Starting phenix.real_space_refine (version: dev) on Tue Dec 13 11:18:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/12_2022/6lyp_30017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/12_2022/6lyp_30017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/12_2022/6lyp_30017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/12_2022/6lyp_30017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/12_2022/6lyp_30017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/12_2022/6lyp_30017.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "E ARG 257": "NH1" <-> "NH2" Residue "E ARG 265": "NH1" <-> "NH2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "F ARG 257": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F ARG 342": "NH1" <-> "NH2" Residue "F PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 444": "NH1" <-> "NH2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "G ARG 257": "NH1" <-> "NH2" Residue "G ARG 265": "NH1" <-> "NH2" Residue "G ARG 342": "NH1" <-> "NH2" Residue "G PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G ARG 460": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 15169 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 8.82, per 1000 atoms: 0.58 Number of scatterers: 15169 At special positions: 0 Unit cell: (102.96, 100.88, 123.76, 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 2793 8.00 N 2548 7.00 C 9744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.56 Conformation dependent library (CDL) restraints added in 2.6 seconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3710 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 21 sheets defined 48.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.641A pdb=" N ALA A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.779A pdb=" N THR A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 327 through 342 removed outlier: 4.063A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.698A pdb=" N SER A 385 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.676A pdb=" N LYS A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.639A pdb=" N ALA B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.644A pdb=" N ILE B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.700A pdb=" N SER B 385 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 386' Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 474 " --> pdb=" O GLN B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.641A pdb=" N ALA C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 251 through 266 removed outlier: 4.493A pdb=" N ARG C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.643A pdb=" N ILE C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR C 312 " --> pdb=" O GLN C 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER C 385 " --> pdb=" O ASN C 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 386' Processing helix chain 'C' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 474 " --> pdb=" O GLN C 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 223 removed outlier: 3.640A pdb=" N ALA D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG D 257 " --> pdb=" O TRP D 253 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 262 " --> pdb=" O TRP D 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 282 removed outlier: 3.779A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR D 312 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER D 385 " --> pdb=" O ASN D 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 381 through 386' Processing helix chain 'D' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS D 422 " --> pdb=" O SER D 418 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 469 " --> pdb=" O GLU D 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 474 " --> pdb=" O GLN D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 223 removed outlier: 3.640A pdb=" N ALA E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG E 257 " --> pdb=" O TRP E 253 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 262 " --> pdb=" O TRP E 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE E 263 " --> pdb=" O LYS E 259 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 282 removed outlier: 3.779A pdb=" N THR E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 287 Processing helix chain 'E' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR E 312 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 324 Processing helix chain 'E' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER E 385 " --> pdb=" O ASN E 381 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 381 through 386' Processing helix chain 'E' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS E 422 " --> pdb=" O SER E 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 469 " --> pdb=" O GLU E 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 474 " --> pdb=" O GLN E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.641A pdb=" N ALA F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 251 through 266 removed outlier: 4.493A pdb=" N ARG F 257 " --> pdb=" O TRP F 253 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 262 " --> pdb=" O TRP F 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 Processing helix chain 'F' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR F 312 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 327 through 342 removed outlier: 4.063A pdb=" N GLN F 339 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE F 340 " --> pdb=" O LEU F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER F 385 " --> pdb=" O ASN F 381 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 381 through 386' Processing helix chain 'F' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS F 422 " --> pdb=" O SER F 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 469 " --> pdb=" O GLU F 465 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU F 474 " --> pdb=" O GLN F 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.640A pdb=" N ALA G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE G 220 " --> pdb=" O LEU G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG G 257 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL G 262 " --> pdb=" O TRP G 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 287 Processing helix chain 'G' and resid 289 through 303 removed outlier: 3.537A pdb=" N ILE G 294 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU G 301 " --> pdb=" O MET G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 removed outlier: 3.644A pdb=" N ILE G 310 " --> pdb=" O ALA G 306 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR G 312 " --> pdb=" O GLN G 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 313 " --> pdb=" O SER G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 324 Processing helix chain 'G' and resid 327 through 342 removed outlier: 4.063A pdb=" N GLN G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE G 340 " --> pdb=" O LEU G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER G 385 " --> pdb=" O ASN G 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER G 386 " --> pdb=" O SER G 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 381 through 386' Processing helix chain 'G' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS G 422 " --> pdb=" O SER G 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER G 427 " --> pdb=" O GLU G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN G 468 " --> pdb=" O GLU G 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR G 469 " --> pdb=" O GLU G 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU G 474 " --> pdb=" O GLN G 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 350 removed outlier: 6.682A pdb=" N SER A 368 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET A 362 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 389 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.650A pdb=" N ILE A 389 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET B 362 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER B 368 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR A 441 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER A 487 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.648A pdb=" N ILE B 389 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR C 366 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET C 362 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER C 368 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 399 through 401 removed outlier: 3.861A pdb=" N TYR B 441 " --> pdb=" O THR B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER B 487 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.626A pdb=" N ILE C 389 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR D 366 " --> pdb=" O MET D 362 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET D 362 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER D 368 " --> pdb=" O ILE D 360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR C 441 " --> pdb=" O THR C 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER C 487 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.637A pdb=" N ILE D 389 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET E 362 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER E 368 " --> pdb=" O ILE E 360 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 399 through 401 removed outlier: 3.861A pdb=" N TYR D 441 " --> pdb=" O THR D 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 406 through 407 removed outlier: 3.748A pdb=" N SER D 487 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 389 through 390 removed outlier: 7.202A pdb=" N THR F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET F 362 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER F 368 " --> pdb=" O ILE F 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR E 441 " --> pdb=" O THR E 453 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 406 through 407 removed outlier: 3.746A pdb=" N SER E 487 " --> pdb=" O GLN E 407 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 389 through 390 removed outlier: 3.561A pdb=" N ILE F 389 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR G 366 " --> pdb=" O MET G 362 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET G 362 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER G 368 " --> pdb=" O ILE G 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 399 through 401 removed outlier: 3.861A pdb=" N TYR F 441 " --> pdb=" O THR F 453 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER F 487 " --> pdb=" O GLN F 407 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR G 441 " --> pdb=" O THR G 453 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER G 487 " --> pdb=" O GLN G 407 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1743 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: 4.51 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2973 1.33 - 1.45: 3346 1.45 - 1.57: 8941 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 15407 Sorted by residual: bond pdb=" C PHE B 375 " pdb=" N PRO B 376 " ideal model delta sigma weight residual 1.334 1.205 0.129 2.34e-02 1.83e+03 3.05e+01 bond pdb=" C PHE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.334 1.205 0.129 2.34e-02 1.83e+03 3.02e+01 bond pdb=" C PHE E 375 " pdb=" N PRO E 376 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 3.01e+01 bond pdb=" C PHE C 375 " pdb=" N PRO C 376 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 3.00e+01 bond pdb=" C PHE F 375 " pdb=" N PRO F 376 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 3.00e+01 ... (remaining 15402 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.83: 447 106.83 - 113.94: 8795 113.94 - 121.06: 7404 121.06 - 128.17: 4102 128.17 - 135.28: 105 Bond angle restraints: 20853 Sorted by residual: angle pdb=" C LYS C 374 " pdb=" N PHE C 375 " pdb=" CA PHE C 375 " ideal model delta sigma weight residual 121.83 135.28 -13.45 1.56e+00 4.11e-01 7.43e+01 angle pdb=" C LYS D 374 " pdb=" N PHE D 375 " pdb=" CA PHE D 375 " ideal model delta sigma weight residual 121.83 135.26 -13.43 1.56e+00 4.11e-01 7.41e+01 angle pdb=" C LYS F 374 " pdb=" N PHE F 375 " pdb=" CA PHE F 375 " ideal model delta sigma weight residual 121.83 135.25 -13.42 1.56e+00 4.11e-01 7.40e+01 angle pdb=" C LYS E 374 " pdb=" N PHE E 375 " pdb=" CA PHE E 375 " ideal model delta sigma weight residual 121.83 135.23 -13.40 1.56e+00 4.11e-01 7.38e+01 angle pdb=" C LYS G 374 " pdb=" N PHE G 375 " pdb=" CA PHE G 375 " ideal model delta sigma weight residual 121.83 135.20 -13.37 1.56e+00 4.11e-01 7.35e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.59: 7795 10.59 - 21.17: 1081 21.17 - 31.76: 287 31.76 - 42.34: 105 42.34 - 52.93: 42 Dihedral angle restraints: 9310 sinusoidal: 3563 harmonic: 5747 Sorted by residual: dihedral pdb=" CA TRP E 253 " pdb=" C TRP E 253 " pdb=" N PHE E 254 " pdb=" CA PHE E 254 " ideal model delta harmonic sigma weight residual 180.00 149.23 30.77 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA TRP B 253 " pdb=" C TRP B 253 " pdb=" N PHE B 254 " pdb=" CA PHE B 254 " ideal model delta harmonic sigma weight residual 180.00 149.31 30.69 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA TRP G 253 " pdb=" C TRP G 253 " pdb=" N PHE G 254 " pdb=" CA PHE G 254 " ideal model delta harmonic sigma weight residual 180.00 149.33 30.67 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 9307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1556 0.059 - 0.117: 621 0.117 - 0.176: 283 0.176 - 0.234: 53 0.234 - 0.293: 14 Chirality restraints: 2527 Sorted by residual: chirality pdb=" CB ILE G 459 " pdb=" CA ILE G 459 " pdb=" CG1 ILE G 459 " pdb=" CG2 ILE G 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE F 459 " pdb=" CA ILE F 459 " pdb=" CG1 ILE F 459 " pdb=" CG2 ILE F 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE A 459 " pdb=" CA ILE A 459 " pdb=" CG1 ILE A 459 " pdb=" CG2 ILE A 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 2524 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 355 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C VAL F 355 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL F 355 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU F 356 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 355 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C VAL B 355 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL B 355 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 356 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 355 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" C VAL A 355 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL A 355 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 356 " 0.018 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 587 2.70 - 3.25: 14426 3.25 - 3.80: 23785 3.80 - 4.35: 31622 4.35 - 4.90: 51212 Nonbonded interactions: 121632 Sorted by model distance: nonbonded pdb=" OG1 THR A 491 " pdb=" OE2 GLU G 446 " model vdw 2.148 2.440 nonbonded pdb=" OE2 GLU C 446 " pdb=" OG1 THR D 491 " model vdw 2.215 2.440 nonbonded pdb=" OE2 GLU B 446 " pdb=" OG1 THR C 491 " model vdw 2.234 2.440 nonbonded pdb=" OE2 GLU F 446 " pdb=" OG1 THR G 491 " model vdw 2.249 2.440 nonbonded pdb=" OE2 GLU E 446 " pdb=" OG1 THR F 491 " model vdw 2.253 2.440 ... (remaining 121627 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9744 2.51 5 N 2548 2.21 5 O 2793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.020 Extract box with map and model: 4.890 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.120 Process input model: 41.790 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.129 15407 Z= 0.719 Angle : 1.350 13.450 20853 Z= 0.725 Chirality : 0.076 0.293 2527 Planarity : 0.007 0.046 2604 Dihedral : 11.789 52.927 5600 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -6.19 (0.13), residues: 1995 helix: -4.35 (0.08), residues: 973 sheet: -2.72 (0.30), residues: 224 loop : -4.01 (0.18), residues: 798 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 298 time to evaluate : 1.888 Fit side-chains outliers start: 23 outliers final: 0 residues processed: 316 average time/residue: 0.2899 time to fit residues: 132.0181 Evaluate side-chains 191 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 407 GLN B 358 GLN B 407 GLN B 470 GLN C 358 GLN C 407 GLN C 470 GLN D 358 GLN D 470 GLN E 358 GLN E 407 GLN F 358 GLN G 358 GLN G 407 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 15407 Z= 0.228 Angle : 0.719 9.550 20853 Z= 0.373 Chirality : 0.047 0.155 2527 Planarity : 0.005 0.035 2604 Dihedral : 6.548 22.611 2114 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 4.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.15), residues: 1995 helix: -3.08 (0.13), residues: 973 sheet: -1.92 (0.31), residues: 238 loop : -4.33 (0.17), residues: 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 235 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 41 residues processed: 296 average time/residue: 0.2572 time to fit residues: 114.1885 Evaluate side-chains 250 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 209 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1479 time to fit residues: 13.3539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 143 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN A 470 GLN B 358 GLN B 470 GLN C 457 ASN C 470 GLN D 339 GLN D 358 GLN D 484 HIS F 457 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15407 Z= 0.216 Angle : 0.666 7.232 20853 Z= 0.342 Chirality : 0.046 0.142 2527 Planarity : 0.004 0.026 2604 Dihedral : 5.939 18.788 2114 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer Outliers : 4.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.16), residues: 1995 helix: -2.26 (0.15), residues: 959 sheet: -2.19 (0.30), residues: 266 loop : -4.16 (0.17), residues: 770 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 216 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 45 residues processed: 281 average time/residue: 0.2616 time to fit residues: 110.4218 Evaluate side-chains 238 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 193 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.1592 time to fit residues: 15.0493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 119 optimal weight: 0.0370 chunk 178 optimal weight: 0.0770 chunk 189 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 470 GLN B 470 GLN C 470 GLN C 484 HIS D 484 HIS E 358 GLN F 470 GLN G 358 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 15407 Z= 0.157 Angle : 0.609 8.704 20853 Z= 0.315 Chirality : 0.044 0.137 2527 Planarity : 0.003 0.026 2604 Dihedral : 5.554 17.118 2114 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.17), residues: 1995 helix: -1.65 (0.17), residues: 924 sheet: -2.13 (0.30), residues: 266 loop : -4.11 (0.16), residues: 805 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 24 residues processed: 242 average time/residue: 0.2532 time to fit residues: 91.8545 Evaluate side-chains 203 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1424 time to fit residues: 9.6635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 96 optimal weight: 0.3980 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN C 358 GLN C 484 HIS D 484 HIS E 339 GLN F 358 GLN F 470 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15407 Z= 0.191 Angle : 0.614 6.901 20853 Z= 0.315 Chirality : 0.045 0.145 2527 Planarity : 0.003 0.024 2604 Dihedral : 5.494 17.019 2114 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.17), residues: 1995 helix: -1.49 (0.17), residues: 924 sheet: -2.04 (0.30), residues: 266 loop : -4.05 (0.17), residues: 805 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 1.615 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 216 average time/residue: 0.2505 time to fit residues: 80.7009 Evaluate side-chains 203 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1260 time to fit residues: 6.9666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN C 484 HIS E 339 GLN E 470 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15407 Z= 0.171 Angle : 0.586 7.945 20853 Z= 0.302 Chirality : 0.044 0.135 2527 Planarity : 0.003 0.027 2604 Dihedral : 5.343 16.165 2114 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.17), residues: 1995 helix: -1.20 (0.17), residues: 910 sheet: -1.87 (0.31), residues: 266 loop : -3.99 (0.17), residues: 819 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.516 Fit side-chains outliers start: 28 outliers final: 18 residues processed: 209 average time/residue: 0.2906 time to fit residues: 92.7242 Evaluate side-chains 191 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1383 time to fit residues: 7.3121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 0.0020 chunk 87 optimal weight: 2.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN C 484 HIS D 484 HIS E 339 GLN F 471 GLN ** F 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15407 Z= 0.222 Angle : 0.619 8.399 20853 Z= 0.317 Chirality : 0.046 0.249 2527 Planarity : 0.003 0.025 2604 Dihedral : 5.433 17.635 2114 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.17), residues: 1995 helix: -1.25 (0.16), residues: 952 sheet: -1.78 (0.31), residues: 266 loop : -3.97 (0.17), residues: 777 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 178 time to evaluate : 1.762 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 189 average time/residue: 0.2680 time to fit residues: 76.0505 Evaluate side-chains 176 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1339 time to fit residues: 4.3706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.1980 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN C 484 HIS D 484 HIS E 339 GLN F 471 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15407 Z= 0.181 Angle : 0.601 11.851 20853 Z= 0.306 Chirality : 0.045 0.222 2527 Planarity : 0.003 0.028 2604 Dihedral : 5.289 17.122 2114 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.17), residues: 1995 helix: -1.03 (0.17), residues: 938 sheet: -1.72 (0.32), residues: 266 loop : -3.89 (0.17), residues: 791 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 1.744 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 185 average time/residue: 0.2603 time to fit residues: 72.6594 Evaluate side-chains 175 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.726 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1364 time to fit residues: 3.4159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.0570 chunk 180 optimal weight: 0.2980 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 138 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN F 471 GLN ** G 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 15407 Z= 0.150 Angle : 0.595 12.181 20853 Z= 0.301 Chirality : 0.044 0.202 2527 Planarity : 0.003 0.030 2604 Dihedral : 5.051 16.559 2114 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.18), residues: 1995 helix: -0.89 (0.17), residues: 952 sheet: -1.68 (0.31), residues: 266 loop : -3.75 (0.18), residues: 777 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.861 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 185 average time/residue: 0.2548 time to fit residues: 73.0391 Evaluate side-chains 168 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1253 time to fit residues: 4.1705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.0070 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 0.0670 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 195 optimal weight: 0.0670 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 120 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 overall best weight: 0.1274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN C 484 HIS D 358 GLN D 484 HIS E 339 GLN F 471 GLN ** G 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 15407 Z= 0.135 Angle : 0.602 12.807 20853 Z= 0.300 Chirality : 0.043 0.208 2527 Planarity : 0.003 0.033 2604 Dihedral : 4.796 17.211 2114 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.18), residues: 1995 helix: -0.56 (0.17), residues: 945 sheet: -1.59 (0.31), residues: 266 loop : -3.57 (0.18), residues: 784 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.864 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 172 average time/residue: 0.2536 time to fit residues: 66.4703 Evaluate side-chains 156 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1326 time to fit residues: 3.4935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 HIS C 339 GLN F 470 GLN F 471 GLN ** F 484 HIS ** 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 = 0.4181 r_free = 0.4181 target = 0.201529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155789 restraints weight = 14164.062| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.39 r_work: 0.3365 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 15407 Z= 0.363 Angle : 0.739 12.042 20853 Z= 0.370 Chirality : 0.050 0.249 2527 Planarity : 0.004 0.059 2604 Dihedral : 5.641 19.081 2114 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.17), residues: 1995 helix: -1.04 (0.16), residues: 987 sheet: -1.63 (0.32), residues: 266 loop : -3.83 (0.18), residues: 742 =============================================================================== Job complete usr+sys time: 2873.81 seconds wall clock time: 53 minutes 19.84 seconds (3199.84 seconds total)