Starting phenix.real_space_refine on Fri Feb 16 09:04:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnm_27574/02_2024/8dnm_27574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnm_27574/02_2024/8dnm_27574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnm_27574/02_2024/8dnm_27574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnm_27574/02_2024/8dnm_27574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnm_27574/02_2024/8dnm_27574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnm_27574/02_2024/8dnm_27574.pdb" } resolution = 2.76 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= 0.021 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 72 5.16 5 C 9368 2.51 5 N 2556 2.21 5 O 2884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 229": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3720 Classifications: {'peptide': 483} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Chain: "B" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3720 Classifications: {'peptide': 483} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Chain: "C" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3720 Classifications: {'peptide': 483} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Chain: "D" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3720 Classifications: {'peptide': 483} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Time building chain proxies: 7.94, per 1000 atoms: 0.53 Number of scatterers: 14880 At special positions: 0 Unit cell: (129.47, 90.95, 99.51, 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 72 16.00 O 2884 8.00 N 2556 7.00 C 9368 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: 6.27 Conformation dependent library (CDL) restraints added in 3.0 seconds 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 43.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.556A pdb=" N THR A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 131 Processing helix chain 'A' and resid 145 through 159 removed outlier: 4.083A pdb=" N GLN A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 227 removed outlier: 4.030A pdb=" N HIS A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 247 removed outlier: 4.263A pdb=" N GLU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 286 through 292 removed outlier: 4.152A pdb=" N HIS A 289 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.615A pdb=" N PHE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 360 through 370 Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.618A pdb=" N LYS A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 removed outlier: 3.556A pdb=" N THR B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 131 Processing helix chain 'B' and resid 145 through 159 removed outlier: 4.085A pdb=" N GLN B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 219 through 227 removed outlier: 4.030A pdb=" N HIS B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 247 removed outlier: 4.263A pdb=" N GLU B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 286 through 292 removed outlier: 4.152A pdb=" N HIS B 289 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.615A pdb=" N PHE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 385 through 392 Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.618A pdb=" N LYS B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 99 removed outlier: 3.556A pdb=" N THR C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 131 Processing helix chain 'C' and resid 145 through 159 removed outlier: 4.083A pdb=" N GLN C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 219 through 227 removed outlier: 4.031A pdb=" N HIS C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 247 removed outlier: 4.263A pdb=" N GLU C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 286 through 292 removed outlier: 4.152A pdb=" N HIS C 289 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.616A pdb=" N PHE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 360 through 370 Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 385 through 392 Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.619A pdb=" N LYS C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.556A pdb=" N THR D 93 " --> pdb=" O PHE D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'D' and resid 145 through 159 removed outlier: 4.083A pdb=" N GLN D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 219 through 227 removed outlier: 4.030A pdb=" N HIS D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 224 " --> pdb=" O PRO D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 247 removed outlier: 4.262A pdb=" N GLU D 232 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 279 through 285 Processing helix chain 'D' and resid 286 through 292 removed outlier: 4.152A pdb=" N HIS D 289 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 301 removed outlier: 3.616A pdb=" N PHE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 385 through 392 Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.618A pdb=" N LYS D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE D 482 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR A 36 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A 45 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 34 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR A 36 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A 45 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 34 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL A 65 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS A 23 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL A 25 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 64 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 409 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL A 446 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 411 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP A 415 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG A 440 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL A 417 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU A 438 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LEU A 444 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU A 455 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 446 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.841A pdb=" N GLY A 69 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE A 104 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP A 71 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP A 106 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N HIS A 73 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N VAL A 108 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A 102 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N SER A 136 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 104 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS A 138 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP A 106 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP A 140 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 108 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER A 163 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR A 167 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE A 164 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N HIS A 198 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 166 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA A 195 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 253 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 197 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 255 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR A 275 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR A 253 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU A 277 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR B 36 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 45 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 34 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR B 36 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 45 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 34 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL B 65 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS B 23 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N VAL B 25 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET B 64 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU B 409 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL B 446 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 411 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP B 415 " --> pdb=" O ARG B 440 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG B 440 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL B 417 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU B 438 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LEU B 444 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 455 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 446 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 69 through 74 removed outlier: 6.841A pdb=" N GLY B 69 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE B 104 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP B 71 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP B 106 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS B 73 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N VAL B 108 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR B 102 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N SER B 136 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE B 104 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N HIS B 138 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP B 106 " --> pdb=" O HIS B 138 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP B 140 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 108 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER B 163 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR B 167 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE B 164 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N HIS B 198 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL B 166 " --> pdb=" O HIS B 198 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA B 195 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR B 253 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 197 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL B 255 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR B 275 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR B 253 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU B 277 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR C 36 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 45 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 34 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR C 36 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 45 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 34 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL C 65 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS C 23 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL C 25 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C 64 " --> pdb=" O TRP C 412 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 409 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 446 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 411 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP C 415 " --> pdb=" O ARG C 440 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG C 440 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C 417 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU C 438 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LEU C 444 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU C 455 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 446 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 74 removed outlier: 6.842A pdb=" N GLY C 69 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE C 104 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP C 71 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP C 106 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS C 73 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N VAL C 108 " --> pdb=" O HIS C 73 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR C 102 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER C 136 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 104 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS C 138 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP C 106 " --> pdb=" O HIS C 138 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP C 140 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 108 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER C 163 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR C 167 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE C 164 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N HIS C 198 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL C 166 " --> pdb=" O HIS C 198 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA C 195 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 253 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 197 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL C 255 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR C 275 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR C 253 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU C 277 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AB4, first strand: chain 'D' and resid 41 through 46 removed outlier: 6.672A pdb=" N TYR D 36 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 45 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP D 34 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 41 through 46 removed outlier: 6.672A pdb=" N TYR D 36 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 45 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP D 34 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL D 65 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS D 23 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL D 25 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET D 64 " --> pdb=" O TRP D 412 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU D 409 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL D 446 " --> pdb=" O LEU D 409 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 411 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP D 415 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG D 440 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL D 417 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N GLU D 438 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LEU D 444 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU D 455 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL D 446 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 69 through 74 removed outlier: 6.842A pdb=" N GLY D 69 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE D 104 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP D 71 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP D 106 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS D 73 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N VAL D 108 " --> pdb=" O HIS D 73 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR D 102 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER D 136 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE D 104 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS D 138 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP D 106 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP D 140 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 108 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER D 163 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR D 167 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE D 164 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N HIS D 198 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL D 166 " --> pdb=" O HIS D 198 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA D 195 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR D 253 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 197 " --> pdb=" O THR D 253 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL D 255 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR D 275 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR D 253 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU D 277 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 79 through 80 648 hydrogen bonds defined for protein. 1800 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: 5.36 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2584 1.31 - 1.43: 3729 1.43 - 1.55: 8736 1.55 - 1.68: 19 1.68 - 1.80: 116 Bond restraints: 15184 Sorted by residual: bond pdb=" C VAL A 494 " pdb=" N PRO A 495 " ideal model delta sigma weight residual 1.333 1.364 -0.030 1.01e-02 9.80e+03 9.07e+00 bond pdb=" C VAL C 494 " pdb=" N PRO C 495 " ideal model delta sigma weight residual 1.333 1.364 -0.030 1.01e-02 9.80e+03 8.86e+00 bond pdb=" C VAL B 494 " pdb=" N PRO B 495 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.01e-02 9.80e+03 8.58e+00 bond pdb=" C VAL D 494 " pdb=" N PRO D 495 " ideal model delta sigma weight residual 1.333 1.363 -0.029 1.01e-02 9.80e+03 8.37e+00 bond pdb=" CA VAL B 494 " pdb=" C VAL B 494 " ideal model delta sigma weight residual 1.524 1.553 -0.029 1.05e-02 9.07e+03 7.39e+00 ... (remaining 15179 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 394 106.15 - 113.13: 8213 113.13 - 120.11: 5427 120.11 - 127.09: 6377 127.09 - 134.07: 189 Bond angle restraints: 20600 Sorted by residual: angle pdb=" N LEU A 488 " pdb=" CA LEU A 488 " pdb=" C LEU A 488 " ideal model delta sigma weight residual 111.82 117.04 -5.22 1.16e+00 7.43e-01 2.02e+01 angle pdb=" N LEU B 488 " pdb=" CA LEU B 488 " pdb=" C LEU B 488 " ideal model delta sigma weight residual 111.82 117.01 -5.19 1.16e+00 7.43e-01 2.01e+01 angle pdb=" N LEU D 488 " pdb=" CA LEU D 488 " pdb=" C LEU D 488 " ideal model delta sigma weight residual 111.82 117.01 -5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" N LEU C 488 " pdb=" CA LEU C 488 " pdb=" C LEU C 488 " ideal model delta sigma weight residual 111.82 116.98 -5.16 1.16e+00 7.43e-01 1.98e+01 angle pdb=" N GLU C 229 " pdb=" CA GLU C 229 " pdb=" C GLU C 229 " ideal model delta sigma weight residual 112.23 106.63 5.60 1.26e+00 6.30e-01 1.98e+01 ... (remaining 20595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 8396 17.55 - 35.11: 580 35.11 - 52.66: 99 52.66 - 70.21: 29 70.21 - 87.77: 12 Dihedral angle restraints: 9116 sinusoidal: 3588 harmonic: 5528 Sorted by residual: dihedral pdb=" C VAL C 224 " pdb=" N VAL C 224 " pdb=" CA VAL C 224 " pdb=" CB VAL C 224 " ideal model delta harmonic sigma weight residual -122.00 -134.71 12.71 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" C VAL B 224 " pdb=" N VAL B 224 " pdb=" CA VAL B 224 " pdb=" CB VAL B 224 " ideal model delta harmonic sigma weight residual -122.00 -134.68 12.68 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" C VAL A 224 " pdb=" N VAL A 224 " pdb=" CA VAL A 224 " pdb=" CB VAL A 224 " ideal model delta harmonic sigma weight residual -122.00 -134.66 12.66 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 9113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1932 0.066 - 0.133: 331 0.133 - 0.199: 45 0.199 - 0.265: 12 0.265 - 0.332: 4 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA VAL A 224 " pdb=" N VAL A 224 " pdb=" C VAL A 224 " pdb=" CB VAL A 224 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA VAL B 224 " pdb=" N VAL B 224 " pdb=" C VAL B 224 " pdb=" CB VAL B 224 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA VAL C 224 " pdb=" N VAL C 224 " pdb=" C VAL C 224 " pdb=" CB VAL C 224 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 2321 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 227 " 0.062 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO C 228 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 227 " 0.062 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO D 228 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 228 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 228 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 227 " -0.061 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO A 228 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.051 5.00e-02 4.00e+02 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2190 2.75 - 3.29: 15410 3.29 - 3.83: 27094 3.83 - 4.36: 34524 4.36 - 4.90: 55753 Nonbonded interactions: 134971 Sorted by model distance: nonbonded pdb=" NZ LYS D 258 " pdb=" OG1 THR D 312 " model vdw 2.217 2.520 nonbonded pdb=" NZ LYS A 258 " pdb=" OG1 THR A 312 " model vdw 2.217 2.520 nonbonded pdb=" NZ LYS C 258 " pdb=" OG1 THR C 312 " model vdw 2.217 2.520 nonbonded pdb=" NZ LYS B 258 " pdb=" OG1 THR B 312 " model vdw 2.217 2.520 nonbonded pdb=" OG1 THR C 419 " pdb=" OE1 GLU C 438 " model vdw 2.273 2.440 ... (remaining 134966 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' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 6.460 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 43.060 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 0.048 15184 Z= 0.381 Angle : 0.853 10.729 20600 Z= 0.522 Chirality : 0.053 0.332 2324 Planarity : 0.007 0.094 2684 Dihedral : 12.930 87.767 5564 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.86 % Allowed : 1.23 % Favored : 97.90 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 9.09 % 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: -1.12 (0.18), residues: 1924 helix: 0.66 (0.19), residues: 748 sheet: -2.12 (0.27), residues: 304 loop : -1.42 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 412 HIS 0.008 0.002 HIS A 425 PHE 0.009 0.001 PHE C 380 TYR 0.015 0.002 TYR B 275 ARG 0.007 0.001 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 1.722 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 210 average time/residue: 1.7813 time to fit residues: 402.3553 Evaluate side-chains 86 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 247 ASN B 77 GLN B 247 ASN B 266 GLN C 77 GLN C 247 ASN C 266 GLN D 77 GLN D 247 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15184 Z= 0.210 Angle : 0.519 4.874 20600 Z= 0.279 Chirality : 0.042 0.124 2324 Planarity : 0.005 0.053 2684 Dihedral : 4.382 20.125 2060 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.49 % Allowed : 8.77 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.46 (0.19), residues: 1924 helix: 1.17 (0.19), residues: 764 sheet: -1.53 (0.27), residues: 344 loop : -1.11 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 295 HIS 0.006 0.001 HIS D 138 PHE 0.016 0.001 PHE C 316 TYR 0.010 0.001 TYR A 290 ARG 0.008 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.800 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 128 average time/residue: 1.4696 time to fit residues: 206.3895 Evaluate side-chains 92 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 289 HIS A 379 GLN B 247 ASN B 289 HIS B 379 GLN C 247 ASN C 289 HIS C 379 GLN D 247 ASN D 289 HIS D 379 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 15184 Z= 0.380 Angle : 0.557 5.661 20600 Z= 0.296 Chirality : 0.044 0.146 2324 Planarity : 0.004 0.031 2684 Dihedral : 4.327 20.629 2060 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.36 % Allowed : 10.56 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.19 (0.19), residues: 1924 helix: 1.35 (0.19), residues: 764 sheet: -1.20 (0.33), residues: 256 loop : -1.08 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.007 0.001 HIS B 425 PHE 0.009 0.001 PHE A 316 TYR 0.012 0.002 TYR A 251 ARG 0.004 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.620 Fit side-chains outliers start: 22 outliers final: 4 residues processed: 112 average time/residue: 1.6529 time to fit residues: 201.2723 Evaluate side-chains 92 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15184 Z= 0.202 Angle : 0.473 4.958 20600 Z= 0.251 Chirality : 0.041 0.124 2324 Planarity : 0.003 0.029 2684 Dihedral : 4.068 20.558 2060 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.86 % Allowed : 11.98 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.18 (0.19), residues: 1924 helix: 1.66 (0.19), residues: 764 sheet: -1.14 (0.33), residues: 248 loop : -0.83 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 295 HIS 0.005 0.001 HIS B 425 PHE 0.008 0.001 PHE D 316 TYR 0.007 0.001 TYR C 479 ARG 0.002 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.617 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 94 average time/residue: 1.5760 time to fit residues: 162.1504 Evaluate side-chains 89 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15184 Z= 0.200 Angle : 0.462 4.923 20600 Z= 0.244 Chirality : 0.041 0.124 2324 Planarity : 0.003 0.028 2684 Dihedral : 3.935 20.090 2060 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.99 % Allowed : 12.41 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.49 (0.19), residues: 1924 helix: 1.78 (0.19), residues: 764 sheet: -1.04 (0.35), residues: 228 loop : -0.51 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.005 0.001 HIS A 425 PHE 0.008 0.001 PHE A 380 TYR 0.008 0.001 TYR C 251 ARG 0.007 0.000 ARG C 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 1.732 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 105 average time/residue: 1.5165 time to fit residues: 174.4443 Evaluate side-chains 91 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 365 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 overall best weight: 1.6484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 15184 Z= 0.329 Angle : 0.529 7.559 20600 Z= 0.276 Chirality : 0.043 0.128 2324 Planarity : 0.004 0.031 2684 Dihedral : 4.075 20.485 2060 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.05 % Allowed : 12.59 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.31 (0.19), residues: 1924 helix: 1.77 (0.19), residues: 764 sheet: -1.54 (0.31), residues: 296 loop : -0.50 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 295 HIS 0.008 0.001 HIS C 425 PHE 0.009 0.001 PHE B 380 TYR 0.011 0.002 TYR D 251 ARG 0.008 0.001 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 1.872 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 95 average time/residue: 1.4586 time to fit residues: 152.7734 Evaluate side-chains 92 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15184 Z= 0.287 Angle : 0.506 6.088 20600 Z= 0.265 Chirality : 0.042 0.125 2324 Planarity : 0.003 0.030 2684 Dihedral : 4.043 20.536 2060 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.11 % Allowed : 12.16 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.61 (0.19), residues: 1924 helix: 1.83 (0.19), residues: 764 sheet: -1.23 (0.38), residues: 200 loop : -0.35 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.006 0.001 HIS A 425 PHE 0.009 0.001 PHE D 380 TYR 0.009 0.001 TYR C 251 ARG 0.007 0.001 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.977 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 98 average time/residue: 1.3948 time to fit residues: 151.8148 Evaluate side-chains 92 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 17 optimal weight: 0.0670 chunk 145 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15184 Z= 0.184 Angle : 0.472 5.904 20600 Z= 0.245 Chirality : 0.041 0.123 2324 Planarity : 0.003 0.027 2684 Dihedral : 3.913 20.212 2060 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.30 % Allowed : 12.53 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.76 (0.19), residues: 1924 helix: 1.98 (0.19), residues: 764 sheet: -1.07 (0.34), residues: 236 loop : -0.26 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 295 HIS 0.005 0.001 HIS A 425 PHE 0.008 0.001 PHE D 380 TYR 0.007 0.001 TYR D 251 ARG 0.007 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.860 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 101 average time/residue: 1.3793 time to fit residues: 154.5482 Evaluate side-chains 92 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 ASN C 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 15184 Z= 0.460 Angle : 0.564 6.003 20600 Z= 0.297 Chirality : 0.045 0.142 2324 Planarity : 0.004 0.055 2684 Dihedral : 4.171 20.459 2060 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.86 % Allowed : 13.46 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.58 (0.19), residues: 1924 helix: 1.78 (0.19), residues: 764 sheet: -1.18 (0.39), residues: 200 loop : -0.37 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 295 HIS 0.010 0.002 HIS A 425 PHE 0.010 0.002 PHE D 380 TYR 0.012 0.002 TYR B 251 ARG 0.014 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 2.009 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 94 average time/residue: 1.4442 time to fit residues: 149.9873 Evaluate side-chains 92 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15184 Z= 0.206 Angle : 0.482 5.719 20600 Z= 0.252 Chirality : 0.042 0.124 2324 Planarity : 0.004 0.053 2684 Dihedral : 4.001 20.658 2060 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.11 % Allowed : 13.27 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.70 (0.19), residues: 1924 helix: 1.93 (0.19), residues: 764 sheet: -0.78 (0.34), residues: 256 loop : -0.39 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 295 HIS 0.005 0.001 HIS A 425 PHE 0.008 0.001 PHE D 380 TYR 0.007 0.001 TYR A 251 ARG 0.013 0.001 ARG A 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 1.875 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 98 average time/residue: 1.4120 time to fit residues: 154.2625 Evaluate side-chains 92 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.062180 restraints weight = 28847.163| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.73 r_work: 0.2734 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15184 Z= 0.281 Angle : 0.493 5.480 20600 Z= 0.261 Chirality : 0.043 0.127 2324 Planarity : 0.004 0.051 2684 Dihedral : 4.046 20.599 2060 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.80 % Allowed : 13.83 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.69 (0.19), residues: 1924 helix: 1.87 (0.19), residues: 764 sheet: -1.28 (0.39), residues: 196 loop : -0.26 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 295 HIS 0.007 0.001 HIS A 425 PHE 0.009 0.001 PHE A 380 TYR 0.008 0.001 TYR D 251 ARG 0.013 0.001 ARG A 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3872.66 seconds wall clock time: 70 minutes 45.25 seconds (4245.25 seconds total)