Starting phenix.real_space_refine on Mon Jan 13 20:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5i_19736/01_2025/8s5i_19736_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5i_19736/01_2025/8s5i_19736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s5i_19736/01_2025/8s5i_19736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5i_19736/01_2025/8s5i_19736.map" model { file = "/net/cci-nas-00/data/ceres_data/8s5i_19736/01_2025/8s5i_19736_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5i_19736/01_2025/8s5i_19736_trim.cif" } resolution = 3.1 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= 0.004 sd= 0.284 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 6 7.16 5 P 6 5.49 5 S 132 5.16 5 C 15162 2.51 5 N 4152 2.21 5 O 4470 1.98 5 H 23952 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 47880 Number of models: 1 Model: "" Number of chains: 12 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: "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} Time building chain proxies: 16.53, per 1000 atoms: 0.35 Number of scatterers: 47880 At special positions: 0 Unit cell: (147.56, 138.88, 226.765, 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 6 26.01 S 132 16.00 P 6 15.00 O 4470 8.00 N 4152 7.00 C 15162 6.00 H 23952 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.37 Conformation dependent library (CDL) restraints added in 2.9 seconds 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5592 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 28 sheets defined 47.0% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 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 93 through 99 removed outlier: 4.271A pdb=" N LYS A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.826A 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 235 removed outlier: 3.747A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.669A pdb=" N GLN A 295 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.505A pdb=" N VAL A 319 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.753A 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: 3.964A pdb=" N ASN A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 4.118A 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 405 removed outlier: 4.020A pdb=" N LYS A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 4.363A 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 440 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.671A 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 547 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 removed outlier: 4.270A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) 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 133 Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.826A 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 235 removed outlier: 3.747A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 258 through 272 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.668A pdb=" N GLN B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.505A pdb=" N VAL B 319 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 343 Processing helix chain 'B' and resid 347 through 361 removed outlier: 3.753A 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: 3.963A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 398 through 405 removed outlier: 4.020A pdb=" N LYS B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.363A 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 440 Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.671A pdb=" N LYS B 481 " --> pdb=" O GLN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 535 through 547 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' 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 185 removed outlier: 3.781A pdb=" N VAL C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.799A 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 Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.540A pdb=" N GLN C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.634A pdb=" N VAL C 319 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 343 Processing helix chain 'C' and resid 347 through 361 removed outlier: 4.305A 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: 4.001A pdb=" N ASN C 380 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 4.047A 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: 4.389A 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: 3.517A pdb=" N LYS C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.695A pdb=" N LYS C 481 " --> pdb=" O GLN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 535 through 547 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 79 through 84 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 removed outlier: 3.613A pdb=" N GLY D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.735A 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: 3.866A pdb=" N HIS D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 245 Processing helix chain 'D' and resid 258 through 272 Processing helix chain 'D' and resid 290 through 295 removed outlier: 3.644A pdb=" N GLN D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.664A pdb=" N VAL D 319 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 342 Processing helix chain 'D' and resid 347 through 361 removed outlier: 4.038A 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: 3.882A pdb=" N ASN D 380 " --> pdb=" O SER D 377 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET D 382 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 394 Processing helix chain 'D' and resid 398 through 405 removed outlier: 4.323A pdb=" N LYS D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 removed outlier: 3.856A 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 442 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.606A pdb=" N LYS D 481 " --> pdb=" O GLN D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 535 through 547 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 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 148 through 161 removed outlier: 3.730A pdb=" N GLY E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.934A pdb=" N VAL E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 212 Processing helix chain 'E' and resid 226 through 235 removed outlier: 3.909A pdb=" N HIS E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 245 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.754A pdb=" N GLN E 295 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 320 removed outlier: 3.594A pdb=" N VAL E 319 " --> pdb=" O ASP E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 removed outlier: 3.503A pdb=" N ALA E 331 " --> pdb=" O ASN E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 361 removed outlier: 4.234A 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: 3.794A pdb=" N ASN E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET E 382 " --> pdb=" O ARG E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 394 Processing helix chain 'E' and resid 398 through 404 Processing helix chain 'E' and resid 407 through 412 removed outlier: 4.057A 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 Processing helix chain 'E' and resid 461 through 470 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 547 Processing helix chain 'F' and resid 59 through 63 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 94 through 99 Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' 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: 3.832A pdb=" N VAL F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 214 Processing helix chain 'F' and resid 226 through 235 removed outlier: 3.885A 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 Processing helix chain 'F' and resid 290 through 295 removed outlier: 3.579A pdb=" N GLN F 295 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.714A pdb=" N VAL F 319 " --> pdb=" O ASP F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 341 Processing helix chain 'F' and resid 347 through 361 removed outlier: 4.326A 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: 4.032A pdb=" N ASN F 380 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 3.947A 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: 4.274A 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 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'F' and resid 478 through 482 removed outlier: 3.696A pdb=" N LYS F 481 " --> pdb=" O GLN F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 535 through 547 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.771A pdb=" N LEU A 105 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER A 254 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 251 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL A 280 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA A 253 " --> pdb=" O VAL A 280 " (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 423 through 425 removed outlier: 6.462A pdb=" N LYS F 488 " --> pdb=" O LEU F 510 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL F 512 " --> pdb=" O LYS F 488 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE F 490 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLU F 514 " --> pdb=" O ILE F 490 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 423 through 425 removed outlier: 6.352A pdb=" N ALA F 509 " --> pdb=" O VAL F 533 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL F 533 " --> pdb=" O ALA F 509 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL F 511 " --> pdb=" O PHE F 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 449 removed outlier: 7.355A pdb=" N ALA A 446 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N MET A 458 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 448 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.280A pdb=" N ALA A 509 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 533 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 511 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490 removed outlier: 7.699A pdb=" N THR F 424 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE A 516 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 92 removed outlier: 4.771A pdb=" N LEU B 105 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER B 254 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 251 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL B 280 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA B 253 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 191 Processing sheet with id=AB1, first strand: chain 'B' and resid 423 through 425 Processing sheet with id=AB2, first strand: chain 'B' and resid 423 through 425 removed outlier: 4.170A pdb=" N GLY C 532 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N HIS C 513 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL C 530 " --> pdb=" O HIS C 513 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLN C 515 " --> pdb=" O GLN C 528 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLN C 528 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN C 517 " --> pdb=" O GLN C 526 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLN C 526 " --> pdb=" O GLN C 517 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 449 removed outlier: 7.355A pdb=" N ALA B 446 " --> pdb=" O MET B 458 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N MET B 458 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 448 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.280A pdb=" N ALA B 509 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL B 533 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 511 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 490 removed outlier: 7.752A pdb=" N THR C 424 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE B 516 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 76 through 77 removed outlier: 5.397A pdb=" N SER D 254 " --> pdb=" O ILE D 373 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 322 through 326 removed outlier: 5.103A pdb=" N SER C 254 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU C 104 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL C 372 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU C 106 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU C 374 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS C 108 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET C 89 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 187 through 191 Processing sheet with id=AB9, first strand: chain 'C' and resid 445 through 449 removed outlier: 7.202A pdb=" N ALA C 446 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N MET C 458 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 448 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 187 through 191 Processing sheet with id=AC2, first strand: chain 'D' and resid 445 through 449 Processing sheet with id=AC3, first strand: chain 'D' and resid 488 through 491 removed outlier: 5.976A pdb=" N HIS D 513 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL D 530 " --> pdb=" O HIS D 513 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLN D 515 " --> pdb=" O GLN D 528 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLN D 528 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN D 517 " --> pdb=" O GLN D 526 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLN D 526 " --> pdb=" O GLN D 517 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 76 through 77 removed outlier: 7.328A pdb=" N LEU E 77 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER F 254 " --> pdb=" O ILE F 373 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE F 277 " --> pdb=" O LYS F 322 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE F 324 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY F 279 " --> pdb=" O PHE F 324 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N SER F 326 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP F 281 " --> pdb=" O SER F 326 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 322 through 326 removed outlier: 5.342A pdb=" N SER E 254 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU E 104 " --> pdb=" O CYS E 370 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL E 372 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU E 106 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU E 374 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS E 108 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET E 89 " --> pdb=" O LEU F 77 " (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: 7.099A pdb=" N ALA E 446 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N MET E 458 " --> pdb=" O ALA E 446 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL E 448 " --> pdb=" O LEU E 456 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 488 through 491 removed outlier: 3.762A pdb=" N GLY E 532 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N HIS E 513 " --> pdb=" O VAL E 530 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL E 530 " --> pdb=" O HIS E 513 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLN E 515 " --> pdb=" O GLN E 528 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLN E 528 " --> pdb=" O GLN E 515 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN E 517 " --> pdb=" O GLN E 526 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLN E 526 " --> pdb=" O GLN E 517 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 187 through 191 Processing sheet with id=AD1, first strand: chain 'F' and resid 445 through 449 removed outlier: 7.191A pdb=" N ALA F 446 " --> pdb=" O MET F 458 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N MET F 458 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL F 448 " --> pdb=" O LEU F 456 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2805 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: 16.75 Time building geometry restraints manager: 11.45 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: 23798 1.08 - 1.32: 4354 1.32 - 1.56: 19992 1.56 - 1.81: 182 1.81 - 2.05: 52 Bond restraints: 48378 Sorted by residual: bond pdb=" C4' LLP A 119 " pdb="H4'1 LLP A 119 " ideal model delta sigma weight residual 0.930 1.084 -0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C4' LLP F 119 " pdb="H4'1 LLP F 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 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 5.86e+01 bond pdb=" C4' LLP B 119 " pdb="H4'1 LLP B 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.84e+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 5.84e+01 ... (remaining 48373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 87244 2.04 - 4.07: 509 4.07 - 6.11: 41 6.11 - 8.15: 8 8.15 - 10.18: 8 Bond angle restraints: 87810 Sorted by residual: angle pdb=" OP1 LLP E 119 " pdb=" P LLP E 119 " pdb=" OP4 LLP E 119 " ideal model delta sigma weight residual 100.47 109.49 -9.02 3.00e+00 1.11e-01 9.04e+00 angle pdb=" OP1 LLP D 119 " pdb=" P LLP D 119 " pdb=" OP4 LLP D 119 " ideal model delta sigma weight residual 100.47 109.46 -8.99 3.00e+00 1.11e-01 8.98e+00 angle pdb=" OP1 LLP C 119 " pdb=" P LLP C 119 " pdb=" OP4 LLP C 119 " ideal model delta sigma weight residual 100.47 109.44 -8.97 3.00e+00 1.11e-01 8.94e+00 angle pdb=" OP1 LLP F 119 " pdb=" P LLP F 119 " pdb=" OP4 LLP F 119 " ideal model delta sigma weight residual 100.47 109.37 -8.90 3.00e+00 1.11e-01 8.80e+00 angle pdb=" OP1 LLP A 119 " pdb=" P LLP A 119 " pdb=" OP4 LLP A 119 " ideal model delta sigma weight residual 100.47 109.26 -8.79 3.00e+00 1.11e-01 8.59e+00 ... (remaining 87805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 20390 17.91 - 35.83: 1285 35.83 - 53.74: 541 53.74 - 71.66: 158 71.66 - 89.57: 48 Dihedral angle restraints: 22422 sinusoidal: 12600 harmonic: 9822 Sorted by residual: dihedral pdb=" CA LYS D 384 " pdb=" C LYS D 384 " pdb=" N PHE D 385 " pdb=" CA PHE D 385 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LYS C 384 " pdb=" C LYS C 384 " pdb=" N PHE C 385 " pdb=" CA PHE C 385 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LYS B 384 " pdb=" C LYS B 384 " pdb=" N PHE B 385 " pdb=" CA PHE B 385 " ideal model delta harmonic sigma weight residual -180.00 -162.07 -17.93 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 22419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2362 0.027 - 0.055: 857 0.055 - 0.082: 201 0.082 - 0.109: 197 0.109 - 0.136: 103 Chirality restraints: 3720 Sorted by residual: chirality pdb=" CA ILE C 311 " pdb=" N ILE C 311 " pdb=" C ILE C 311 " pdb=" CB ILE C 311 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE C 214 " pdb=" N ILE C 214 " pdb=" C ILE C 214 " pdb=" CB ILE C 214 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE F 311 " pdb=" N ILE F 311 " pdb=" C ILE F 311 " pdb=" CB ILE F 311 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 3717 not shown) Planarity restraints: 7128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP C 119 " 0.025 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C LLP C 119 " -0.086 2.00e-02 2.50e+03 pdb=" O LLP C 119 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP C 120 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP F 119 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C LLP F 119 " 0.055 2.00e-02 2.50e+03 pdb=" O LLP F 119 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP F 120 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP B 119 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.78e+00 pdb=" C LLP B 119 " -0.034 2.00e-02 2.50e+03 pdb=" O LLP B 119 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP B 120 " 0.011 2.00e-02 2.50e+03 ... (remaining 7125 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1734 2.15 - 2.76: 93623 2.76 - 3.38: 139278 3.38 - 3.99: 180597 3.99 - 4.60: 285618 Nonbonded interactions: 700850 Sorted by model distance: nonbonded pdb=" HH TYR A 484 " pdb=" OE2 GLU B 201 " model vdw 1.540 2.450 nonbonded pdb=" OE2 GLU A 201 " pdb=" HH TYR B 484 " model vdw 1.543 2.450 nonbonded pdb=" OE2 GLU C 304 " pdb=" HZ2 LYS C 384 " model vdw 1.585 2.450 nonbonded pdb=" O SER A 520 " pdb=" HG1 THR A 521 " model vdw 1.589 2.450 nonbonded pdb=" O SER B 520 " pdb=" HG1 THR B 521 " model vdw 1.589 2.450 ... (remaining 700845 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.600 Extract box with map and model: 1.270 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 76.070 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 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:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 0.081 24426 Z= 0.268 Angle : 0.575 10.184 33174 Z= 0.290 Chirality : 0.040 0.136 3720 Planarity : 0.004 0.050 4242 Dihedral : 13.531 89.574 9090 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.93 % Favored : 97.84 % Rotamer: Outliers : 0.58 % Allowed : 5.18 % Favored : 94.24 % 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: 0.50 (0.16), residues: 3012 helix: 0.25 (0.16), residues: 1186 sheet: 0.01 (0.23), residues: 536 loop : 0.84 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 390 HIS 0.006 0.001 HIS B 203 PHE 0.025 0.001 PHE C 531 TYR 0.009 0.001 TYR A 233 ARG 0.002 0.000 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 472 time to evaluate : 2.785 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: A 413 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8094 (mtm180) REVERT: A 415 GLN cc_start: 0.6892 (pp30) cc_final: 0.6143 (pp30) REVERT: B 415 GLN cc_start: 0.7118 (pp30) cc_final: 0.6853 (pp30) REVERT: C 329 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: C 401 ASP cc_start: 0.4123 (m-30) cc_final: 0.3739 (t0) REVERT: C 458 MET cc_start: 0.8025 (tpt) cc_final: 0.7816 (tpt) REVERT: C 540 LEU cc_start: 0.8316 (tt) cc_final: 0.8089 (mm) REVERT: D 382 MET cc_start: 0.7481 (mmm) cc_final: 0.7129 (mmt) REVERT: D 494 ASP cc_start: 0.3012 (m-30) cc_final: 0.2149 (m-30) REVERT: D 529 MET cc_start: 0.2543 (ttp) cc_final: 0.1578 (tpt) REVERT: E 140 ASP cc_start: 0.2591 (m-30) cc_final: 0.1679 (m-30) REVERT: E 320 VAL cc_start: 0.5660 (t) cc_final: 0.5459 (t) REVERT: E 529 MET cc_start: 0.2312 (ttp) cc_final: 0.1386 (tpt) REVERT: F 59 PRO cc_start: 0.0742 (Cg_endo) cc_final: 0.0456 (Cg_exo) REVERT: F 173 MET cc_start: 0.5538 (mmt) cc_final: 0.5293 (mmp) REVERT: F 415 GLN cc_start: 0.6775 (pp30) cc_final: 0.6539 (pp30) REVERT: F 469 LEU cc_start: 0.7438 (mm) cc_final: 0.6886 (tt) REVERT: F 491 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6567 (mtm-85) REVERT: F 527 ARG cc_start: 0.6726 (mmt90) cc_final: 0.6430 (mmt-90) REVERT: F 548 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.5281 (mmt-90) outliers start: 15 outliers final: 3 residues processed: 481 average time/residue: 0.8363 time to fit residues: 600.2418 Evaluate side-chains 285 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 279 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain F residue 491 ARG Chi-restraints excluded: chain F residue 548 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN C 415 GLN C 513 HIS E 113 ASN E 216 ASN F 113 ASN ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.220234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156615 restraints weight = 83837.391| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.26 r_work: 0.3326 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 24426 Z= 0.365 Angle : 0.610 13.344 33174 Z= 0.305 Chirality : 0.045 0.198 3720 Planarity : 0.005 0.045 4242 Dihedral : 8.741 89.441 3354 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Rotamer: Outliers : 1.48 % Allowed : 8.76 % Favored : 89.76 % 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: 0.71 (0.16), residues: 3012 helix: 0.50 (0.16), residues: 1150 sheet: 0.19 (0.24), residues: 476 loop : 0.80 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 390 HIS 0.008 0.002 HIS C 232 PHE 0.020 0.002 PHE F 531 TYR 0.014 0.002 TYR F 484 ARG 0.005 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 309 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 GLN cc_start: 0.7817 (pp30) cc_final: 0.7099 (pp30) REVERT: B 415 GLN cc_start: 0.7815 (pp30) cc_final: 0.7342 (pp30) REVERT: C 232 HIS cc_start: 0.5613 (m-70) cc_final: 0.5356 (m90) REVERT: C 329 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6223 (tt0) REVERT: C 416 GLU cc_start: 0.7789 (tt0) cc_final: 0.7422 (tp30) REVERT: C 540 LEU cc_start: 0.8585 (tt) cc_final: 0.8288 (mm) REVERT: D 337 MET cc_start: 0.7105 (mmt) cc_final: 0.6770 (mmm) REVERT: D 364 LEU cc_start: 0.5973 (mt) cc_final: 0.5625 (mt) REVERT: D 494 ASP cc_start: 0.3836 (m-30) cc_final: 0.3005 (m-30) REVERT: D 529 MET cc_start: 0.2085 (ttp) cc_final: 0.1028 (tpt) REVERT: E 250 MET cc_start: 0.4324 (ttp) cc_final: 0.4011 (tpp) REVERT: E 341 GLN cc_start: 0.7902 (mt0) cc_final: 0.7505 (mm110) REVERT: E 494 ASP cc_start: 0.4389 (m-30) cc_final: 0.3862 (m-30) REVERT: E 529 MET cc_start: 0.2124 (ttp) cc_final: 0.1348 (tpt) REVERT: F 232 HIS cc_start: 0.6444 (m-70) cc_final: 0.6018 (m-70) REVERT: F 415 GLN cc_start: 0.7555 (pp30) cc_final: 0.7189 (pp30) REVERT: F 491 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7280 (mtm-85) REVERT: F 548 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5633 (mmt-90) outliers start: 38 outliers final: 30 residues processed: 337 average time/residue: 0.7246 time to fit residues: 378.7731 Evaluate side-chains 292 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 491 ARG Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 548 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 170 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 ASN E 216 ASN F 113 ASN ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.219437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159582 restraints weight = 83957.881| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.06 r_work: 0.3372 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24426 Z= 0.273 Angle : 0.538 9.488 33174 Z= 0.268 Chirality : 0.043 0.173 3720 Planarity : 0.004 0.048 4242 Dihedral : 8.426 89.674 3350 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 1.21 % Allowed : 9.85 % Favored : 88.94 % 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: 0.85 (0.16), residues: 3012 helix: 0.70 (0.16), residues: 1140 sheet: 0.14 (0.24), residues: 470 loop : 0.84 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 390 HIS 0.006 0.001 HIS B 203 PHE 0.015 0.002 PHE F 99 TYR 0.013 0.001 TYR C 484 ARG 0.004 0.000 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 2.800 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: A 415 GLN cc_start: 0.7760 (pp30) cc_final: 0.6932 (pp30) REVERT: A 547 GLU cc_start: 0.7795 (tt0) cc_final: 0.7575 (tt0) REVERT: B 547 GLU cc_start: 0.7763 (tt0) cc_final: 0.7545 (tt0) REVERT: C 416 GLU cc_start: 0.7700 (tt0) cc_final: 0.7277 (tp30) REVERT: C 533 VAL cc_start: 0.9065 (m) cc_final: 0.8827 (t) REVERT: C 540 LEU cc_start: 0.8639 (tt) cc_final: 0.8328 (mm) REVERT: D 250 MET cc_start: 0.4128 (ttp) cc_final: 0.3444 (tpp) REVERT: D 276 ARG cc_start: 0.5915 (mmm160) cc_final: 0.5300 (mtm180) REVERT: D 337 MET cc_start: 0.7168 (mmt) cc_final: 0.6821 (mmm) REVERT: D 494 ASP cc_start: 0.3942 (m-30) cc_final: 0.3159 (m-30) REVERT: D 529 MET cc_start: 0.2155 (ttp) cc_final: 0.1089 (tpt) REVERT: E 250 MET cc_start: 0.4121 (ttp) cc_final: 0.3560 (tpp) REVERT: E 276 ARG cc_start: 0.6054 (mmm160) cc_final: 0.5663 (mtm180) REVERT: E 341 GLN cc_start: 0.7619 (mt0) cc_final: 0.7317 (mm110) REVERT: E 494 ASP cc_start: 0.4296 (m-30) cc_final: 0.3657 (m-30) REVERT: E 529 MET cc_start: 0.1294 (ttp) cc_final: 0.0955 (tpt) REVERT: F 304 GLU cc_start: 0.6375 (mp0) cc_final: 0.6048 (mp0) REVERT: F 415 GLN cc_start: 0.7480 (pp30) cc_final: 0.6966 (pp30) REVERT: F 491 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7288 (mtm-85) REVERT: F 540 LEU cc_start: 0.8636 (tt) cc_final: 0.8316 (mm) outliers start: 31 outliers final: 23 residues processed: 302 average time/residue: 0.6988 time to fit residues: 330.4234 Evaluate side-chains 276 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 491 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 91 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 272 optimal weight: 30.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN C 507 HIS E 216 ASN ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.219020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158785 restraints weight = 83445.709| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.98 r_work: 0.3343 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24426 Z= 0.323 Angle : 0.553 10.747 33174 Z= 0.275 Chirality : 0.043 0.191 3720 Planarity : 0.004 0.044 4242 Dihedral : 8.199 89.856 3340 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 1.48 % Allowed : 10.67 % Favored : 87.85 % 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: 0.78 (0.16), residues: 3012 helix: 0.72 (0.16), residues: 1124 sheet: 0.06 (0.23), residues: 478 loop : 0.74 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 390 HIS 0.007 0.001 HIS B 203 PHE 0.037 0.002 PHE C 531 TYR 0.010 0.002 TYR A 233 ARG 0.004 0.000 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 2.824 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: A 415 GLN cc_start: 0.7771 (pp30) cc_final: 0.6830 (pp30) REVERT: A 547 GLU cc_start: 0.7737 (tt0) cc_final: 0.7456 (tt0) REVERT: B 216 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.8082 (m-40) REVERT: B 415 GLN cc_start: 0.7943 (pp30) cc_final: 0.7409 (pp30) REVERT: B 547 GLU cc_start: 0.7695 (tt0) cc_final: 0.7412 (tt0) REVERT: C 264 ILE cc_start: 0.5522 (mt) cc_final: 0.5217 (tp) REVERT: C 304 GLU cc_start: 0.6089 (mp0) cc_final: 0.5862 (mp0) REVERT: C 416 GLU cc_start: 0.7746 (tt0) cc_final: 0.7458 (tp30) REVERT: C 540 LEU cc_start: 0.8642 (tt) cc_final: 0.8292 (mm) REVERT: D 250 MET cc_start: 0.4154 (ttp) cc_final: 0.3412 (tpp) REVERT: D 276 ARG cc_start: 0.5921 (mmm160) cc_final: 0.5308 (mtm180) REVERT: D 337 MET cc_start: 0.7178 (mmt) cc_final: 0.6811 (mmm) REVERT: D 494 ASP cc_start: 0.4024 (m-30) cc_final: 0.3397 (m-30) REVERT: D 529 MET cc_start: 0.1733 (ttp) cc_final: 0.0916 (tpt) REVERT: E 250 MET cc_start: 0.4160 (ttp) cc_final: 0.3502 (tpp) REVERT: E 276 ARG cc_start: 0.6037 (mmm160) cc_final: 0.5624 (mtm180) REVERT: E 341 GLN cc_start: 0.7697 (mt0) cc_final: 0.7418 (mm-40) REVERT: E 494 ASP cc_start: 0.4660 (m-30) cc_final: 0.4378 (p0) REVERT: F 415 GLN cc_start: 0.7473 (pp30) cc_final: 0.6895 (pp30) REVERT: F 433 HIS cc_start: 0.7460 (m-70) cc_final: 0.7184 (m-70) REVERT: F 491 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7282 (mtm-85) REVERT: F 540 LEU cc_start: 0.8637 (tt) cc_final: 0.8276 (mm) outliers start: 38 outliers final: 33 residues processed: 301 average time/residue: 0.6643 time to fit residues: 316.4147 Evaluate side-chains 284 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 483 ILE Chi-restraints excluded: chain F residue 491 ARG Chi-restraints excluded: chain F residue 533 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 109 optimal weight: 0.0040 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.0570 chunk 101 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 249 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 ASN B 517 GLN E 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.221179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162620 restraints weight = 83507.778| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.07 r_work: 0.3368 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24426 Z= 0.174 Angle : 0.495 9.151 33174 Z= 0.244 Chirality : 0.041 0.145 3720 Planarity : 0.004 0.043 4242 Dihedral : 7.943 89.446 3340 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 1.13 % Allowed : 11.45 % Favored : 87.42 % 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: 1.07 (0.16), residues: 3012 helix: 0.98 (0.16), residues: 1136 sheet: 0.13 (0.23), residues: 470 loop : 0.92 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 390 HIS 0.006 0.001 HIS B 519 PHE 0.029 0.001 PHE C 531 TYR 0.006 0.001 TYR C 484 ARG 0.003 0.000 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 2.979 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: A 415 GLN cc_start: 0.7681 (pp30) cc_final: 0.6617 (pp30) REVERT: A 547 GLU cc_start: 0.7740 (tt0) cc_final: 0.7476 (tt0) REVERT: B 547 GLU cc_start: 0.7755 (tt0) cc_final: 0.7499 (tt0) REVERT: C 264 ILE cc_start: 0.5515 (mt) cc_final: 0.5205 (tp) REVERT: C 304 GLU cc_start: 0.6046 (mp0) cc_final: 0.5833 (mp0) REVERT: C 416 GLU cc_start: 0.7761 (tt0) cc_final: 0.7353 (tp30) REVERT: C 540 LEU cc_start: 0.8618 (tt) cc_final: 0.8315 (mm) REVERT: D 250 MET cc_start: 0.3914 (ttp) cc_final: 0.3174 (tpp) REVERT: D 276 ARG cc_start: 0.5906 (mmm160) cc_final: 0.5339 (mtm180) REVERT: D 337 MET cc_start: 0.7113 (mmt) cc_final: 0.6753 (mmm) REVERT: D 529 MET cc_start: 0.1785 (ttp) cc_final: 0.0937 (tpt) REVERT: E 250 MET cc_start: 0.4487 (ttp) cc_final: 0.3909 (tpp) REVERT: E 276 ARG cc_start: 0.5966 (mmm160) cc_final: 0.5561 (mtm180) REVERT: E 327 ASN cc_start: 0.7221 (p0) cc_final: 0.6301 (t0) REVERT: E 341 GLN cc_start: 0.7640 (mt0) cc_final: 0.7326 (mm-40) REVERT: E 494 ASP cc_start: 0.4597 (m-30) cc_final: 0.4351 (p0) REVERT: F 415 GLN cc_start: 0.7400 (pp30) cc_final: 0.6709 (pp30) REVERT: F 433 HIS cc_start: 0.7399 (m-70) cc_final: 0.7053 (m-70) REVERT: F 435 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7215 (mt) REVERT: F 491 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7164 (mtm-85) REVERT: F 540 LEU cc_start: 0.8629 (tt) cc_final: 0.8290 (mm) outliers start: 29 outliers final: 21 residues processed: 285 average time/residue: 0.6838 time to fit residues: 312.5084 Evaluate side-chains 270 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 491 ARG Chi-restraints excluded: chain F residue 533 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 57 optimal weight: 2.9990 chunk 275 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 291 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.216658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156694 restraints weight = 83691.885| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.93 r_work: 0.3264 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 24426 Z= 0.409 Angle : 0.574 10.478 33174 Z= 0.288 Chirality : 0.045 0.215 3720 Planarity : 0.005 0.051 4242 Dihedral : 8.175 91.687 3340 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 1.79 % Allowed : 11.60 % Favored : 86.60 % 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: 0.74 (0.16), residues: 3012 helix: 0.77 (0.16), residues: 1124 sheet: -0.06 (0.23), residues: 472 loop : 0.68 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 390 HIS 0.007 0.001 HIS D 203 PHE 0.024 0.002 PHE C 531 TYR 0.013 0.002 TYR B 484 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 2.774 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: A 415 GLN cc_start: 0.7658 (pp30) cc_final: 0.6610 (pp30) REVERT: A 547 GLU cc_start: 0.7786 (tt0) cc_final: 0.7496 (tt0) REVERT: B 547 GLU cc_start: 0.7815 (tt0) cc_final: 0.7540 (tt0) REVERT: C 416 GLU cc_start: 0.7740 (tt0) cc_final: 0.7358 (tp30) REVERT: C 540 LEU cc_start: 0.8653 (tt) cc_final: 0.8294 (mm) REVERT: D 250 MET cc_start: 0.3933 (ttp) cc_final: 0.3300 (tpp) REVERT: D 276 ARG cc_start: 0.5872 (mmm160) cc_final: 0.5317 (mtm180) REVERT: D 337 MET cc_start: 0.7130 (mmt) cc_final: 0.6775 (mmm) REVERT: D 494 ASP cc_start: 0.5710 (OUTLIER) cc_final: 0.5234 (m-30) REVERT: D 529 MET cc_start: 0.1709 (ttp) cc_final: 0.0950 (tpt) REVERT: E 250 MET cc_start: 0.4398 (ttp) cc_final: 0.3939 (tpp) REVERT: E 276 ARG cc_start: 0.5881 (mmm160) cc_final: 0.5521 (mtm180) REVERT: E 337 MET cc_start: 0.7159 (mmt) cc_final: 0.6944 (mmm) REVERT: E 341 GLN cc_start: 0.7635 (mt0) cc_final: 0.7308 (mm-40) REVERT: F 415 GLN cc_start: 0.7430 (pp30) cc_final: 0.6716 (pp30) REVERT: F 435 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7343 (mt) REVERT: F 436 GLU cc_start: 0.7240 (pt0) cc_final: 0.6935 (pt0) REVERT: F 540 LEU cc_start: 0.8708 (tt) cc_final: 0.8317 (mm) outliers start: 46 outliers final: 34 residues processed: 278 average time/residue: 0.7037 time to fit residues: 305.3978 Evaluate side-chains 273 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 489 GLN Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 483 ILE Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 534 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 217 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 232 optimal weight: 30.0000 chunk 296 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 237 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 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 = 0.4428 r_free = 0.4428 target = 0.217597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156379 restraints weight = 83761.837| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.82 r_work: 0.3328 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24426 Z= 0.294 Angle : 0.529 9.911 33174 Z= 0.264 Chirality : 0.043 0.180 3720 Planarity : 0.004 0.051 4242 Dihedral : 8.040 90.345 3336 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 1.40 % Allowed : 12.34 % Favored : 86.25 % 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: 0.78 (0.16), residues: 3012 helix: 0.83 (0.16), residues: 1136 sheet: -0.07 (0.23), residues: 470 loop : 0.68 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 390 HIS 0.007 0.001 HIS A 203 PHE 0.025 0.001 PHE C 531 TYR 0.009 0.001 TYR A 233 ARG 0.005 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 2.759 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: A 415 GLN cc_start: 0.7681 (pp30) cc_final: 0.6559 (pp30) REVERT: A 547 GLU cc_start: 0.7746 (tt0) cc_final: 0.7453 (tt0) REVERT: B 547 GLU cc_start: 0.7753 (tt0) cc_final: 0.7460 (tt0) REVERT: C 416 GLU cc_start: 0.7721 (tt0) cc_final: 0.7500 (tp30) REVERT: C 540 LEU cc_start: 0.8637 (tt) cc_final: 0.8256 (mm) REVERT: D 250 MET cc_start: 0.3779 (ttp) cc_final: 0.3229 (tpp) REVERT: D 276 ARG cc_start: 0.5935 (mmm160) cc_final: 0.5384 (mtm180) REVERT: D 337 MET cc_start: 0.7163 (mmt) cc_final: 0.6803 (mmm) REVERT: D 529 MET cc_start: 0.2207 (ttp) cc_final: 0.1306 (tpt) REVERT: E 250 MET cc_start: 0.4450 (ttp) cc_final: 0.3936 (tpp) REVERT: E 276 ARG cc_start: 0.5911 (mmm160) cc_final: 0.5611 (mtm180) REVERT: E 341 GLN cc_start: 0.7589 (mt0) cc_final: 0.7278 (mm-40) REVERT: F 415 GLN cc_start: 0.7504 (pp30) cc_final: 0.6696 (pp30) REVERT: F 435 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7313 (mt) REVERT: F 540 LEU cc_start: 0.8680 (tt) cc_final: 0.8276 (mm) outliers start: 36 outliers final: 28 residues processed: 275 average time/residue: 0.6881 time to fit residues: 299.0979 Evaluate side-chains 268 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 385 PHE Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 483 ILE Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 534 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 158 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 257 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 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 = 0.4429 r_free = 0.4429 target = 0.217681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158719 restraints weight = 83739.509| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.95 r_work: 0.3297 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24426 Z= 0.289 Angle : 0.529 9.633 33174 Z= 0.263 Chirality : 0.043 0.182 3720 Planarity : 0.004 0.042 4242 Dihedral : 8.016 90.037 3336 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 1.64 % Allowed : 12.38 % Favored : 85.98 % 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: 0.82 (0.16), residues: 3012 helix: 0.93 (0.16), residues: 1124 sheet: -0.10 (0.23), residues: 470 loop : 0.67 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 410 HIS 0.007 0.001 HIS F 232 PHE 0.022 0.001 PHE C 531 TYR 0.010 0.001 TYR C 163 ARG 0.003 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 2.789 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: A 415 GLN cc_start: 0.7708 (pp30) cc_final: 0.6607 (pp30) REVERT: A 547 GLU cc_start: 0.7883 (tt0) cc_final: 0.7593 (tt0) REVERT: B 547 GLU cc_start: 0.7838 (tt0) cc_final: 0.7547 (tt0) REVERT: C 271 LYS cc_start: 0.5328 (mmtm) cc_final: 0.4554 (tmtt) REVERT: C 416 GLU cc_start: 0.7763 (tt0) cc_final: 0.7536 (tp30) REVERT: D 250 MET cc_start: 0.3778 (ttp) cc_final: 0.3180 (tpp) REVERT: D 276 ARG cc_start: 0.5860 (mmm160) cc_final: 0.5343 (mtm180) REVERT: D 337 MET cc_start: 0.7152 (mmt) cc_final: 0.6792 (mmm) REVERT: D 494 ASP cc_start: 0.5882 (OUTLIER) cc_final: 0.5335 (m-30) REVERT: D 529 MET cc_start: 0.1943 (ttp) cc_final: 0.1061 (tpt) REVERT: E 250 MET cc_start: 0.4300 (ttp) cc_final: 0.3825 (tpp) REVERT: E 276 ARG cc_start: 0.5861 (mmm160) cc_final: 0.5583 (mtm180) REVERT: E 327 ASN cc_start: 0.7192 (p0) cc_final: 0.6345 (t0) REVERT: E 341 GLN cc_start: 0.7570 (mt0) cc_final: 0.7212 (mm-40) REVERT: F 232 HIS cc_start: 0.5578 (m170) cc_final: 0.5361 (m170) REVERT: F 415 GLN cc_start: 0.7496 (pp30) cc_final: 0.6699 (pp30) REVERT: F 435 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7355 (mt) REVERT: F 540 LEU cc_start: 0.8734 (tt) cc_final: 0.8327 (mm) outliers start: 42 outliers final: 34 residues processed: 283 average time/residue: 0.6715 time to fit residues: 300.6049 Evaluate side-chains 280 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 489 GLN Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 385 PHE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 483 ILE Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 534 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 29 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 133 optimal weight: 0.0370 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 515 GLN F 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.218421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.161643 restraints weight = 83220.733| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.00 r_work: 0.3349 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24426 Z= 0.235 Angle : 0.511 9.443 33174 Z= 0.252 Chirality : 0.042 0.166 3720 Planarity : 0.004 0.043 4242 Dihedral : 7.931 89.264 3336 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.49 % Favored : 97.44 % Rotamer: Outliers : 1.17 % Allowed : 13.16 % Favored : 85.67 % 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: 0.94 (0.16), residues: 3012 helix: 1.03 (0.16), residues: 1136 sheet: -0.06 (0.23), residues: 470 loop : 0.75 (0.18), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 323 HIS 0.006 0.001 HIS B 203 PHE 0.022 0.001 PHE C 531 TYR 0.010 0.001 TYR F 163 ARG 0.004 0.000 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 2.775 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: A 415 GLN cc_start: 0.7695 (pp30) cc_final: 0.6662 (pp30) REVERT: A 547 GLU cc_start: 0.7605 (tt0) cc_final: 0.7307 (tt0) REVERT: B 547 GLU cc_start: 0.7558 (tt0) cc_final: 0.7264 (tt0) REVERT: C 271 LYS cc_start: 0.5365 (mmtm) cc_final: 0.4562 (tmtt) REVERT: D 250 MET cc_start: 0.3796 (ttp) cc_final: 0.3182 (tpp) REVERT: D 276 ARG cc_start: 0.5815 (mmm160) cc_final: 0.5415 (mtm180) REVERT: D 337 MET cc_start: 0.7126 (mmt) cc_final: 0.6813 (mmm) REVERT: D 494 ASP cc_start: 0.5750 (OUTLIER) cc_final: 0.5234 (m-30) REVERT: D 529 MET cc_start: 0.2155 (ttp) cc_final: 0.1269 (tpt) REVERT: E 250 MET cc_start: 0.4342 (ttp) cc_final: 0.3898 (tpp) REVERT: E 276 ARG cc_start: 0.5880 (mmm160) cc_final: 0.5669 (mtm180) REVERT: E 327 ASN cc_start: 0.7169 (p0) cc_final: 0.6357 (t0) REVERT: E 478 GLN cc_start: 0.4185 (mm-40) cc_final: 0.3887 (mm-40) REVERT: F 400 GLU cc_start: 0.4326 (pm20) cc_final: 0.3896 (pm20) REVERT: F 415 GLN cc_start: 0.7474 (pp30) cc_final: 0.6795 (pp30) REVERT: F 435 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7312 (mt) REVERT: F 540 LEU cc_start: 0.8684 (tt) cc_final: 0.8267 (mm) outliers start: 30 outliers final: 28 residues processed: 273 average time/residue: 0.6676 time to fit residues: 287.2067 Evaluate side-chains 275 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 385 PHE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 483 ILE Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 534 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 162 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.4446 r_free = 0.4446 target = 0.219482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160573 restraints weight = 83826.132| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.10 r_work: 0.3342 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24426 Z= 0.207 Angle : 0.503 8.990 33174 Z= 0.247 Chirality : 0.042 0.160 3720 Planarity : 0.004 0.044 4242 Dihedral : 7.854 88.800 3336 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 1.17 % Allowed : 13.28 % Favored : 85.55 % 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: 1.06 (0.16), residues: 3012 helix: 1.15 (0.16), residues: 1136 sheet: -0.06 (0.24), residues: 458 loop : 0.81 (0.18), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 323 HIS 0.005 0.001 HIS B 203 PHE 0.020 0.001 PHE C 531 TYR 0.009 0.001 TYR C 163 ARG 0.003 0.000 ARG E 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 2.867 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: A 415 GLN cc_start: 0.7689 (pp30) cc_final: 0.6621 (pp30) REVERT: A 547 GLU cc_start: 0.7801 (tt0) cc_final: 0.7507 (tt0) REVERT: B 547 GLU cc_start: 0.7742 (tt0) cc_final: 0.7443 (tt0) REVERT: C 540 LEU cc_start: 0.8659 (tt) cc_final: 0.8258 (mm) REVERT: D 250 MET cc_start: 0.3777 (ttp) cc_final: 0.3165 (tpp) REVERT: D 276 ARG cc_start: 0.5902 (mmm160) cc_final: 0.5544 (mtm180) REVERT: D 337 MET cc_start: 0.7127 (mmt) cc_final: 0.6807 (mmm) REVERT: D 494 ASP cc_start: 0.5925 (OUTLIER) cc_final: 0.5322 (m-30) REVERT: D 529 MET cc_start: 0.2192 (ttp) cc_final: 0.1575 (tpp) REVERT: E 250 MET cc_start: 0.4431 (ttp) cc_final: 0.3955 (tpp) REVERT: E 276 ARG cc_start: 0.5986 (mmm160) cc_final: 0.5765 (mtm180) REVERT: E 327 ASN cc_start: 0.7160 (p0) cc_final: 0.6362 (t0) REVERT: E 478 GLN cc_start: 0.4198 (mm-40) cc_final: 0.3904 (mm-40) REVERT: F 400 GLU cc_start: 0.4251 (pm20) cc_final: 0.3823 (pm20) REVERT: F 415 GLN cc_start: 0.7475 (pp30) cc_final: 0.6758 (pp30) REVERT: F 540 LEU cc_start: 0.8673 (tt) cc_final: 0.8269 (mm) outliers start: 30 outliers final: 29 residues processed: 271 average time/residue: 0.6929 time to fit residues: 296.9983 Evaluate side-chains 275 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 385 PHE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 534 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 63 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 103 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 507 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 = 0.4447 r_free = 0.4447 target = 0.219575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.159340 restraints weight = 83722.929| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.08 r_work: 0.3322 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24426 Z= 0.209 Angle : 0.498 8.896 33174 Z= 0.244 Chirality : 0.042 0.162 3720 Planarity : 0.004 0.042 4242 Dihedral : 7.782 88.914 3336 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.59 % Favored : 97.34 % Rotamer: Outliers : 1.36 % Allowed : 13.12 % Favored : 85.51 % 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: 1.15 (0.16), residues: 3012 helix: 1.24 (0.16), residues: 1136 sheet: -0.01 (0.23), residues: 458 loop : 0.84 (0.18), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 323 HIS 0.006 0.001 HIS B 203 PHE 0.019 0.001 PHE C 531 TYR 0.012 0.001 TYR D 233 ARG 0.004 0.000 ARG A 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23253.37 seconds wall clock time: 396 minutes 20.14 seconds (23780.14 seconds total)