Starting phenix.real_space_refine on Sat Mar 16 17:41:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/03_2024/6cxc_7774_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/03_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_7774/03_2024/6cxc_7774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/03_2024/6cxc_7774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/03_2024/6cxc_7774_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cxc_7774/03_2024/6cxc_7774_neut.pdb" } 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 Residue "X ARG 38": "NH1" <-> "NH2" Residue "X ARG 96": "NH1" <-> "NH2" Residue "Y ARG 132": "NH1" <-> "NH2" Residue "Y ARG 144": "NH1" <-> "NH2" Residue "Y ARG 152": "NH1" <-> "NH2" Residue "Y ARG 168": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 179": "NH1" <-> "NH2" Residue "Y ARG 222": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "J ARG 132": "NH1" <-> "NH2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 175": "NH1" <-> "NH2" Residue "J ARG 179": "NH1" <-> "NH2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "K ARG 132": "NH1" <-> "NH2" Residue "K ARG 144": "NH1" <-> "NH2" Residue "K ARG 152": "NH1" <-> "NH2" Residue "K ARG 168": "NH1" <-> "NH2" Residue "K ARG 175": "NH1" <-> "NH2" Residue "K ARG 179": "NH1" <-> "NH2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "B PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "F ARG 507": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.50, per 1000 atoms: 0.56 Number of scatterers: 15196 At special positions: 0 Unit cell: (153.061, 139.261, 190.699, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2989 8.00 N 2541 7.00 C 9582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS X 20 " - pdb=" SG CYS X 94 " distance=2.04 Simple disulfide: pdb=" SG CYS G 20 " - pdb=" SG CYS G 94 " distance=2.04 Simple disulfide: pdb=" SG CYS I 20 " - pdb=" SG CYS I 94 " distance=2.04 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.04 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS D 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 322 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 358 " - pdb=" SG CYS D 367 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 393 " distance=2.03 Simple disulfide: pdb=" SG CYS D 416 " - pdb=" SG CYS D 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS F 439 " distance=2.03 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS F 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 322 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 367 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 393 " distance=2.03 Simple disulfide: pdb=" SG CYS F 416 " - pdb=" SG CYS F 422 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 70 " " NAG C 601 " - " ASN C 70 " " NAG E 601 " - " ASN E 70 " Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 2.9 seconds 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 34 sheets defined 27.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 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: 4.77 Time building geometry restraints manager: 6.34 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: 97.74 - 105.01: 218 105.01 - 112.27: 7985 112.27 - 119.54: 5146 119.54 - 126.81: 7419 126.81 - 134.07: 149 Bond angle restraints: 20917 Sorted by residual: angle pdb=" C ALA B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta sigma weight residual 120.77 128.68 -7.91 1.31e+00 5.83e-01 3.65e+01 angle pdb=" N ASP B 401 " pdb=" CA ASP B 401 " pdb=" C ASP B 401 " ideal model delta sigma weight residual 107.93 115.36 -7.43 1.65e+00 3.67e-01 2.03e+01 angle pdb=" N THR B 267 " pdb=" CA THR B 267 " pdb=" C THR B 267 " ideal model delta sigma weight residual 110.43 116.07 -5.64 1.31e+00 5.83e-01 1.85e+01 angle pdb=" N LYS F 399 " pdb=" CA LYS F 399 " pdb=" C LYS F 399 " ideal model delta sigma weight residual 113.18 107.60 5.58 1.33e+00 5.65e-01 1.76e+01 angle pdb=" N LYS D 399 " pdb=" CA LYS D 399 " pdb=" C LYS D 399 " ideal model delta sigma weight residual 113.18 107.61 5.57 1.33e+00 5.65e-01 1.75e+01 ... (remaining 20912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 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 2.440 nonbonded pdb=" O ILE B 499 " pdb=" OG SER B 502 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR B 198 " pdb=" O VAL F 482 " model vdw 2.249 2.440 nonbonded pdb=" O VAL B 482 " pdb=" OH TYR D 198 " model vdw 2.253 2.440 nonbonded pdb=" O VAL F 187 " pdb=" OG SER F 190 " model vdw 2.259 2.440 ... (remaining 118721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 97 or resid 601)) selection = chain 'C' selection = (chain 'E' and (resid 26 through 97 or resid 601)) } ncs_group { reference = (chain 'B' and (resid 155 through 514 or resid 800)) selection = (chain 'D' and (resid 155 through 322 or resid 333 through 514 or resid 800)) selection = (chain 'F' and (resid 155 through 322 or resid 333 through 514 or resid 800)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 1.130 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: 4.570 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 41.970 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.090 ------------------------------------------------------------------------------- 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 : 1.906 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: 0.3340 time to fit residues: 295.9186 Evaluate side-chains 306 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 80 GLN Y 141 GLN Y 169 HIS ** Y 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 205 HIS J 167 ASN J 169 HIS J 205 HIS ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS A 67 ASN A 98 GLN B 159 HIS ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 268 ASN B 371 ASN B 496 ASN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN D 496 ASN F 159 HIS ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 ASN F 268 ASN F 496 ASN F 500 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15451 Z= 0.192 Angle : 0.723 11.137 20917 Z= 0.374 Chirality : 0.048 0.508 2454 Planarity : 0.005 0.041 2631 Dihedral : 7.653 68.742 2188 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.05 % Allowed : 17.41 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.17), residues: 1915 helix: -2.24 (0.19), residues: 459 sheet: -1.69 (0.22), residues: 502 loop : -2.20 (0.18), residues: 954 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 0.023 0.002 PHE B 505 TYR 0.027 0.002 TYR B 391 ARG 0.011 0.001 ARG X 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: 53 poor density : 375 time to evaluate : 1.872 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: Y 200 TYR cc_start: 0.7226 (m-80) cc_final: 0.5767 (m-80) REVERT: Y 205 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7457 (t70) REVERT: G 31 TRP cc_start: 0.4882 (m100) cc_final: 0.4572 (m100) REVERT: J 144 ARG cc_start: 0.6780 (mpt90) cc_final: 0.6316 (mmt180) REVERT: K 200 TYR cc_start: 0.7160 (m-80) cc_final: 0.6192 (m-80) REVERT: K 205 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7740 (t70) REVERT: B 156 LYS cc_start: 0.7207 (mmmm) cc_final: 0.6880 (mmmt) REVERT: B 161 GLU cc_start: 0.9113 (pt0) cc_final: 0.8630 (mp0) REVERT: B 280 ILE cc_start: 0.7939 (mm) cc_final: 0.7727 (mt) REVERT: B 400 THR cc_start: 0.6936 (OUTLIER) cc_final: 0.6609 (p) REVERT: B 486 ASP cc_start: 0.7027 (p0) cc_final: 0.6808 (p0) REVERT: B 507 ARG cc_start: 0.8900 (tpm170) cc_final: 0.8573 (tpp-160) REVERT: C 82 GLU cc_start: 0.6805 (tp30) cc_final: 0.6308 (tp30) REVERT: E 82 GLU cc_start: 0.6953 (tp30) cc_final: 0.6195 (tp30) REVERT: F 289 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6393 (ttp) REVERT: F 507 ARG cc_start: 0.8824 (tpm170) cc_final: 0.8557 (tpp-160) outliers start: 53 outliers final: 21 residues processed: 410 average time/residue: 0.2731 time to fit residues: 161.4094 Evaluate side-chains 306 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 281 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 182 SER Chi-restraints excluded: chain B residue 260 LEU 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 182 SER Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 338 ASP 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: 10.0000 chunk 53 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 81 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN B 501 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 GLN E 81 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN F 501 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15451 Z= 0.358 Angle : 0.795 11.927 20917 Z= 0.417 Chirality : 0.050 0.481 2454 Planarity : 0.005 0.092 2631 Dihedral : 7.305 55.205 2188 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 5.23 % Allowed : 19.48 % Favored : 75.29 % 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: -2.73 (0.17), residues: 1915 helix: -1.40 (0.22), residues: 450 sheet: -1.22 (0.23), residues: 478 loop : -2.33 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 34 HIS 0.018 0.003 HIS J 205 PHE 0.020 0.002 PHE J 201 TYR 0.019 0.003 TYR G 78 ARG 0.008 0.001 ARG I 38 *********************** 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 380 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 289 time to evaluate : 1.780 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: Y 159 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8390 (mmmt) REVERT: Y 185 PHE cc_start: 0.6710 (m-80) cc_final: 0.6347 (m-80) REVERT: Y 200 TYR cc_start: 0.6966 (m-80) cc_final: 0.6033 (m-80) REVERT: Y 205 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7433 (t-170) REVERT: G 10 VAL cc_start: 0.5735 (m) cc_final: 0.5064 (p) REVERT: G 49 LEU cc_start: 0.7057 (tp) cc_final: 0.6821 (tp) REVERT: J 162 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8748 (tp) REVERT: J 195 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: K 200 TYR cc_start: 0.7297 (m-80) cc_final: 0.6608 (m-80) REVERT: K 205 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.8058 (t-170) REVERT: B 156 LYS cc_start: 0.7444 (mmmm) cc_final: 0.7140 (mmmt) REVERT: B 161 GLU cc_start: 0.9150 (pt0) cc_final: 0.8728 (mp0) REVERT: B 289 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6588 (ptt) REVERT: B 400 THR cc_start: 0.6815 (OUTLIER) cc_final: 0.6478 (p) REVERT: C 82 GLU cc_start: 0.7197 (tp30) cc_final: 0.6865 (tp30) REVERT: E 82 GLU cc_start: 0.7265 (tp30) cc_final: 0.7047 (tp30) REVERT: F 171 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8844 (tt) outliers start: 91 outliers final: 54 residues processed: 355 average time/residue: 0.2510 time to fit residues: 132.1078 Evaluate side-chains 315 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 254 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 202 CYS Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 167 ASN 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 202 CYS Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 46 SER 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 257 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 357 THR 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 D residue 214 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 366 PHE 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 69 CYS Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain F residue 343 CYS Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 392 ASP 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: 0.5980 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 205 HIS J 205 HIS ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS A 67 ASN B 183 ASN B 501 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15451 Z= 0.199 Angle : 0.697 12.425 20917 Z= 0.351 Chirality : 0.047 0.479 2454 Planarity : 0.004 0.039 2631 Dihedral : 6.316 53.101 2188 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.31 % Allowed : 21.61 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.18), residues: 1915 helix: -1.08 (0.23), residues: 453 sheet: -1.18 (0.23), residues: 500 loop : -2.08 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 104 HIS 0.002 0.001 HIS Y 205 PHE 0.033 0.002 PHE G 103 TYR 0.016 0.002 TYR Y 150 ARG 0.005 0.001 ARG I 38 *********************** 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 369 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 294 time to evaluate : 1.918 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: 0.8673 (mmtt) cc_final: 0.8310 (mmmt) REVERT: Y 185 PHE cc_start: 0.6565 (m-80) cc_final: 0.6159 (m-10) REVERT: Y 205 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7412 (t70) REVERT: J 162 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8491 (tp) REVERT: J 164 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7815 (tp) REVERT: J 195 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: I 68 LEU cc_start: 0.8136 (tp) cc_final: 0.7829 (tp) REVERT: K 149 TRP cc_start: 0.6177 (m100) cc_final: 0.5322 (m-10) REVERT: K 159 LYS cc_start: 0.8938 (mptt) cc_final: 0.8567 (mmtm) REVERT: K 200 TYR cc_start: 0.7187 (m-80) cc_final: 0.6392 (m-80) REVERT: K 205 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7775 (t70) REVERT: B 156 LYS cc_start: 0.7439 (mmmm) cc_final: 0.7128 (mmmt) REVERT: B 161 GLU cc_start: 0.9000 (pt0) cc_final: 0.8697 (mp0) REVERT: B 400 THR cc_start: 0.6738 (OUTLIER) cc_final: 0.6443 (p) REVERT: B 408 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7811 (p) REVERT: C 82 GLU cc_start: 0.7199 (tp30) cc_final: 0.6908 (tp30) REVERT: E 82 GLU cc_start: 0.7069 (tp30) cc_final: 0.6819 (tp30) REVERT: F 171 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8900 (tt) REVERT: F 289 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6842 (ptt) outliers start: 75 outliers final: 42 residues processed: 345 average time/residue: 0.2613 time to fit residues: 133.5413 Evaluate side-chains 312 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 261 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain Y residue 184 ASP 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 164 LEU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 202 CYS 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 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 197 LEU Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 382 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 D residue 193 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 366 PHE 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 171 LEU Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain F residue 343 CYS 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: 0.9980 chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 205 HIS J 205 HIS ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS A 67 ASN B 501 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15451 Z= 0.234 Angle : 0.686 11.125 20917 Z= 0.350 Chirality : 0.047 0.473 2454 Planarity : 0.004 0.047 2631 Dihedral : 6.098 53.816 2188 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.06 % Allowed : 21.38 % Favored : 73.56 % 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: -2.37 (0.18), residues: 1915 helix: -0.94 (0.23), residues: 455 sheet: -1.19 (0.23), residues: 506 loop : -2.08 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 104 HIS 0.004 0.001 HIS Y 205 PHE 0.029 0.002 PHE G 103 TYR 0.020 0.002 TYR I 78 ARG 0.008 0.001 ARG F 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 364 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 276 time to evaluate : 1.948 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: Y 159 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8373 (mmtt) REVERT: Y 185 PHE cc_start: 0.6806 (m-80) cc_final: 0.6347 (m-10) REVERT: Y 205 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7734 (t70) REVERT: J 162 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8514 (tp) REVERT: J 164 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7760 (tp) REVERT: J 195 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: J 200 TYR cc_start: 0.6734 (m-80) cc_final: 0.6475 (m-80) REVERT: I 53 ASP cc_start: 0.6804 (p0) cc_final: 0.6602 (p0) REVERT: K 151 GLN cc_start: 0.7518 (pp30) cc_final: 0.7213 (pp30) REVERT: K 159 LYS cc_start: 0.8975 (mptt) cc_final: 0.8444 (mptt) REVERT: K 205 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.7782 (t70) REVERT: A 68 LYS cc_start: 0.7319 (mmpt) cc_final: 0.6998 (mttm) REVERT: B 156 LYS cc_start: 0.7393 (mmmm) cc_final: 0.7074 (mmmt) REVERT: B 161 GLU cc_start: 0.8977 (pt0) cc_final: 0.8654 (mp0) REVERT: B 171 LEU cc_start: 0.9133 (mp) cc_final: 0.8833 (tt) REVERT: B 173 SER cc_start: 0.9340 (m) cc_final: 0.9076 (p) REVERT: B 400 THR cc_start: 0.6974 (OUTLIER) cc_final: 0.6674 (p) REVERT: C 82 GLU cc_start: 0.7186 (tp30) cc_final: 0.6895 (tp30) REVERT: E 82 GLU cc_start: 0.7220 (tp30) cc_final: 0.6975 (tp30) outliers start: 88 outliers final: 55 residues processed: 338 average time/residue: 0.2497 time to fit residues: 126.8921 Evaluate side-chains 321 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 260 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 184 ASP Chi-restraints excluded: chain Y residue 197 LEU 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 164 LEU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 202 CYS Chi-restraints excluded: chain J residue 203 LEU 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 167 ASN 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 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL 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 408 THR 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 55 SER Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 220 VAL 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 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 F residue 182 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain F residue 357 THR 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: 0.5980 chunk 164 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 151 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7635 moved from start: 0.6245 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= 0.181 Angle : 0.663 10.928 20917 Z= 0.331 Chirality : 0.046 0.472 2454 Planarity : 0.004 0.037 2631 Dihedral : 5.669 53.225 2188 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.48 % Allowed : 22.53 % Favored : 72.99 % 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: -2.19 (0.18), residues: 1915 helix: -0.77 (0.24), residues: 452 sheet: -1.05 (0.23), residues: 477 loop : -1.99 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Y 149 HIS 0.004 0.001 HIS Y 205 PHE 0.023 0.002 PHE G 103 TYR 0.014 0.002 TYR Y 150 ARG 0.009 0.001 ARG Y 179 *********************** 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 359 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 281 time to evaluate : 2.063 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: Y 159 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8223 (mmtt) REVERT: Y 185 PHE cc_start: 0.6506 (m-80) cc_final: 0.6169 (m-10) REVERT: G 92 TYR cc_start: 0.6788 (m-80) cc_final: 0.6370 (m-80) REVERT: J 162 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8532 (tp) REVERT: J 164 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7716 (tp) REVERT: J 195 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: I 53 ASP cc_start: 0.6874 (p0) cc_final: 0.6598 (p0) REVERT: K 151 GLN cc_start: 0.7455 (pp30) cc_final: 0.7138 (pp30) REVERT: K 159 LYS cc_start: 0.9034 (mptt) cc_final: 0.8337 (mptt) REVERT: K 205 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7736 (t70) REVERT: A 68 LYS cc_start: 0.7337 (mmpt) cc_final: 0.6999 (mttm) REVERT: B 156 LYS cc_start: 0.7396 (mmmm) cc_final: 0.7095 (mmmt) REVERT: B 161 GLU cc_start: 0.8986 (pt0) cc_final: 0.8660 (mp0) REVERT: B 173 SER cc_start: 0.9311 (m) cc_final: 0.9019 (p) REVERT: B 218 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: B 400 THR cc_start: 0.6889 (OUTLIER) cc_final: 0.6617 (p) REVERT: C 58 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7615 (m) REVERT: C 82 GLU cc_start: 0.6946 (tp30) cc_final: 0.6662 (tp30) REVERT: D 408 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7640 (p) REVERT: E 82 GLU cc_start: 0.7106 (tp30) cc_final: 0.6887 (tp30) REVERT: F 173 SER cc_start: 0.9190 (m) cc_final: 0.8955 (p) REVERT: F 250 TYR cc_start: 0.7084 (m-10) cc_final: 0.6732 (m-10) REVERT: F 408 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7879 (p) outliers start: 78 outliers final: 54 residues processed: 339 average time/residue: 0.2495 time to fit residues: 126.5448 Evaluate side-chains 320 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 257 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 197 LEU Chi-restraints excluded: chain Y residue 202 CYS Chi-restraints excluded: chain Y residue 203 LEU 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 164 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 202 CYS Chi-restraints excluded: chain J residue 203 LEU 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 153 LYS Chi-restraints excluded: chain K residue 167 ASN 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 205 HIS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL 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 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 55 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 357 THR 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 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 338 ASP 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: 10.0000 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 122 GLN Y 205 HIS J 205 HIS ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7658 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15451 Z= 0.206 Angle : 0.679 11.080 20917 Z= 0.340 Chirality : 0.046 0.468 2454 Planarity : 0.004 0.054 2631 Dihedral : 5.649 53.552 2188 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.06 % Allowed : 22.93 % Favored : 72.01 % 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: -2.18 (0.18), residues: 1915 helix: -0.70 (0.24), residues: 451 sheet: -1.22 (0.22), residues: 512 loop : -1.92 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP Y 149 HIS 0.005 0.001 HIS Y 205 PHE 0.021 0.002 PHE I 103 TYR 0.015 0.002 TYR G 78 ARG 0.005 0.001 ARG Y 179 *********************** 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 352 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 264 time to evaluate : 1.923 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: Y 159 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8194 (mmtt) REVERT: Y 205 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7700 (t70) REVERT: G 92 TYR cc_start: 0.6731 (m-80) cc_final: 0.6369 (m-80) REVERT: J 162 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8522 (tp) REVERT: J 164 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7768 (tp) REVERT: J 195 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8261 (pm20) REVERT: I 53 ASP cc_start: 0.6945 (p0) cc_final: 0.6648 (p0) REVERT: I 56 ILE cc_start: 0.7699 (tp) cc_final: 0.7345 (tp) REVERT: K 159 LYS cc_start: 0.9176 (mptt) cc_final: 0.8521 (mptt) REVERT: A 68 LYS cc_start: 0.7367 (mmpt) cc_final: 0.7015 (mttm) REVERT: B 156 LYS cc_start: 0.7415 (mmmm) cc_final: 0.7112 (mmmt) REVERT: B 161 GLU cc_start: 0.9000 (pt0) cc_final: 0.8679 (mp0) REVERT: B 173 SER cc_start: 0.9282 (m) cc_final: 0.8982 (p) REVERT: B 218 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: B 400 THR cc_start: 0.6840 (OUTLIER) cc_final: 0.6580 (p) REVERT: B 507 ARG cc_start: 0.9036 (tpm170) cc_final: 0.8713 (tpp-160) REVERT: C 58 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7698 (m) REVERT: C 82 GLU cc_start: 0.7175 (tp30) cc_final: 0.6873 (tp30) REVERT: D 264 MET cc_start: 0.7090 (mmm) cc_final: 0.6831 (mmm) REVERT: D 408 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7658 (p) REVERT: E 82 GLU cc_start: 0.7186 (tp30) cc_final: 0.6982 (tp30) REVERT: F 173 SER cc_start: 0.9150 (m) cc_final: 0.8943 (p) REVERT: F 250 TYR cc_start: 0.7108 (m-10) cc_final: 0.6762 (m-10) REVERT: F 408 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7914 (p) outliers start: 88 outliers final: 64 residues processed: 330 average time/residue: 0.2408 time to fit residues: 120.7083 Evaluate side-chains 326 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 253 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain Y residue 197 LEU 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 164 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 202 CYS Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain J residue 205 HIS 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 167 ASN Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 184 ASP 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 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL 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 408 THR 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 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 214 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 357 THR 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 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 338 ASP 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: 30.0000 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 165 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 205 HIS J 205 HIS K 205 HIS B 371 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7740 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15451 Z= 0.322 Angle : 0.749 10.065 20917 Z= 0.384 Chirality : 0.048 0.468 2454 Planarity : 0.004 0.058 2631 Dihedral : 6.218 54.197 2188 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.00 % Allowed : 23.45 % 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: -2.41 (0.18), residues: 1915 helix: -0.87 (0.23), residues: 458 sheet: -1.20 (0.23), residues: 497 loop : -2.18 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP Y 149 HIS 0.016 0.002 HIS Y 205 PHE 0.023 0.002 PHE K 212 TYR 0.023 0.002 TYR B 250 ARG 0.006 0.001 ARG B 336 *********************** 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 330 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 243 time to evaluate : 2.032 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: Y 159 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8327 (mmtt) REVERT: Y 205 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7961 (t70) REVERT: J 164 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7927 (tp) REVERT: J 195 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: I 53 ASP cc_start: 0.7061 (p0) cc_final: 0.6859 (p0) REVERT: K 159 LYS cc_start: 0.9126 (mptt) cc_final: 0.8756 (mmpt) REVERT: A 68 LYS cc_start: 0.7492 (mmpt) cc_final: 0.7003 (mttm) REVERT: B 173 SER cc_start: 0.9292 (m) cc_final: 0.8989 (p) REVERT: B 218 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: B 400 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6762 (p) REVERT: B 507 ARG cc_start: 0.9062 (tpm170) cc_final: 0.8720 (tpp-160) REVERT: C 82 GLU cc_start: 0.7361 (tp30) cc_final: 0.6992 (tp30) REVERT: D 264 MET cc_start: 0.6958 (mmm) cc_final: 0.6655 (mmm) REVERT: D 408 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7863 (p) REVERT: E 82 GLU cc_start: 0.7455 (tp30) cc_final: 0.7231 (tp30) REVERT: F 173 SER cc_start: 0.9142 (m) cc_final: 0.8941 (p) REVERT: F 396 MET cc_start: 0.7580 (tpt) cc_final: 0.7367 (tpt) REVERT: F 486 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6986 (p0) outliers start: 87 outliers final: 66 residues processed: 309 average time/residue: 0.2535 time to fit residues: 119.4185 Evaluate side-chains 307 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 234 time to evaluate : 2.803 ------------------------------------------------------------------------------- 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 81 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 199 ASP 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 164 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 202 CYS Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN 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 167 ASN Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 184 ASP 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 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL 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 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 511 GLU Chi-restraints excluded: chain C residue 55 SER 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 269 ASP Chi-restraints excluded: chain D residue 357 THR 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 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 486 ASP 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: 0.9990 chunk 169 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 0.0370 chunk 52 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 205 HIS J 205 HIS ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7641 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15451 Z= 0.180 Angle : 0.700 11.662 20917 Z= 0.346 Chirality : 0.047 0.468 2454 Planarity : 0.004 0.046 2631 Dihedral : 5.675 52.786 2188 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.91 % Allowed : 25.11 % Favored : 70.98 % 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: -2.18 (0.18), residues: 1915 helix: -0.77 (0.24), residues: 462 sheet: -1.19 (0.22), residues: 519 loop : -1.91 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP Y 149 HIS 0.010 0.001 HIS Y 205 PHE 0.018 0.002 PHE B 505 TYR 0.026 0.002 TYR J 210 ARG 0.005 0.001 ARG D 336 *********************** 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 338 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 270 time to evaluate : 1.808 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: Y 159 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8281 (mmtt) REVERT: Y 205 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7244 (t70) REVERT: G 92 TYR cc_start: 0.6705 (m-80) cc_final: 0.6339 (m-80) REVERT: J 164 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7783 (tp) REVERT: K 200 TYR cc_start: 0.7170 (m-80) cc_final: 0.6695 (m-80) REVERT: K 205 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7633 (t70) REVERT: A 68 LYS cc_start: 0.7604 (mmpt) cc_final: 0.7055 (mttm) REVERT: B 161 GLU cc_start: 0.8961 (pt0) cc_final: 0.8649 (mp0) REVERT: B 173 SER cc_start: 0.9230 (m) cc_final: 0.8947 (p) REVERT: B 218 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8068 (pm20) REVERT: B 370 MET cc_start: 0.8233 (tpt) cc_final: 0.8023 (tpp) REVERT: B 507 ARG cc_start: 0.9008 (tpm170) cc_final: 0.8658 (tpp-160) REVERT: C 58 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7763 (m) REVERT: C 77 LYS cc_start: 0.7132 (mmmt) cc_final: 0.6767 (mmmm) REVERT: C 82 GLU cc_start: 0.7072 (tp30) cc_final: 0.6799 (tp30) REVERT: D 264 MET cc_start: 0.6669 (mmm) cc_final: 0.6367 (mmm) REVERT: D 408 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7674 (p) REVERT: E 82 GLU cc_start: 0.7177 (tp30) cc_final: 0.6973 (tp30) REVERT: F 173 SER cc_start: 0.9056 (m) cc_final: 0.8785 (t) REVERT: F 250 TYR cc_start: 0.6979 (m-10) cc_final: 0.6743 (m-80) REVERT: F 408 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7976 (p) outliers start: 68 outliers final: 47 residues processed: 319 average time/residue: 0.2443 time to fit residues: 117.5527 Evaluate side-chains 303 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 81 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR 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 164 LEU Chi-restraints excluded: chain J residue 167 ASN Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 203 LEU 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 184 ASP 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 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 220 VAL 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 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 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 289 MET 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 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 338 ASP 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: 8.9990 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 188 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 159 optimal weight: 0.0870 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15451 Z= 0.196 Angle : 0.711 11.178 20917 Z= 0.351 Chirality : 0.048 0.462 2454 Planarity : 0.004 0.049 2631 Dihedral : 5.610 53.292 2188 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.62 % Allowed : 26.15 % Favored : 70.23 % 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: -2.16 (0.18), residues: 1915 helix: -0.72 (0.24), residues: 460 sheet: -1.22 (0.22), residues: 530 loop : -1.88 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Y 149 HIS 0.009 0.001 HIS J 205 PHE 0.017 0.002 PHE K 212 TYR 0.020 0.002 TYR G 78 ARG 0.007 0.001 ARG D 429 ********************** 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 314 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 251 time to evaluate : 1.810 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: Y 159 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8250 (mmtt) REVERT: J 164 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7682 (tp) REVERT: A 68 LYS cc_start: 0.7584 (mmpt) cc_final: 0.7028 (mttm) REVERT: B 161 GLU cc_start: 0.8957 (pt0) cc_final: 0.8643 (mp0) REVERT: B 173 SER cc_start: 0.9193 (m) cc_final: 0.8943 (p) REVERT: B 402 VAL cc_start: 0.6632 (OUTLIER) cc_final: 0.6333 (m) REVERT: B 507 ARG cc_start: 0.8999 (tpm170) cc_final: 0.8642 (tpp-160) REVERT: C 58 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7758 (m) REVERT: C 77 LYS cc_start: 0.7139 (mmmt) cc_final: 0.6766 (mmmm) REVERT: C 82 GLU cc_start: 0.7015 (tp30) cc_final: 0.6729 (tp30) REVERT: D 264 MET cc_start: 0.6732 (mmm) cc_final: 0.6463 (mmm) REVERT: D 408 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7652 (p) REVERT: E 82 GLU cc_start: 0.7084 (tp30) cc_final: 0.6852 (tp30) REVERT: F 173 SER cc_start: 0.9071 (m) cc_final: 0.8851 (p) REVERT: F 250 TYR cc_start: 0.7004 (m-10) cc_final: 0.6757 (m-80) REVERT: F 408 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7947 (p) REVERT: F 486 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6830 (p0) outliers start: 63 outliers final: 52 residues processed: 295 average time/residue: 0.2460 time to fit residues: 109.8347 Evaluate side-chains 299 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 241 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 81 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 197 LEU Chi-restraints excluded: chain Y residue 199 ASP Chi-restraints excluded: chain Y residue 203 LEU 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 164 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 203 LEU 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 184 ASP 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 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 220 VAL 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 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 C residue 55 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 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 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 F residue 193 LEU 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 338 ASP 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 486 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 154 optimal weight: 20.0000 chunk 19 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 205 HIS J 205 HIS ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.069770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.062054 restraints weight = 98648.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.062783 restraints weight = 69487.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.062978 restraints weight = 55036.988| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15451 Z= 0.234 Angle : 0.728 10.959 20917 Z= 0.364 Chirality : 0.048 0.462 2454 Planarity : 0.004 0.047 2631 Dihedral : 5.742 53.721 2188 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.85 % Allowed : 25.75 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.18), residues: 1915 helix: -0.72 (0.24), residues: 460 sheet: -1.32 (0.23), residues: 497 loop : -1.88 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Y 149 HIS 0.006 0.001 HIS Y 205 PHE 0.015 0.002 PHE I 103 TYR 0.020 0.002 TYR J 210 ARG 0.007 0.001 ARG D 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.57 seconds wall clock time: 62 minutes 4.35 seconds (3724.35 seconds total)