Starting phenix.real_space_refine on Mon Sep 23 17:42:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5i_19736/09_2024/8s5i_19736_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5i_19736/09_2024/8s5i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5i_19736/09_2024/8s5i_19736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5i_19736/09_2024/8s5i_19736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5i_19736/09_2024/8s5i_19736_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5i_19736/09_2024/8s5i_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-5461/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: 17.52, per 1000 atoms: 0.37 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: 9.44 Conformation dependent library (CDL) restraints added in 2.8 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: 3.56 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: 16.28 Time building geometry restraints manager: 11.59 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: 0.00 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: 0.010 Construct map_model_manager: 0.620 Extract box with map and model: 1.290 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 78.470 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.150 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.650 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 15 poor density : 472 time to evaluate : 2.783 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: 0.8433 time to fit residues: 602.8052 Evaluate side-chains 285 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 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 fitting. rotamer outliers: 38 poor density : 309 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7304 (pp30) cc_final: 0.6400 (pp30) REVERT: B 415 GLN cc_start: 0.7256 (pp30) cc_final: 0.6738 (pp30) REVERT: C 416 GLU cc_start: 0.7550 (tt0) cc_final: 0.7085 (tp30) REVERT: C 540 LEU cc_start: 0.8353 (tt) cc_final: 0.8053 (mm) REVERT: D 364 LEU cc_start: 0.5454 (mt) cc_final: 0.5144 (mt) REVERT: D 494 ASP cc_start: 0.2931 (m-30) cc_final: 0.2083 (m-30) REVERT: D 529 MET cc_start: 0.1950 (ttp) cc_final: 0.1059 (tpt) REVERT: E 494 ASP cc_start: 0.3985 (m-30) cc_final: 0.3012 (m-30) REVERT: E 529 MET cc_start: 0.2235 (ttp) cc_final: 0.1579 (tpt) REVERT: F 59 PRO cc_start: 0.0420 (Cg_endo) cc_final: 0.0172 (Cg_exo) REVERT: F 415 GLN cc_start: 0.7057 (pp30) cc_final: 0.6538 (pp30) REVERT: F 491 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6708 (mtm-85) REVERT: F 511 VAL cc_start: 0.8615 (t) cc_final: 0.8363 (m) REVERT: F 548 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5603 (mmt-90) outliers start: 38 outliers final: 30 residues processed: 337 average time/residue: 0.7374 time to fit residues: 386.9358 Evaluate side-chains 289 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 257 time to evaluate : 2.742 ------------------------------------------------------------------------------- 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 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 151 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 chunk 185 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 272 optimal weight: 20.0000 chunk 294 optimal weight: 2.9990 chunk 243 optimal weight: 20.0000 chunk 270 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN B 216 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN F 113 ASN ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24426 Z= 0.195 Angle : 0.514 9.131 33174 Z= 0.254 Chirality : 0.042 0.149 3720 Planarity : 0.004 0.050 4242 Dihedral : 8.299 89.941 3347 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.89 % Favored : 98.04 % Rotamer: Outliers : 0.90 % Allowed : 10.05 % Favored : 89.06 % 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: 1.01 (0.16), residues: 3012 helix: 0.83 (0.16), residues: 1140 sheet: 0.22 (0.24), residues: 470 loop : 0.93 (0.18), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 54 HIS 0.010 0.001 HIS F 232 PHE 0.012 0.001 PHE C 531 TYR 0.011 0.001 TYR C 484 ARG 0.005 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 306 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 283 time to evaluate : 2.786 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: A 415 GLN cc_start: 0.7134 (pp30) cc_final: 0.6107 (pp30) REVERT: A 547 GLU cc_start: 0.7356 (tt0) cc_final: 0.7111 (tt0) REVERT: B 547 GLU cc_start: 0.7279 (tt0) cc_final: 0.7038 (tt0) REVERT: C 416 GLU cc_start: 0.7479 (tt0) cc_final: 0.6954 (tp30) REVERT: C 533 VAL cc_start: 0.8942 (m) cc_final: 0.8701 (t) REVERT: C 540 LEU cc_start: 0.8340 (tt) cc_final: 0.8045 (mm) REVERT: D 494 ASP cc_start: 0.3064 (m-30) cc_final: 0.2315 (m-30) REVERT: D 529 MET cc_start: 0.2070 (ttp) cc_final: 0.1223 (tpt) REVERT: E 327 ASN cc_start: 0.6679 (p0) cc_final: 0.6012 (t0) REVERT: E 478 GLN cc_start: 0.3675 (mm-40) cc_final: 0.3090 (mm-40) REVERT: E 494 ASP cc_start: 0.3794 (m-30) cc_final: 0.2885 (m-30) REVERT: E 529 MET cc_start: 0.1731 (ttp) cc_final: 0.1495 (tpt) REVERT: F 59 PRO cc_start: 0.0555 (Cg_endo) cc_final: 0.0314 (Cg_exo) REVERT: F 415 GLN cc_start: 0.6899 (pp30) cc_final: 0.6287 (pp30) REVERT: F 477 ASP cc_start: 0.4856 (m-30) cc_final: 0.4290 (t0) REVERT: F 491 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6682 (mtm-85) REVERT: F 540 LEU cc_start: 0.8377 (tt) cc_final: 0.8044 (mm) outliers start: 23 outliers final: 18 residues processed: 298 average time/residue: 0.6844 time to fit residues: 320.3632 Evaluate side-chains 267 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 248 time to evaluate : 2.756 ------------------------------------------------------------------------------- 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 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 252 VAL 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 269 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 507 HIS C 541 ASN E 216 ASN ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 24426 Z= 0.480 Angle : 0.627 11.674 33174 Z= 0.316 Chirality : 0.046 0.240 3720 Planarity : 0.005 0.053 4242 Dihedral : 8.414 94.029 3340 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 1.79 % Allowed : 10.83 % Favored : 87.38 % 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: 0.49 (0.15), residues: 3012 helix: 0.45 (0.16), residues: 1124 sheet: -0.02 (0.23), residues: 472 loop : 0.57 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 390 HIS 0.015 0.002 HIS F 232 PHE 0.033 0.002 PHE C 531 TYR 0.016 0.002 TYR B 484 ARG 0.006 0.000 ARG E 276 *********************** 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 302 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 2.807 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 128 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7686 (mt-10) REVERT: A 415 GLN cc_start: 0.7253 (pp30) cc_final: 0.6188 (pp30) REVERT: A 547 GLU cc_start: 0.7637 (tt0) cc_final: 0.7339 (tt0) REVERT: B 128 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7667 (mt-10) REVERT: B 547 GLU cc_start: 0.7615 (tt0) cc_final: 0.7303 (tt0) REVERT: C 416 GLU cc_start: 0.7608 (tt0) cc_final: 0.7075 (tp30) REVERT: C 533 VAL cc_start: 0.8919 (m) cc_final: 0.8663 (t) REVERT: C 540 LEU cc_start: 0.8396 (tt) cc_final: 0.8037 (mm) REVERT: D 529 MET cc_start: 0.1693 (ttp) cc_final: 0.1096 (tpt) REVERT: F 415 GLN cc_start: 0.7061 (pp30) cc_final: 0.6298 (pp30) REVERT: F 433 HIS cc_start: 0.7412 (m-70) cc_final: 0.7173 (m-70) REVERT: F 435 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7181 (mt) REVERT: F 491 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6889 (mtm-85) REVERT: F 540 LEU cc_start: 0.8420 (tt) cc_final: 0.8040 (mm) outliers start: 46 outliers final: 38 residues processed: 293 average time/residue: 0.7216 time to fit residues: 335.6218 Evaluate side-chains 277 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 237 time to evaluate : 2.787 ------------------------------------------------------------------------------- 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 456 LEU Chi-restraints excluded: chain A residue 531 PHE 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 44 ILE 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 203 HIS 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 202 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 473 VAL 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 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 466 SER 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 241 optimal weight: 30.0000 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 260 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 517 GLN E 216 ASN ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24426 Z= 0.251 Angle : 0.527 9.838 33174 Z= 0.262 Chirality : 0.042 0.166 3720 Planarity : 0.004 0.043 4242 Dihedral : 8.126 89.834 3340 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % Rotamer: Outliers : 1.17 % Allowed : 11.99 % Favored : 86.84 % 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: 0.72 (0.16), residues: 3012 helix: 0.72 (0.16), residues: 1136 sheet: 0.05 (0.23), residues: 478 loop : 0.65 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 390 HIS 0.015 0.001 HIS F 232 PHE 0.035 0.001 PHE C 531 TYR 0.010 0.001 TYR C 163 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 288 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 258 time to evaluate : 2.790 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 128 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7622 (mt-10) REVERT: A 415 GLN cc_start: 0.7116 (pp30) cc_final: 0.5896 (pp30) REVERT: A 547 GLU cc_start: 0.7523 (tt0) cc_final: 0.7212 (tt0) REVERT: B 128 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7618 (mt-10) REVERT: B 547 GLU cc_start: 0.7537 (tt0) cc_final: 0.7237 (tt0) REVERT: C 416 GLU cc_start: 0.7534 (tt0) cc_final: 0.7016 (tp30) REVERT: C 540 LEU cc_start: 0.8378 (tt) cc_final: 0.8019 (mm) REVERT: D 529 MET cc_start: 0.1833 (ttp) cc_final: 0.1170 (tpt) REVERT: F 415 GLN cc_start: 0.7003 (pp30) cc_final: 0.6210 (pp30) REVERT: F 491 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6720 (mtm-85) REVERT: F 540 LEU cc_start: 0.8404 (tt) cc_final: 0.8030 (mm) outliers start: 30 outliers final: 24 residues processed: 280 average time/residue: 0.6723 time to fit residues: 295.1968 Evaluate side-chains 267 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 242 time to evaluate : 2.789 ------------------------------------------------------------------------------- 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 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 248 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 489 GLN Chi-restraints excluded: chain D residue 495 THR 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 495 THR 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 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 97 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 240 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 96 optimal weight: 0.0570 chunk 152 optimal weight: 6.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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** ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24426 Z= 0.260 Angle : 0.524 9.941 33174 Z= 0.260 Chirality : 0.042 0.186 3720 Planarity : 0.004 0.040 4242 Dihedral : 8.031 88.603 3340 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 1.40 % Allowed : 11.88 % Favored : 86.72 % 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: 0.83 (0.16), residues: 3012 helix: 0.87 (0.16), residues: 1124 sheet: 0.03 (0.23), residues: 470 loop : 0.69 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 390 HIS 0.016 0.001 HIS F 232 PHE 0.029 0.001 PHE C 531 TYR 0.008 0.001 TYR B 233 ARG 0.002 0.000 ARG D 161 *********************** 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 285 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 249 time to evaluate : 2.814 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 128 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7669 (mt-10) REVERT: A 415 GLN cc_start: 0.7104 (pp30) cc_final: 0.5835 (pp30) REVERT: A 547 GLU cc_start: 0.7574 (tt0) cc_final: 0.7254 (tt0) REVERT: B 128 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7660 (mt-10) REVERT: B 547 GLU cc_start: 0.7534 (tt0) cc_final: 0.7225 (tt0) REVERT: C 416 GLU cc_start: 0.7473 (tt0) cc_final: 0.7158 (tp30) REVERT: C 540 LEU cc_start: 0.8384 (tt) cc_final: 0.8018 (mm) REVERT: D 529 MET cc_start: 0.1830 (ttp) cc_final: 0.1162 (tpt) REVERT: E 327 ASN cc_start: 0.6651 (p0) cc_final: 0.6011 (t0) REVERT: F 415 GLN cc_start: 0.6990 (pp30) cc_final: 0.6149 (pp30) REVERT: F 491 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6808 (mtm-85) REVERT: F 540 LEU cc_start: 0.8408 (tt) cc_final: 0.8030 (mm) outliers start: 36 outliers final: 30 residues processed: 273 average time/residue: 0.6941 time to fit residues: 299.6172 Evaluate side-chains 270 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 239 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU 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 466 SER 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 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 252 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 495 THR 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 168 VAL Chi-restraints excluded: chain F residue 264 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 289 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** F 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24426 Z= 0.249 Angle : 0.515 9.790 33174 Z= 0.255 Chirality : 0.042 0.172 3720 Planarity : 0.004 0.041 4242 Dihedral : 7.955 88.254 3340 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 1.75 % Allowed : 11.95 % Favored : 86.29 % 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: 0.93 (0.16), residues: 3012 helix: 0.97 (0.16), residues: 1136 sheet: 0.02 (0.23), residues: 470 loop : 0.75 (0.18), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 390 HIS 0.015 0.001 HIS F 232 PHE 0.023 0.001 PHE C 531 TYR 0.010 0.001 TYR C 163 ARG 0.003 0.000 ARG A 413 *********************** 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 300 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 255 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 128 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7667 (mt-10) REVERT: A 547 GLU cc_start: 0.7549 (tt0) cc_final: 0.7226 (tt0) REVERT: B 128 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7706 (mt-10) REVERT: B 416 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8521 (tp30) REVERT: B 547 GLU cc_start: 0.7541 (tt0) cc_final: 0.7220 (tt0) REVERT: C 416 GLU cc_start: 0.7490 (tt0) cc_final: 0.7114 (tp30) REVERT: C 540 LEU cc_start: 0.8391 (tt) cc_final: 0.8016 (mm) REVERT: D 494 ASP cc_start: 0.5153 (OUTLIER) cc_final: 0.4290 (m-30) REVERT: D 529 MET cc_start: 0.1977 (ttp) cc_final: 0.1306 (tpt) REVERT: E 126 MET cc_start: 0.6838 (mtp) cc_final: 0.6459 (mtp) REVERT: E 327 ASN cc_start: 0.6551 (p0) cc_final: 0.6089 (t0) REVERT: F 415 GLN cc_start: 0.7011 (pp30) cc_final: 0.6590 (pp30) REVERT: F 435 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7186 (mt) REVERT: F 436 GLU cc_start: 0.7013 (pt0) cc_final: 0.6811 (pt0) REVERT: F 540 LEU cc_start: 0.8430 (tt) cc_final: 0.8032 (mm) outliers start: 45 outliers final: 35 residues processed: 290 average time/residue: 0.6445 time to fit residues: 297.7060 Evaluate side-chains 277 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 239 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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 416 GLU 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 449 VAL 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 D residue 495 THR 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** C 515 GLN F 515 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 24426 Z= 0.403 Angle : 0.580 11.619 33174 Z= 0.290 Chirality : 0.045 0.216 3720 Planarity : 0.005 0.050 4242 Dihedral : 8.164 92.988 3336 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.91 % Allowed : 12.38 % Favored : 85.71 % 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: 0.63 (0.16), residues: 3012 helix: 0.74 (0.16), residues: 1124 sheet: -0.09 (0.24), residues: 458 loop : 0.54 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 410 HIS 0.016 0.001 HIS F 232 PHE 0.022 0.002 PHE C 531 TYR 0.012 0.002 TYR B 484 ARG 0.004 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 305 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 256 time to evaluate : 2.813 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: 0.7246 (pp30) cc_final: 0.6235 (pp30) REVERT: A 547 GLU cc_start: 0.7594 (tt0) cc_final: 0.7263 (tt0) REVERT: B 416 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8522 (tp30) REVERT: B 547 GLU cc_start: 0.7617 (tt0) cc_final: 0.7282 (tt0) REVERT: C 416 GLU cc_start: 0.7573 (tt0) cc_final: 0.7207 (tp30) REVERT: D 494 ASP cc_start: 0.5627 (OUTLIER) cc_final: 0.5247 (p0) REVERT: D 529 MET cc_start: 0.1650 (ttp) cc_final: 0.1407 (tpt) REVERT: E 478 GLN cc_start: 0.4459 (mm-40) cc_final: 0.4124 (mm-40) REVERT: F 415 GLN cc_start: 0.7150 (pp30) cc_final: 0.6563 (pp30) REVERT: F 436 GLU cc_start: 0.7111 (pt0) cc_final: 0.6898 (pt0) REVERT: F 540 LEU cc_start: 0.8350 (tt) cc_final: 0.8014 (mm) outliers start: 49 outliers final: 40 residues processed: 295 average time/residue: 0.6947 time to fit residues: 323.6649 Evaluate side-chains 287 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 245 time to evaluate : 2.777 ------------------------------------------------------------------------------- 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 216 ASN 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 416 GLU 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 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 202 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 495 THR 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 202 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 385 PHE Chi-restraints excluded: chain F residue 67 HIS 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 277 optimal weight: 20.0000 chunk 252 optimal weight: 0.5980 chunk 269 optimal weight: 20.0000 chunk 276 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 254 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24426 Z= 0.335 Angle : 0.551 10.458 33174 Z= 0.275 Chirality : 0.044 0.190 3720 Planarity : 0.004 0.045 4242 Dihedral : 8.077 91.406 3336 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 1.71 % Allowed : 13.05 % Favored : 85.24 % 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: 0.64 (0.16), residues: 3012 helix: 0.80 (0.16), residues: 1124 sheet: -0.13 (0.24), residues: 458 loop : 0.52 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 323 HIS 0.017 0.001 HIS F 232 PHE 0.023 0.002 PHE C 531 TYR 0.011 0.002 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 293 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 249 time to evaluate : 2.794 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: A 415 GLN cc_start: 0.7296 (pp30) cc_final: 0.6200 (pp30) REVERT: A 547 GLU cc_start: 0.7591 (tt0) cc_final: 0.7250 (tt0) REVERT: B 416 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8515 (tp30) REVERT: B 547 GLU cc_start: 0.7569 (tt0) cc_final: 0.7236 (tt0) REVERT: C 416 GLU cc_start: 0.7517 (tt0) cc_final: 0.7165 (tp30) REVERT: D 494 ASP cc_start: 0.5651 (OUTLIER) cc_final: 0.5255 (p0) REVERT: D 529 MET cc_start: 0.2144 (ttp) cc_final: 0.1700 (tpp) REVERT: E 327 ASN cc_start: 0.6636 (p0) cc_final: 0.6300 (t0) REVERT: E 478 GLN cc_start: 0.4552 (mm-40) cc_final: 0.4228 (mm-40) REVERT: F 415 GLN cc_start: 0.7191 (pp30) cc_final: 0.6488 (pp30) REVERT: F 436 GLU cc_start: 0.7067 (pt0) cc_final: 0.6811 (pt0) REVERT: F 540 LEU cc_start: 0.8353 (tt) cc_final: 0.8002 (mm) outliers start: 44 outliers final: 42 residues processed: 282 average time/residue: 0.6769 time to fit residues: 304.2152 Evaluate side-chains 286 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 242 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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 216 ASN 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 416 GLU 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 202 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 495 THR 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 202 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 LEU 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 286 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 7.9990 chunk 284 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24426 Z= 0.302 Angle : 0.541 9.784 33174 Z= 0.268 Chirality : 0.043 0.186 3720 Planarity : 0.004 0.041 4242 Dihedral : 7.989 90.467 3336 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 1.79 % Allowed : 13.12 % Favored : 85.09 % 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: 0.70 (0.16), residues: 3012 helix: 0.88 (0.16), residues: 1124 sheet: -0.12 (0.24), residues: 458 loop : 0.52 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 323 HIS 0.018 0.001 HIS F 232 PHE 0.022 0.001 PHE C 531 TYR 0.009 0.001 TYR C 163 ARG 0.003 0.000 ARG A 413 ********************** 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 291 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 2.802 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: 0.7243 (pp30) cc_final: 0.6115 (pp30) REVERT: A 547 GLU cc_start: 0.7586 (tt0) cc_final: 0.7245 (tt0) REVERT: B 416 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8525 (tp30) REVERT: B 547 GLU cc_start: 0.7565 (tt0) cc_final: 0.7231 (tt0) REVERT: C 275 CYS cc_start: 0.4062 (m) cc_final: 0.3524 (t) REVERT: C 416 GLU cc_start: 0.7544 (tt0) cc_final: 0.7218 (tp30) REVERT: D 494 ASP cc_start: 0.5636 (OUTLIER) cc_final: 0.5386 (p0) REVERT: D 529 MET cc_start: 0.2149 (ttp) cc_final: 0.1656 (tpp) REVERT: E 327 ASN cc_start: 0.6586 (p0) cc_final: 0.6271 (t0) REVERT: F 304 GLU cc_start: 0.6015 (mp0) cc_final: 0.5806 (mp0) REVERT: F 415 GLN cc_start: 0.7162 (pp30) cc_final: 0.6469 (pp30) outliers start: 46 outliers final: 43 residues processed: 278 average time/residue: 0.6647 time to fit residues: 295.8491 Evaluate side-chains 281 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 236 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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 216 ASN 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 416 GLU 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 C residue 460 THR 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 326 SER Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 495 THR 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 202 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 LEU 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 286 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 20.0000 chunk 253 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 219 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.218157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.158401 restraints weight = 83587.722| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.93 r_work: 0.3586 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4299 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= 0.284 Angle : 0.533 9.285 33174 Z= 0.264 Chirality : 0.043 0.180 3720 Planarity : 0.004 0.043 4242 Dihedral : 7.916 89.659 3336 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 1.79 % Allowed : 13.28 % Favored : 84.93 % 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: 0.77 (0.16), residues: 3012 helix: 0.95 (0.16), residues: 1124 sheet: -0.08 (0.24), residues: 458 loop : 0.54 (0.18), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 323 HIS 0.016 0.001 HIS F 232 PHE 0.021 0.001 PHE C 531 TYR 0.013 0.001 TYR D 233 ARG 0.003 0.000 ARG A 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8490.66 seconds wall clock time: 146 minutes 41.94 seconds (8801.94 seconds total)