004 0.044 2631 Dihedral : 6.440 53.572 2188 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.43 % Allowed : 19.31 % Favored : 76.26 % 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: -2.66 (0.17), residues: 1915 helix: -1.43 (0.22), residues: 460 sheet: -1.24 (0.23), residues: 481 loop : -2.20 (0.17), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 104 HIS 0.010 0.001 HIS Y 205 PHE 0.032 0.002 PHE I 103 TYR 0.015 0.002 TYR Y 150 ARG 0.005 0.001 ARG B 429 *********************** 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 358 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 281 time to evaluate : 1.916 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: Y 159 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8229 (mmpt) REVERT: Y 185 PHE cc_start: 0.6438 (m-80) cc_final: 0.6021 (m-10) REVERT: Y 200 TYR cc_start: 0.7130 (m-80) cc_final: 0.6460 (m-80) REVERT: J 162 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8524 (tp) REVERT: K 149 TRP cc_start: 0.6466 (m100) cc_final: 0.5572 (m-10) REVERT: K 151 GLN cc_start: 0.7155 (pp30) cc_final: 0.6755 (pm20) REVERT: K 159 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8426 (mmmt) REVERT: K 200 TYR cc_start: 0.7643 (m-80) cc_final: 0.7051 (m-80) REVERT: K 205 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7919 (t70) REVERT: B 400 THR cc_start: 0.6678 (OUTLIER) cc_final: 0.6410 (p) REVERT: D 410 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.6878 (tp) REVERT: F 250 TYR cc_start: 0.6987 (m-10) cc_final: 0.6720 (m-10) REVERT: F 264 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7354 (mmm) REVERT: F 289 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6827 (ptt) REVERT: F 391 TYR cc_start: 0.4809 (t80) cc_final: 0.4428 (t80) outliers start: 77 outliers final: 51 residues processed: 336 average time/residue: 0.2659 time to fit residues: 135.9471 Evaluate side-chains 311 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 253 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 126 optimal weight: 0.0870 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 0.4980 chunk 163 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 overall best weight: 3.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 205 HIS ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 ASN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15451 Z= 0.288 Angle : 0.748 10.989 20917 Z= 0.384 Chirality : 0.048 0.461 2454 Planarity : 0.004 0.041 2631 Dihedral : 6.366 54.290 2188 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.29 % Allowed : 20.23 % Favored : 74.48 % 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: -2.60 (0.18), residues: 1915 helix: -1.22 (0.22), residues: 455 sheet: -1.31 (0.23), residues: 496 loop : -2.19 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP G 104 HIS 0.012 0.002 HIS J 205 PHE 0.032 0.002 PHE G 103 TYR 0.018 0.002 TYR K 150 ARG 0.003 0.001 ARG D 336 *********************** 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 353 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 261 time to evaluate : 1.753 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: Y 159 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8532 (mmtt) REVERT: Y 185 PHE cc_start: 0.6819 (m-80) cc_final: 0.6499 (m-10) REVERT: Y 200 TYR cc_start: 0.6851 (m-80) cc_final: 0.6122 (m-80) REVERT: Y 205 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7511 (t70) REVERT: G 49 LEU cc_start: 0.6985 (tp) cc_final: 0.6738 (tp) REVERT: J 162 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8632 (tp) REVERT: I 53 ASP cc_start: 0.7003 (p0) cc_final: 0.6703 (p0) REVERT: I 84 LEU cc_start: 0.4477 (mm) cc_final: 0.4034 (mm) REVERT: K 200 TYR cc_start: 0.7354 (m-80) cc_final: 0.6465 (m-80) REVERT: K 205 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7750 (t-170) REVERT: A 68 LYS cc_start: 0.7362 (mmpt) cc_final: 0.7009 (mttm) REVERT: B 173 SER cc_start: 0.9310 (m) cc_final: 0.9046 (p) REVERT: B 289 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6637 (ptt) REVERT: B 400 THR cc_start: 0.6879 (OUTLIER) cc_final: 0.6575 (p) REVERT: B 408 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7685 (p) REVERT: B 410 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7866 (mt) REVERT: C 82 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: D 410 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7169 (tp) REVERT: F 250 TYR cc_start: 0.6987 (m-10) cc_final: 0.6598 (m-10) REVERT: F 264 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7549 (mmm) outliers start: 92 outliers final: 62 residues processed: 327 average time/residue: 0.2494 time to fit residues: 122.6089 Evaluate side-chains 322 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 250 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 111 THR Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 205 HIS K 205 HIS B 228 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15451 Z= 0.232 Angle : 0.721 12.414 20917 Z= 0.365 Chirality : 0.047 0.461 2454 Planarity : 0.004 0.036 2631 Dihedral : 6.041 53.557 2188 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.66 % Allowed : 21.32 % Favored : 74.02 % 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: -2.53 (0.18), residues: 1915 helix: -1.13 (0.22), residues: 462 sheet: -1.27 (0.23), residues: 496 loop : -2.18 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 104 HIS 0.011 0.001 HIS J 205 PHE 0.024 0.002 PHE G 103 TYR 0.016 0.002 TYR J 210 ARG 0.006 0.001 ARG F 336 *********************** 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 342 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 261 time to evaluate : 1.791 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: Y 159 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8491 (mmtt) REVERT: Y 185 PHE cc_start: 0.6885 (m-80) cc_final: 0.6521 (m-80) REVERT: Y 205 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7433 (t70) REVERT: J 162 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8604 (tp) REVERT: I 53 ASP cc_start: 0.7178 (p0) cc_final: 0.6904 (p0) REVERT: K 159 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8506 (mmmt) REVERT: K 203 LEU cc_start: 0.7650 (tp) cc_final: 0.7422 (tp) REVERT: K 205 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7575 (t70) REVERT: A 58 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7953 (m) REVERT: A 68 LYS cc_start: 0.7438 (mmpt) cc_final: 0.7028 (mttm) REVERT: B 173 SER cc_start: 0.9287 (m) cc_final: 0.9053 (p) REVERT: B 289 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6707 (ptt) REVERT: B 400 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6595 (p) REVERT: B 408 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7693 (p) REVERT: C 58 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7800 (m) REVERT: D 408 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7428 (p) REVERT: F 250 TYR cc_start: 0.7044 (m-10) cc_final: 0.6691 (m-10) outliers start: 81 outliers final: 59 residues processed: 319 average time/residue: 0.2418 time to fit residues: 116.4959 Evaluate side-chains 306 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 237 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 147 VAL Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 0.0050 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 205 HIS ** K 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15451 Z= 0.214 Angle : 0.718 16.135 20917 Z= 0.360 Chirality : 0.047 0.461 2454 Planarity : 0.004 0.036 2631 Dihedral : 5.877 53.472 2188 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.00 % Allowed : 22.18 % Favored : 72.82 % 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: -2.42 (0.18), residues: 1915 helix: -0.96 (0.23), residues: 456 sheet: -1.20 (0.23), residues: 482 loop : -2.15 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP G 104 HIS 0.010 0.001 HIS K 205 PHE 0.028 0.002 PHE X 103 TYR 0.024 0.002 TYR G 78 ARG 0.004 0.000 ARG G 48 *********************** 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 355 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 268 time to evaluate : 1.903 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: Y 159 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8547 (mmtt) REVERT: Y 185 PHE cc_start: 0.6927 (m-80) cc_final: 0.6572 (m-80) REVERT: Y 205 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7379 (t70) REVERT: J 159 LYS cc_start: 0.9176 (mttt) cc_final: 0.8959 (mptt) REVERT: J 205 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.7655 (m90) REVERT: I 53 ASP cc_start: 0.7179 (p0) cc_final: 0.6848 (p0) REVERT: I 104 TRP cc_start: 0.6909 (m100) cc_final: 0.6655 (m-90) REVERT: A 68 LYS cc_start: 0.7481 (mmpt) cc_final: 0.6994 (mttm) REVERT: B 173 SER cc_start: 0.9283 (m) cc_final: 0.9040 (p) REVERT: B 289 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6673 (ptt) REVERT: B 408 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7720 (p) REVERT: B 410 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7215 (tp) REVERT: C 58 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7821 (m) REVERT: C 82 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: D 408 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7389 (p) REVERT: D 410 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7280 (tp) REVERT: F 171 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9122 (tt) REVERT: F 218 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: F 250 TYR cc_start: 0.7049 (m-10) cc_final: 0.6766 (m-80) outliers start: 87 outliers final: 60 residues processed: 332 average time/residue: 0.2434 time to fit residues: 122.0762 Evaluate side-chains 315 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 244 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 32 MET Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 147 VAL Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 202 CYS Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 205 HIS K 151 GLN K 205 HIS F 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15451 Z= 0.336 Angle : 0.809 15.972 20917 Z= 0.415 Chirality : 0.049 0.453 2454 Planarity : 0.004 0.041 2631 Dihedral : 6.504 54.537 2188 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 5.46 % Allowed : 22.59 % Favored : 71.95 % 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: -2.60 (0.18), residues: 1915 helix: -1.15 (0.23), residues: 453 sheet: -0.97 (0.24), residues: 443 loop : -2.40 (0.17), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP G 104 HIS 0.015 0.002 HIS J 205 PHE 0.022 0.002 PHE K 212 TYR 0.019 0.003 TYR A 86 ARG 0.004 0.001 ARG G 48 *********************** 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 331 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 236 time to evaluate : 1.964 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: X 53 ASP cc_start: 0.7236 (p0) cc_final: 0.6658 (t0) REVERT: Y 159 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8571 (mmtt) REVERT: Y 205 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7449 (t70) REVERT: A 68 LYS cc_start: 0.7625 (mmpt) cc_final: 0.7004 (mttm) REVERT: B 173 SER cc_start: 0.9296 (m) cc_final: 0.8998 (t) REVERT: B 226 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.7848 (pttt) REVERT: B 289 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6436 (ptt) REVERT: B 410 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7346 (tp) REVERT: C 58 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7796 (m) REVERT: C 82 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: D 408 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7528 (p) REVERT: D 410 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7383 (tp) REVERT: F 171 LEU cc_start: 0.9331 (mm) cc_final: 0.9036 (tt) REVERT: F 218 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: F 250 TYR cc_start: 0.7016 (m-10) cc_final: 0.6724 (m-80) outliers start: 95 outliers final: 69 residues processed: 302 average time/residue: 0.2437 time to fit residues: 111.7193 Evaluate side-chains 305 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 227 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 32 MET Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 147 VAL Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 202 CYS Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 163 TYR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 505 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 169 optimal weight: 0.0870 chunk 102 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 179 optimal weight: 0.2980 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 205 HIS K 151 GLN ** K 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15451 Z= 0.190 Angle : 0.744 17.038 20917 Z= 0.366 Chirality : 0.048 0.465 2454 Planarity : 0.003 0.045 2631 Dihedral : 5.807 52.617 2188 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.74 % Allowed : 24.71 % Favored : 71.55 % 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: -2.45 (0.18), residues: 1915 helix: -1.03 (0.23), residues: 456 sheet: -1.16 (0.23), residues: 477 loop : -2.16 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP Y 149 HIS 0.011 0.001 HIS K 205 PHE 0.017 0.002 PHE K 212 TYR 0.020 0.002 TYR J 210 ARG 0.003 0.000 ARG G 48 *********************** 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 324 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 259 time to evaluate : 1.920 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: X 53 ASP cc_start: 0.7195 (p0) cc_final: 0.6461 (t0) REVERT: Y 159 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8501 (mmtt) REVERT: Y 185 PHE cc_start: 0.6940 (m-10) cc_final: 0.6599 (m-10) REVERT: Y 205 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.7396 (t70) REVERT: G 53 ASP cc_start: 0.7042 (p0) cc_final: 0.6351 (t0) REVERT: J 159 LYS cc_start: 0.9182 (mttt) cc_final: 0.8787 (mmtm) REVERT: J 205 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7620 (m90) REVERT: A 68 LYS cc_start: 0.7723 (mmpt) cc_final: 0.7134 (mttm) REVERT: B 173 SER cc_start: 0.9252 (m) cc_final: 0.9024 (p) REVERT: B 226 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.7670 (pmtt) REVERT: B 410 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7393 (tp) REVERT: C 49 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7038 (tmm-80) REVERT: C 58 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7781 (m) REVERT: D 171 LEU cc_start: 0.9157 (mp) cc_final: 0.8839 (tt) REVERT: D 218 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: D 408 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7464 (p) REVERT: D 410 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7350 (tp) REVERT: F 171 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9068 (tt) REVERT: F 408 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7521 (p) outliers start: 65 outliers final: 41 residues processed: 306 average time/residue: 0.2482 time to fit residues: 114.4301 Evaluate side-chains 286 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 234 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 202 CYS Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 75 ASN ** Y 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS ** K 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.7214 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= 0.195 Angle : 0.732 12.845 20917 Z= 0.364 Chirality : 0.048 0.446 2454 Planarity : 0.004 0.063 2631 Dihedral : 5.608 53.481 2188 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.10 % Allowed : 25.69 % Favored : 71.21 % 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: -2.38 (0.18), residues: 1915 helix: -0.97 (0.23), residues: 456 sheet: -1.19 (0.23), residues: 491 loop : -2.08 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.003 TRP G 104 HIS 0.010 0.001 HIS J 205 PHE 0.017 0.002 PHE K 212 TYR 0.022 0.002 TYR J 210 ARG 0.003 0.000 ARG G 48 ********************** 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 303 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 1.799 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: X 53 ASP cc_start: 0.7114 (p0) cc_final: 0.6377 (t0) REVERT: Y 159 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8529 (mmtt) REVERT: Y 205 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7380 (t70) REVERT: G 53 ASP cc_start: 0.7090 (p0) cc_final: 0.6422 (t0) REVERT: G 96 ARG cc_start: 0.6261 (mtp180) cc_final: 0.5890 (mtm180) REVERT: J 149 TRP cc_start: 0.5920 (m100) cc_final: 0.5151 (m100) REVERT: A 68 LYS cc_start: 0.7648 (mmpt) cc_final: 0.7062 (mttm) REVERT: B 173 SER cc_start: 0.9242 (m) cc_final: 0.9005 (p) REVERT: B 226 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7633 (pmtt) REVERT: B 410 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7333 (tp) REVERT: C 49 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7039 (tmm-80) REVERT: C 58 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7767 (m) REVERT: D 171 LEU cc_start: 0.9148 (mp) cc_final: 0.8848 (tt) REVERT: D 218 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: D 408 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7447 (p) REVERT: D 410 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7231 (tp) REVERT: F 171 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9091 (tt) REVERT: F 408 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7499 (p) outliers start: 54 outliers final: 37 residues processed: 287 average time/residue: 0.2567 time to fit residues: 110.1949 Evaluate side-chains 285 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 202 CYS Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 154 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 0.2980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS ** K 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.071616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.062285 restraints weight = 93415.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.063597 restraints weight = 55545.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.064498 restraints weight = 37538.359| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.7336 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 : 0.758 17.690 20917 Z= 0.369 Chirality : 0.048 0.446 2454 Planarity : 0.004 0.060 2631 Dihedral : 5.448 53.163 2188 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.16 % Allowed : 26.09 % Favored : 70.75 % 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: -2.26 (0.18), residues: 1915 helix: -1.00 (0.23), residues: 455 sheet: -1.02 (0.23), residues: 491 loop : -1.99 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP G 104 HIS 0.006 0.001 HIS J 205 PHE 0.020 0.001 PHE K 212 TYR 0.025 0.002 TYR G 25 ARG 0.006 0.000 ARG J 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3415.42 seconds wall clock time: 61 minutes 59.88 seconds (3719.88 seconds total)