Starting phenix.real_space_refine on Mon Jan 20 03:50:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5k_19738/01_2025/8s5k_19738_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5k_19738/01_2025/8s5k_19738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s5k_19738/01_2025/8s5k_19738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5k_19738/01_2025/8s5k_19738.map" model { file = "/net/cci-nas-00/data/ceres_data/8s5k_19738/01_2025/8s5k_19738_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5k_19738/01_2025/8s5k_19738_trim.cif" } resolution = 3.8 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= 0.012 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: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 8 5.49 5 S 176 5.16 5 C 20216 2.51 5 N 5536 2.21 5 O 5960 1.98 5 H 31936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 63840 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.04, per 1000 atoms: 0.39 Number of scatterers: 63840 At special positions: 0 Unit cell: (161.582, 240.038, 150.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 S 176 16.00 P 8 15.00 O 5960 8.00 N 5536 7.00 C 20216 6.00 H 31936 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.18 Conformation dependent library (CDL) restraints added in 4.0 seconds 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7456 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 38 sheets defined 46.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.157A pdb=" N ILE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.731A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 226 through 244 removed outlier: 3.533A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.969A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.610A pdb=" N ASN A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 398 through 404 Processing helix chain 'A' and resid 405 through 406 No H-bonds generated for 'chain 'A' and resid 405 through 406' Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.814A pdb=" N HIS A 411 " --> pdb=" O TRP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.653A pdb=" N ARG A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.818A pdb=" N LYS A 481 " --> pdb=" O GLN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 99 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 119 through 134 removed outlier: 4.010A pdb=" N ILE B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 162 removed outlier: 4.118A pdb=" N GLY B 153 " --> pdb=" O ASN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.711A pdb=" N VAL B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 226 through 245 removed outlier: 3.888A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 272 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.948A pdb=" N ASN B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.955A pdb=" N VAL B 319 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 341 Processing helix chain 'B' and resid 347 through 361 removed outlier: 3.690A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.993A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 398 through 404 removed outlier: 3.557A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 406 No H-bonds generated for 'chain 'B' and resid 405 through 406' Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.953A pdb=" N HIS B 411 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 430 through 441 removed outlier: 3.749A pdb=" N ARG B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 93 through 99 removed outlier: 3.638A pdb=" N LYS C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 133 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.758A pdb=" N VAL C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.713A pdb=" N TRP C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.934A pdb=" N HIS C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 258 through 272 removed outlier: 4.067A pdb=" N ILE C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 327 through 343 removed outlier: 3.578A pdb=" N ALA C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 361 removed outlier: 3.754A pdb=" N VAL C 356 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.714A pdb=" N ASN C 380 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET C 382 " --> pdb=" O ARG C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 398 through 404 Processing helix chain 'C' and resid 405 through 406 No H-bonds generated for 'chain 'C' and resid 405 through 406' Processing helix chain 'C' and resid 407 through 412 removed outlier: 4.047A pdb=" N HIS C 411 " --> pdb=" O TRP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 430 through 442 removed outlier: 3.652A pdb=" N ARG C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 495 through 504 removed outlier: 3.645A pdb=" N GLU C 504 " --> pdb=" O SER C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 548 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 148 through 162 Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.719A pdb=" N VAL D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.859A pdb=" N HIS D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 Processing helix chain 'D' and resid 258 through 272 removed outlier: 3.611A pdb=" N ILE D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 removed outlier: 3.732A pdb=" N GLN D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 327 through 343 removed outlier: 3.691A pdb=" N ALA D 331 " --> pdb=" O ASN D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 361 removed outlier: 3.740A pdb=" N LYS D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 377 through 382 removed outlier: 3.841A pdb=" N ASN D 380 " --> pdb=" O SER D 377 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET D 382 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 395 Processing helix chain 'D' and resid 398 through 405 removed outlier: 4.587A pdb=" N LYS D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 removed outlier: 4.167A pdb=" N HIS D 411 " --> pdb=" O TRP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 430 through 440 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 535 through 548 removed outlier: 3.627A pdb=" N GLU D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.553A pdb=" N LEU E 124 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.713A pdb=" N VAL E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 214 Processing helix chain 'E' and resid 226 through 235 removed outlier: 3.842A pdb=" N HIS E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 244 Processing helix chain 'E' and resid 258 through 272 removed outlier: 3.608A pdb=" N ILE E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 267 " --> pdb=" O GLY E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 316 through 320 Processing helix chain 'E' and resid 327 through 343 removed outlier: 3.638A pdb=" N ALA E 331 " --> pdb=" O ASN E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 361 removed outlier: 3.820A pdb=" N LYS E 359 " --> pdb=" O ALA E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 377 through 382 removed outlier: 3.783A pdb=" N ASN E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET E 382 " --> pdb=" O ARG E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 395 Processing helix chain 'E' and resid 398 through 404 Processing helix chain 'E' and resid 407 through 412 removed outlier: 4.190A pdb=" N HIS E 411 " --> pdb=" O TRP E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 417 Processing helix chain 'E' and resid 430 through 442 removed outlier: 3.711A pdb=" N LYS E 441 " --> pdb=" O ILE E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 471 Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 535 through 548 Processing helix chain 'F' and resid 59 through 63 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 93 through 99 removed outlier: 3.769A pdb=" N LYS F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 133 Processing helix chain 'F' and resid 148 through 162 Processing helix chain 'F' and resid 174 through 185 removed outlier: 3.745A pdb=" N VAL F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 214 removed outlier: 3.823A pdb=" N TRP F 208 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 235 removed outlier: 3.933A pdb=" N HIS F 232 " --> pdb=" O ASN F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 244 Processing helix chain 'F' and resid 258 through 272 removed outlier: 4.134A pdb=" N ILE F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS F 267 " --> pdb=" O GLY F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 327 through 343 removed outlier: 3.598A pdb=" N ALA F 331 " --> pdb=" O ASN F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 361 removed outlier: 3.752A pdb=" N VAL F 356 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 377 through 382 removed outlier: 3.742A pdb=" N ASN F 380 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET F 382 " --> pdb=" O ARG F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 394 Processing helix chain 'F' and resid 398 through 404 Processing helix chain 'F' and resid 405 through 406 No H-bonds generated for 'chain 'F' and resid 405 through 406' Processing helix chain 'F' and resid 407 through 412 removed outlier: 4.031A pdb=" N HIS F 411 " --> pdb=" O TRP F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 417 Processing helix chain 'F' and resid 430 through 442 removed outlier: 3.693A pdb=" N ARG F 439 " --> pdb=" O ILE F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 471 Processing helix chain 'F' and resid 495 through 504 removed outlier: 3.605A pdb=" N GLU F 504 " --> pdb=" O SER F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 548 Processing helix chain 'G' and resid 59 through 63 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 93 through 99 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 119 through 133 removed outlier: 4.290A pdb=" N ILE G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 162 removed outlier: 4.161A pdb=" N GLY G 153 " --> pdb=" O ASN G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 185 removed outlier: 3.797A pdb=" N VAL G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 Processing helix chain 'G' and resid 226 through 245 removed outlier: 3.516A pdb=" N LEU G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS G 232 " --> pdb=" O ASN G 228 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA G 237 " --> pdb=" O TYR G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 272 Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 316 through 320 removed outlier: 4.121A pdb=" N VAL G 319 " --> pdb=" O ASP G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 341 Processing helix chain 'G' and resid 347 through 361 removed outlier: 3.665A pdb=" N LYS G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 377 through 382 removed outlier: 3.930A pdb=" N ASN G 380 " --> pdb=" O SER G 377 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET G 382 " --> pdb=" O ARG G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 398 through 405 removed outlier: 3.928A pdb=" N LYS G 405 " --> pdb=" O ASP G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 412 removed outlier: 4.001A pdb=" N HIS G 411 " --> pdb=" O TRP G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 417 Processing helix chain 'G' and resid 430 through 441 removed outlier: 3.754A pdb=" N ARG G 439 " --> pdb=" O ILE G 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 471 Processing helix chain 'G' and resid 478 through 482 Processing helix chain 'G' and resid 495 through 504 Processing helix chain 'G' and resid 535 through 548 Processing helix chain 'H' and resid 59 through 63 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 110 through 113 removed outlier: 3.731A pdb=" N ASN H 113 " --> pdb=" O GLU H 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 110 through 113' Processing helix chain 'H' and resid 119 through 134 Processing helix chain 'H' and resid 148 through 162 Processing helix chain 'H' and resid 174 through 184 removed outlier: 3.882A pdb=" N VAL H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 214 Processing helix chain 'H' and resid 226 through 235 Processing helix chain 'H' and resid 235 through 244 Processing helix chain 'H' and resid 258 through 272 Processing helix chain 'H' and resid 290 through 294 Processing helix chain 'H' and resid 327 through 343 removed outlier: 3.580A pdb=" N GLY H 343 " --> pdb=" O ILE H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 361 removed outlier: 3.946A pdb=" N LYS H 359 " --> pdb=" O ALA H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 364 No H-bonds generated for 'chain 'H' and resid 362 through 364' Processing helix chain 'H' and resid 377 through 382 removed outlier: 4.061A pdb=" N MET H 382 " --> pdb=" O ARG H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 395 Processing helix chain 'H' and resid 398 through 404 Processing helix chain 'H' and resid 405 through 406 No H-bonds generated for 'chain 'H' and resid 405 through 406' Processing helix chain 'H' and resid 407 through 412 Processing helix chain 'H' and resid 413 through 417 Processing helix chain 'H' and resid 430 through 442 removed outlier: 3.726A pdb=" N ARG H 439 " --> pdb=" O ILE H 435 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 471 Processing helix chain 'H' and resid 478 through 482 Processing helix chain 'H' and resid 495 through 504 Processing helix chain 'H' and resid 535 through 548 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.004A pdb=" N SER A 254 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 449 removed outlier: 3.524A pdb=" N VAL A 459 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.507A pdb=" N LYS A 488 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A 512 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 490 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLU A 514 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA A 509 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL A 533 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 511 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.803A pdb=" N LEU B 374 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET B 250 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE B 373 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL B 252 " --> pdb=" O ILE B 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.174A pdb=" N ILE B 142 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 168 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU B 144 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 423 through 425 removed outlier: 6.518A pdb=" N LYS C 488 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C 512 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE C 490 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU C 514 " --> pdb=" O ILE C 490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 423 through 425 removed outlier: 3.729A pdb=" N GLY C 532 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS C 513 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL C 530 " --> pdb=" O HIS C 513 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN C 515 " --> pdb=" O GLN C 528 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLN C 528 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN C 517 " --> pdb=" O GLN C 526 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLN C 526 " --> pdb=" O GLN C 517 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 445 through 449 Processing sheet with id=AB1, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.981A pdb=" N ALA B 509 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL B 533 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 511 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 513 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET B 529 " --> pdb=" O HIS B 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 488 through 490 removed outlier: 7.502A pdb=" N THR C 424 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE B 516 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 92 removed outlier: 4.664A pdb=" N LEU C 105 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 187 through 191 removed outlier: 6.582A pdb=" N CYS C 165 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL C 189 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE C 167 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR C 191 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET C 169 " --> pdb=" O THR C 191 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 445 through 449 removed outlier: 7.046A pdb=" N ALA C 446 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N MET C 458 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL C 448 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 5.103A pdb=" N SER D 254 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 253 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE D 277 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N PHE D 324 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY D 279 " --> pdb=" O PHE D 324 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER D 326 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP D 281 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 187 through 191 Processing sheet with id=AB8, first strand: chain 'D' and resid 423 through 425 removed outlier: 6.701A pdb=" N LYS E 488 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL E 512 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE E 490 " --> pdb=" O VAL E 512 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLU E 514 " --> pdb=" O ILE E 490 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 423 through 425 removed outlier: 6.991A pdb=" N ALA E 509 " --> pdb=" O VAL E 533 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL E 533 " --> pdb=" O ALA E 509 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL E 511 " --> pdb=" O PHE E 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 445 through 449 removed outlier: 7.187A pdb=" N ALA D 446 " --> pdb=" O MET D 458 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N MET D 458 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL D 448 " --> pdb=" O LEU D 456 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 488 through 490 removed outlier: 6.648A pdb=" N LYS D 488 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL D 512 " --> pdb=" O LYS D 488 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE D 490 " --> pdb=" O VAL D 512 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLU D 514 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA D 509 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL D 533 " --> pdb=" O ALA D 509 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL D 511 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 488 through 490 removed outlier: 6.648A pdb=" N LYS D 488 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL D 512 " --> pdb=" O LYS D 488 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE D 490 " --> pdb=" O VAL D 512 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLU D 514 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR E 424 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE D 516 " --> pdb=" O THR E 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 76 through 77 removed outlier: 3.522A pdb=" N ARG F 91 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU F 105 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 89 through 91 removed outlier: 5.038A pdb=" N SER E 254 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 253 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE E 277 " --> pdb=" O LYS E 322 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N PHE E 324 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY E 279 " --> pdb=" O PHE E 324 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER E 326 " --> pdb=" O GLY E 279 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP E 281 " --> pdb=" O SER E 326 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 187 through 191 Processing sheet with id=AC7, first strand: chain 'E' and resid 445 through 449 removed outlier: 7.161A pdb=" N ALA E 446 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N MET E 458 " --> pdb=" O ALA E 446 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL E 448 " --> pdb=" O LEU E 456 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 187 through 191 removed outlier: 6.550A pdb=" N CYS F 165 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL F 189 " --> pdb=" O CYS F 165 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE F 167 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N THR F 191 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET F 169 " --> pdb=" O THR F 191 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 423 through 425 Processing sheet with id=AD1, first strand: chain 'F' and resid 423 through 425 removed outlier: 7.136A pdb=" N ALA G 509 " --> pdb=" O VAL G 533 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL G 533 " --> pdb=" O ALA G 509 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL G 511 " --> pdb=" O PHE G 531 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 445 through 449 removed outlier: 7.073A pdb=" N ALA F 446 " --> pdb=" O MET F 458 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N MET F 458 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL F 448 " --> pdb=" O LEU F 456 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 488 through 491 removed outlier: 6.971A pdb=" N ALA F 509 " --> pdb=" O VAL F 533 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL F 533 " --> pdb=" O ALA F 509 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL F 511 " --> pdb=" O PHE F 531 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 488 through 491 removed outlier: 7.403A pdb=" N THR G 424 " --> pdb=" O GLU F 514 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE F 516 " --> pdb=" O THR G 424 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 76 through 77 removed outlier: 6.027A pdb=" N GLU H 104 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL H 372 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU H 106 " --> pdb=" O VAL H 372 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE H 373 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER H 254 " --> pdb=" O ILE H 373 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 322 through 326 removed outlier: 6.663A pdb=" N MET G 250 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE G 373 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL G 252 " --> pdb=" O ILE G 373 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU G 104 " --> pdb=" O CYS G 370 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL G 372 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU G 106 " --> pdb=" O VAL G 372 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU G 374 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LYS G 108 " --> pdb=" O LEU G 374 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 187 through 190 removed outlier: 6.169A pdb=" N ILE G 142 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL G 168 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU G 144 " --> pdb=" O VAL G 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 445 through 449 removed outlier: 3.628A pdb=" N VAL G 459 " --> pdb=" O ALA G 446 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 187 through 191 Processing sheet with id=AE1, first strand: chain 'H' and resid 445 through 449 removed outlier: 6.859A pdb=" N ALA H 446 " --> pdb=" O MET H 458 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N MET H 458 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL H 448 " --> pdb=" O LEU H 456 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 488 through 491 removed outlier: 6.291A pdb=" N LYS H 488 " --> pdb=" O LEU H 510 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL H 512 " --> pdb=" O LYS H 488 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE H 490 " --> pdb=" O VAL H 512 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N GLU H 514 " --> pdb=" O ILE H 490 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA H 509 " --> pdb=" O VAL H 533 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL H 533 " --> pdb=" O ALA H 509 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL H 511 " --> pdb=" O PHE H 531 " (cutoff:3.500A) 1341 hydrogen bonds defined for protein. 3633 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: 22.81 Time building geometry restraints manager: 16.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 31729 1.08 - 1.32: 5797 1.32 - 1.56: 26666 1.56 - 1.81: 233 1.81 - 2.05: 79 Bond restraints: 64504 Sorted by residual: bond pdb=" C6 LLP C 119 " pdb=" H6 LLP C 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C4' LLP E 119 " pdb="H4'1 LLP E 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" C6 LLP F 119 " pdb=" H6 LLP F 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" C4' LLP C 119 " pdb="H4'1 LLP C 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C6 LLP H 119 " pdb=" H6 LLP H 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.86e+01 ... (remaining 64499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.57: 117063 7.57 - 15.13: 10 15.13 - 22.70: 1 22.70 - 30.26: 2 30.26 - 37.83: 4 Bond angle restraints: 117080 Sorted by residual: angle pdb=" O LLP E 119 " pdb=" C LLP E 119 " pdb=" N ASP E 120 " ideal model delta sigma weight residual 123.00 85.17 37.83 1.60e+00 3.91e-01 5.59e+02 angle pdb=" O LLP G 119 " pdb=" C LLP G 119 " pdb=" N ASP G 120 " ideal model delta sigma weight residual 123.00 85.40 37.60 1.60e+00 3.91e-01 5.52e+02 angle pdb=" O LLP D 119 " pdb=" C LLP D 119 " pdb=" N ASP D 120 " ideal model delta sigma weight residual 123.00 85.55 37.45 1.60e+00 3.91e-01 5.48e+02 angle pdb=" O LLP F 119 " pdb=" C LLP F 119 " pdb=" N ASP F 120 " ideal model delta sigma weight residual 123.00 91.76 31.24 1.60e+00 3.91e-01 3.81e+02 angle pdb=" O LLP C 119 " pdb=" C LLP C 119 " pdb=" N ASP C 120 " ideal model delta sigma weight residual 123.00 93.04 29.96 1.60e+00 3.91e-01 3.51e+02 ... (remaining 117075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 27312 20.80 - 41.60: 1860 41.60 - 62.39: 591 62.39 - 83.19: 107 83.19 - 103.99: 26 Dihedral angle restraints: 29896 sinusoidal: 16800 harmonic: 13096 Sorted by residual: dihedral pdb=" CA LYS H 384 " pdb=" C LYS H 384 " pdb=" N PHE H 385 " pdb=" CA PHE H 385 " ideal model delta harmonic sigma weight residual 180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LYS A 384 " pdb=" C LYS A 384 " pdb=" N PHE A 385 " pdb=" CA PHE A 385 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LYS F 384 " pdb=" C LYS F 384 " pdb=" N PHE F 385 " pdb=" CA PHE F 385 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 29893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3271 0.031 - 0.061: 1113 0.061 - 0.092: 268 0.092 - 0.123: 268 0.123 - 0.153: 40 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA PRO D 375 " pdb=" N PRO D 375 " pdb=" C PRO D 375 " pdb=" CB PRO D 375 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA PRO E 375 " pdb=" N PRO E 375 " pdb=" C PRO E 375 " pdb=" CB PRO E 375 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA PRO G 375 " pdb=" N PRO G 375 " pdb=" C PRO G 375 " pdb=" CB PRO G 375 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 4957 not shown) Planarity restraints: 9504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP E 119 " 0.136 2.00e-02 2.50e+03 2.19e-01 4.78e+02 pdb=" C LLP E 119 " -0.378 2.00e-02 2.50e+03 pdb=" O LLP E 119 " 0.131 2.00e-02 2.50e+03 pdb=" N ASP E 120 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP G 119 " -0.135 2.00e-02 2.50e+03 2.17e-01 4.73e+02 pdb=" C LLP G 119 " 0.376 2.00e-02 2.50e+03 pdb=" O LLP G 119 " -0.132 2.00e-02 2.50e+03 pdb=" N ASP G 120 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP D 119 " 0.135 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" C LLP D 119 " -0.376 2.00e-02 2.50e+03 pdb=" O LLP D 119 " 0.130 2.00e-02 2.50e+03 pdb=" N ASP D 120 " 0.110 2.00e-02 2.50e+03 ... (remaining 9501 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1943 2.13 - 2.75: 120731 2.75 - 3.37: 188585 3.37 - 3.98: 239189 3.98 - 4.60: 376442 Nonbonded interactions: 926890 Sorted by model distance: nonbonded pdb=" OE1 GLU F 297 " pdb=" H GLU F 297 " model vdw 1.516 2.450 nonbonded pdb=" O GLN B 415 " pdb="HE21 GLN C 415 " model vdw 1.564 2.450 nonbonded pdb=" H GLY A 115 " pdb=" OD2 ASP A 120 " model vdw 1.575 2.450 nonbonded pdb=" OE2 GLU D 304 " pdb=" HZ2 LYS D 384 " model vdw 1.588 2.450 nonbonded pdb=" H SER B 117 " pdb=" OD2 ASP B 120 " model vdw 1.592 2.450 ... (remaining 926885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 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' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.320 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: 0.890 Extract box with map and model: 2.060 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 105.790 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 : 0.004 0.085 32568 Z= 0.272 Angle : 0.752 37.830 44232 Z= 0.417 Chirality : 0.041 0.153 4960 Planarity : 0.008 0.219 5656 Dihedral : 14.704 103.991 12120 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.04 % Favored : 96.84 % Rotamer: Outliers : 0.15 % Allowed : 10.69 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.58 (0.14), residues: 4016 helix: 0.51 (0.14), residues: 1490 sheet: 0.02 (0.19), residues: 772 loop : 0.71 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.007 0.001 HIS G 232 PHE 0.022 0.001 PHE H 531 TYR 0.012 0.001 TYR C 163 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 248 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 LEU cc_start: 0.7433 (mm) cc_final: 0.7206 (mm) REVERT: E 505 MET cc_start: 0.7080 (mmm) cc_final: 0.6867 (mmt) outliers start: 5 outliers final: 5 residues processed: 250 average time/residue: 0.9128 time to fit residues: 361.6972 Evaluate side-chains 240 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 235 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 146 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 0.6980 chunk 303 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 204 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 233 optimal weight: 0.5980 chunk 363 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.173029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.141024 restraints weight = 185834.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.141668 restraints weight = 309645.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.143236 restraints weight = 206072.687| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32568 Z= 0.200 Angle : 0.550 7.558 44232 Z= 0.280 Chirality : 0.042 0.164 4960 Planarity : 0.004 0.066 5656 Dihedral : 8.606 98.309 4456 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.79 % Allowed : 10.16 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.59 (0.14), residues: 4016 helix: 0.55 (0.14), residues: 1516 sheet: 0.07 (0.19), residues: 772 loop : 0.66 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 409 HIS 0.009 0.001 HIS G 232 PHE 0.014 0.001 PHE B 531 TYR 0.014 0.001 TYR C 163 ARG 0.005 0.000 ARG G 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 4.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 279 average time/residue: 0.9320 time to fit residues: 417.2867 Evaluate side-chains 261 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain H residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 313 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 321 optimal weight: 30.0000 chunk 193 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 340 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.173270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.140848 restraints weight = 184918.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.143873 restraints weight = 305900.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.144206 restraints weight = 181038.744| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32568 Z= 0.275 Angle : 0.549 7.643 44232 Z= 0.280 Chirality : 0.043 0.184 4960 Planarity : 0.004 0.069 5656 Dihedral : 8.538 97.859 4454 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.02 % Allowed : 10.92 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.42 (0.13), residues: 4016 helix: 0.46 (0.14), residues: 1530 sheet: 0.06 (0.20), residues: 684 loop : 0.43 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 390 HIS 0.010 0.001 HIS H 232 PHE 0.014 0.001 PHE B 531 TYR 0.014 0.001 TYR C 163 ARG 0.005 0.000 ARG G 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 3.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 171 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7611 (tm-30) REVERT: F 548 ARG cc_start: 0.4831 (mtm110) cc_final: 0.4615 (mtp-110) outliers start: 35 outliers final: 28 residues processed: 265 average time/residue: 0.8250 time to fit residues: 353.9350 Evaluate side-chains 260 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 320 optimal weight: 20.0000 chunk 321 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS C 415 GLN D 194 ASN E 194 ASN G 489 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.170154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.137517 restraints weight = 184299.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.140330 restraints weight = 318647.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.140841 restraints weight = 190732.775| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 32568 Z= 0.412 Angle : 0.616 7.507 44232 Z= 0.318 Chirality : 0.045 0.222 4960 Planarity : 0.005 0.080 5656 Dihedral : 8.683 98.088 4454 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 1.43 % Allowed : 11.68 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.08 (0.13), residues: 4016 helix: 0.22 (0.13), residues: 1524 sheet: -0.57 (0.19), residues: 714 loop : 0.14 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 54 HIS 0.008 0.001 HIS F 203 PHE 0.019 0.002 PHE D 385 TYR 0.018 0.002 TYR F 163 ARG 0.004 0.001 ARG F 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 4.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 VAL cc_start: 0.5385 (t) cc_final: 0.5117 (t) REVERT: C 382 MET cc_start: 0.9177 (mmm) cc_final: 0.8532 (mmt) outliers start: 49 outliers final: 35 residues processed: 256 average time/residue: 0.8393 time to fit residues: 343.5515 Evaluate side-chains 249 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 384 LYS Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 228 optimal weight: 0.6980 chunk 362 optimal weight: 5.9990 chunk 274 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 320 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 323 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.168268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.135710 restraints weight = 185006.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.138846 restraints weight = 314620.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.138861 restraints weight = 170645.560| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 32568 Z= 0.338 Angle : 0.580 7.997 44232 Z= 0.295 Chirality : 0.043 0.206 4960 Planarity : 0.004 0.076 5656 Dihedral : 8.543 97.522 4454 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 1.40 % Allowed : 12.70 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.05 (0.13), residues: 4016 helix: 0.30 (0.13), residues: 1530 sheet: -0.66 (0.19), residues: 712 loop : 0.15 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 409 HIS 0.007 0.001 HIS F 203 PHE 0.024 0.001 PHE G 531 TYR 0.017 0.002 TYR F 163 ARG 0.004 0.000 ARG E 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 VAL cc_start: 0.5404 (t) cc_final: 0.5122 (t) REVERT: C 382 MET cc_start: 0.9171 (mmm) cc_final: 0.8564 (mmt) outliers start: 48 outliers final: 37 residues processed: 248 average time/residue: 0.9079 time to fit residues: 369.5780 Evaluate side-chains 247 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 384 LYS Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 370 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 390 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 366 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.169581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.136645 restraints weight = 184542.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.138538 restraints weight = 302555.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.139367 restraints weight = 203902.993| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32568 Z= 0.234 Angle : 0.536 8.311 44232 Z= 0.268 Chirality : 0.042 0.171 4960 Planarity : 0.004 0.071 5656 Dihedral : 8.372 96.766 4454 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 1.46 % Allowed : 13.00 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.15 (0.14), residues: 4016 helix: 0.53 (0.14), residues: 1530 sheet: -0.63 (0.19), residues: 712 loop : 0.25 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 409 HIS 0.006 0.001 HIS B 232 PHE 0.022 0.001 PHE C 531 TYR 0.016 0.001 TYR F 163 ARG 0.003 0.000 ARG F 548 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 5.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.7313 (mpp) cc_final: 0.7040 (mpp) REVERT: B 448 VAL cc_start: 0.5372 (t) cc_final: 0.5076 (t) REVERT: C 382 MET cc_start: 0.9132 (mmm) cc_final: 0.8470 (mmt) REVERT: H 483 ILE cc_start: 0.3421 (OUTLIER) cc_final: 0.3207 (mt) outliers start: 50 outliers final: 40 residues processed: 255 average time/residue: 0.9014 time to fit residues: 372.4333 Evaluate side-chains 255 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.8980 chunk 319 optimal weight: 20.0000 chunk 148 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 370 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.170383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.137976 restraints weight = 184841.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.138435 restraints weight = 322655.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.140351 restraints weight = 207926.564| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32568 Z= 0.208 Angle : 0.522 8.248 44232 Z= 0.259 Chirality : 0.042 0.159 4960 Planarity : 0.004 0.066 5656 Dihedral : 8.240 95.923 4454 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 1.52 % Allowed : 12.91 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.29 (0.14), residues: 4016 helix: 0.69 (0.14), residues: 1530 sheet: -0.58 (0.19), residues: 724 loop : 0.30 (0.16), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 390 HIS 0.006 0.001 HIS B 232 PHE 0.017 0.001 PHE C 531 TYR 0.014 0.001 TYR F 163 ARG 0.006 0.000 ARG F 491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 VAL cc_start: 0.5233 (t) cc_final: 0.4936 (t) REVERT: C 382 MET cc_start: 0.9169 (mmm) cc_final: 0.8541 (mmt) REVERT: H 483 ILE cc_start: 0.3453 (OUTLIER) cc_final: 0.3241 (mt) outliers start: 52 outliers final: 44 residues processed: 258 average time/residue: 0.8397 time to fit residues: 351.2572 Evaluate side-chains 266 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 277 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 348 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 193 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.170367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.137464 restraints weight = 184782.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.140305 restraints weight = 301711.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.140697 restraints weight = 182132.828| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32568 Z= 0.213 Angle : 0.520 7.996 44232 Z= 0.257 Chirality : 0.042 0.159 4960 Planarity : 0.004 0.066 5656 Dihedral : 8.169 95.263 4454 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 1.49 % Allowed : 13.03 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.36 (0.14), residues: 4016 helix: 0.76 (0.14), residues: 1530 sheet: -0.57 (0.19), residues: 724 loop : 0.34 (0.16), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 410 HIS 0.006 0.001 HIS B 232 PHE 0.016 0.001 PHE C 531 TYR 0.013 0.001 TYR F 163 ARG 0.005 0.000 ARG F 491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 VAL cc_start: 0.5352 (t) cc_final: 0.5085 (t) REVERT: C 382 MET cc_start: 0.9191 (mmm) cc_final: 0.8544 (mmt) REVERT: H 483 ILE cc_start: 0.3570 (OUTLIER) cc_final: 0.3356 (mt) outliers start: 51 outliers final: 43 residues processed: 257 average time/residue: 0.8268 time to fit residues: 347.1971 Evaluate side-chains 264 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 357 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 386 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.169920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.137141 restraints weight = 184116.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.138587 restraints weight = 308586.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.139716 restraints weight = 203581.482| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32568 Z= 0.240 Angle : 0.529 7.810 44232 Z= 0.263 Chirality : 0.042 0.172 4960 Planarity : 0.004 0.066 5656 Dihedral : 8.151 94.812 4454 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 1.40 % Allowed : 13.32 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.33 (0.14), residues: 4016 helix: 0.74 (0.14), residues: 1530 sheet: -0.61 (0.19), residues: 724 loop : 0.34 (0.16), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 43 HIS 0.006 0.001 HIS B 232 PHE 0.015 0.001 PHE C 531 TYR 0.013 0.001 TYR F 163 ARG 0.005 0.000 ARG F 491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.6743 (tpp) cc_final: 0.6454 (tpp) REVERT: B 448 VAL cc_start: 0.5051 (t) cc_final: 0.4763 (t) REVERT: C 382 MET cc_start: 0.9183 (mmm) cc_final: 0.8570 (mmt) REVERT: H 173 MET cc_start: 0.7058 (tpp) cc_final: 0.6827 (tpp) REVERT: H 483 ILE cc_start: 0.3503 (OUTLIER) cc_final: 0.3280 (mt) outliers start: 48 outliers final: 43 residues processed: 252 average time/residue: 0.8703 time to fit residues: 357.6356 Evaluate side-chains 260 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 155 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 323 optimal weight: 8.9990 chunk 348 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 169 optimal weight: 1.9990 chunk 395 optimal weight: 9.9990 chunk 150 optimal weight: 0.0470 chunk 209 optimal weight: 1.9990 chunk 332 optimal weight: 6.9990 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.168054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.134566 restraints weight = 184684.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.137667 restraints weight = 314214.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.138081 restraints weight = 186968.132| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 32568 Z= 0.344 Angle : 0.576 7.281 44232 Z= 0.291 Chirality : 0.043 0.209 4960 Planarity : 0.004 0.069 5656 Dihedral : 8.251 94.297 4454 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 1.31 % Allowed : 13.55 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.12 (0.14), residues: 4016 helix: 0.57 (0.14), residues: 1530 sheet: -0.75 (0.19), residues: 724 loop : 0.22 (0.16), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 43 HIS 0.007 0.001 HIS F 203 PHE 0.018 0.001 PHE D 385 TYR 0.014 0.001 TYR F 163 ARG 0.004 0.000 ARG F 491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.6768 (tpp) cc_final: 0.6512 (tpp) REVERT: B 448 VAL cc_start: 0.5235 (t) cc_final: 0.4948 (t) REVERT: C 382 MET cc_start: 0.9192 (mmm) cc_final: 0.8628 (mmt) REVERT: H 483 ILE cc_start: 0.3578 (OUTLIER) cc_final: 0.3361 (mt) outliers start: 45 outliers final: 38 residues processed: 248 average time/residue: 0.8381 time to fit residues: 335.4953 Evaluate side-chains 248 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 214 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 264 optimal weight: 0.8980 chunk 246 optimal weight: 0.9980 chunk 256 optimal weight: 0.4980 chunk 395 optimal weight: 8.9990 chunk 369 optimal weight: 10.0000 chunk 379 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.171991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.140125 restraints weight = 183699.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.141788 restraints weight = 302391.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.142773 restraints weight = 198864.771| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32568 Z= 0.189 Angle : 0.523 8.209 44232 Z= 0.256 Chirality : 0.041 0.158 4960 Planarity : 0.004 0.065 5656 Dihedral : 8.093 92.900 4454 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 1.02 % Allowed : 13.93 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.37 (0.14), residues: 4016 helix: 0.77 (0.14), residues: 1530 sheet: -0.63 (0.19), residues: 724 loop : 0.37 (0.16), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 409 HIS 0.006 0.001 HIS B 232 PHE 0.015 0.001 PHE G 531 TYR 0.019 0.001 TYR A 308 ARG 0.004 0.000 ARG F 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12064.28 seconds wall clock time: 210 minutes 2.62 seconds (12602.62 seconds total)