Starting phenix.real_space_refine on Thu Mar 5 20:33:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsy_35008/03_2026/8hsy_35008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsy_35008/03_2026/8hsy_35008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hsy_35008/03_2026/8hsy_35008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsy_35008/03_2026/8hsy_35008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hsy_35008/03_2026/8hsy_35008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsy_35008/03_2026/8hsy_35008.map" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16242 2.51 5 N 4236 2.21 5 O 4734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25320 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.04, per 1000 atoms: 0.20 Number of scatterers: 25320 At special positions: 0 Unit cell: (169.338, 158.184, 94.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4734 8.00 N 4236 7.00 C 16242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 30 sheets defined 36.8% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.552A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.560A pdb=" N LEU A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA A 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.765A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.553A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.560A pdb=" N LEU C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA C 284 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.765A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE C 494 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.552A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.560A pdb=" N LEU B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA B 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.765A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.552A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.560A pdb=" N LEU D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA D 284 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.765A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE D 494 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 87 removed outlier: 3.553A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.559A pdb=" N LEU E 124 " --> pdb=" O PHE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'E' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.892A pdb=" N ALA E 284 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.765A pdb=" N TYR E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 440 through 449 Processing helix chain 'E' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE E 494 " --> pdb=" O PHE E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 533 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 87 removed outlier: 3.552A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.559A pdb=" N LEU F 124 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 153 Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.800A pdb=" N THR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA F 284 " --> pdb=" O LYS F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 340 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.765A pdb=" N TYR F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 406' Processing helix chain 'F' and resid 440 through 449 Processing helix chain 'F' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE F 494 " --> pdb=" O PHE F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN A 243 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER A 266 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 315 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 328 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR A 65 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU A 115 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA A 67 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS A 117 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET A 69 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 171 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.347A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL A 458 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 471 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 460 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL A 469 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN C 243 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER C 266 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 315 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 328 " --> pdb=" O TYR C 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR C 65 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU C 115 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA C 67 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N HIS C 117 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET C 69 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 171 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.347A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AB1, first strand: chain 'C' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 458 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU C 471 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY C 460 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL C 469 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN B 243 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER B 266 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 315 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 328 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR B 65 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU B 115 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA B 67 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS B 117 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N MET B 69 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 171 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.348A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 430 through 431 Processing sheet with id=AB6, first strand: chain 'B' and resid 453 through 461 removed outlier: 6.507A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 458 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 471 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 460 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL B 469 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN D 243 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER D 266 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D 315 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 328 " --> pdb=" O TYR D 318 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR D 65 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU D 115 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA D 67 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N HIS D 117 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N MET D 69 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 171 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.348A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 430 through 431 Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL D 458 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU D 471 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY D 460 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL D 469 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN E 243 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER E 266 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E 315 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER E 328 " --> pdb=" O TYR E 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.952A pdb=" N THR E 65 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU E 115 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA E 67 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS E 117 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET E 69 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 171 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 361 through 363 removed outlier: 5.347A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 430 through 431 Processing sheet with id=AC7, first strand: chain 'E' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL E 458 " --> pdb=" O LEU E 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU E 471 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY E 460 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL E 469 " --> pdb=" O GLY E 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 37 through 40 removed outlier: 3.580A pdb=" N GLN F 243 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER F 266 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE F 315 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER F 328 " --> pdb=" O TYR F 318 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR F 65 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU F 115 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA F 67 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS F 117 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET F 69 " --> pdb=" O HIS F 117 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 171 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 361 through 363 removed outlier: 5.347A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 430 through 431 Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL F 458 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU F 471 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY F 460 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL F 469 " --> pdb=" O GLY F 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4266 1.31 - 1.43: 6527 1.43 - 1.56: 14905 1.56 - 1.68: 0 1.68 - 1.81: 192 Bond restraints: 25890 Sorted by residual: bond pdb=" C ASN E 368 " pdb=" O ASN E 368 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.30e-02 5.92e+03 1.59e+01 bond pdb=" C ASN A 368 " pdb=" O ASN A 368 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.30e-02 5.92e+03 1.57e+01 bond pdb=" C ASN C 368 " pdb=" O ASN C 368 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.30e-02 5.92e+03 1.56e+01 bond pdb=" C ASN F 368 " pdb=" O ASN F 368 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.30e-02 5.92e+03 1.56e+01 bond pdb=" C ASN D 368 " pdb=" O ASN D 368 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.30e-02 5.92e+03 1.56e+01 ... (remaining 25885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 34253 2.05 - 4.10: 769 4.10 - 6.15: 84 6.15 - 8.20: 6 8.20 - 10.25: 6 Bond angle restraints: 35118 Sorted by residual: angle pdb=" N MET C 367 " pdb=" CA MET C 367 " pdb=" C MET C 367 " ideal model delta sigma weight residual 111.02 121.27 -10.25 1.25e+00 6.40e-01 6.72e+01 angle pdb=" N MET B 367 " pdb=" CA MET B 367 " pdb=" C MET B 367 " ideal model delta sigma weight residual 111.02 121.26 -10.24 1.25e+00 6.40e-01 6.71e+01 angle pdb=" N MET F 367 " pdb=" CA MET F 367 " pdb=" C MET F 367 " ideal model delta sigma weight residual 111.02 121.25 -10.23 1.25e+00 6.40e-01 6.70e+01 angle pdb=" N MET E 367 " pdb=" CA MET E 367 " pdb=" C MET E 367 " ideal model delta sigma weight residual 111.02 121.24 -10.22 1.25e+00 6.40e-01 6.68e+01 angle pdb=" N MET A 367 " pdb=" CA MET A 367 " pdb=" C MET A 367 " ideal model delta sigma weight residual 111.02 121.23 -10.21 1.25e+00 6.40e-01 6.67e+01 ... (remaining 35113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 13796 17.30 - 34.59: 1228 34.59 - 51.89: 390 51.89 - 69.18: 78 69.18 - 86.48: 30 Dihedral angle restraints: 15522 sinusoidal: 6252 harmonic: 9270 Sorted by residual: dihedral pdb=" C MET B 367 " pdb=" N MET B 367 " pdb=" CA MET B 367 " pdb=" CB MET B 367 " ideal model delta harmonic sigma weight residual -122.60 -132.28 9.68 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C MET C 367 " pdb=" N MET C 367 " pdb=" CA MET C 367 " pdb=" CB MET C 367 " ideal model delta harmonic sigma weight residual -122.60 -132.27 9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C MET E 367 " pdb=" N MET E 367 " pdb=" CA MET E 367 " pdb=" CB MET E 367 " ideal model delta harmonic sigma weight residual -122.60 -132.25 9.65 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 15519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3840 0.113 - 0.225: 120 0.225 - 0.338: 12 0.338 - 0.450: 0 0.450 - 0.563: 6 Chirality restraints: 3978 Sorted by residual: chirality pdb=" CA MET C 367 " pdb=" N MET C 367 " pdb=" C MET C 367 " pdb=" CB MET C 367 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" CA MET B 367 " pdb=" N MET B 367 " pdb=" C MET B 367 " pdb=" CB MET B 367 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" CA MET E 367 " pdb=" N MET E 367 " pdb=" C MET E 367 " pdb=" CB MET E 367 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 3975 not shown) Planarity restraints: 4476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 340 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C ASP B 340 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP B 340 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL B 341 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 340 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C ASP C 340 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP C 340 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL C 341 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 340 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C ASP D 340 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP D 340 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL D 341 " -0.014 2.00e-02 2.50e+03 ... (remaining 4473 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 618 2.70 - 3.25: 24383 3.25 - 3.80: 40376 3.80 - 4.35: 55483 4.35 - 4.90: 89973 Nonbonded interactions: 210833 Sorted by model distance: nonbonded pdb=" OD1 ASP C 416 " pdb=" N ASP C 417 " model vdw 2.153 3.120 nonbonded pdb=" OD1 ASP B 416 " pdb=" N ASP B 417 " model vdw 2.153 3.120 nonbonded pdb=" OD1 ASP A 416 " pdb=" N ASP A 417 " model vdw 2.153 3.120 nonbonded pdb=" OD1 ASP E 416 " pdb=" N ASP E 417 " model vdw 2.153 3.120 nonbonded pdb=" OD1 ASP D 416 " pdb=" N ASP D 417 " model vdw 2.153 3.120 ... (remaining 210828 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.020 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 0.052 25890 Z= 0.267 Angle : 0.707 10.246 35118 Z= 0.440 Chirality : 0.055 0.563 3978 Planarity : 0.004 0.037 4476 Dihedral : 15.459 86.476 9558 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.25 % Favored : 93.56 % Rotamer: Outliers : 0.80 % Allowed : 12.87 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3168 helix: 0.67 (0.16), residues: 1062 sheet: -0.73 (0.20), residues: 612 loop : -1.21 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 130 TYR 0.010 0.001 TYR C 148 PHE 0.011 0.001 PHE E 225 TRP 0.011 0.001 TRP F 290 HIS 0.003 0.001 HIS F 45 Details of bonding type rmsd covalent geometry : bond 0.00397 (25890) covalent geometry : angle 0.70730 (35118) hydrogen bonds : bond 0.16884 ( 918) hydrogen bonds : angle 7.11939 ( 2574) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.958 Fit side-chains REVERT: C 364 ASP cc_start: 0.7111 (p0) cc_final: 0.6665 (p0) REVERT: D 92 MET cc_start: 0.8890 (mtm) cc_final: 0.8503 (mtp) REVERT: E 92 MET cc_start: 0.8904 (mtm) cc_final: 0.8558 (mtp) outliers start: 22 outliers final: 1 residues processed: 258 average time/residue: 0.7543 time to fit residues: 221.3774 Evaluate side-chains 203 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 243 GLN A 368 ASN C 17 ASN C 243 GLN B 17 ASN B 243 GLN B 368 ASN D 243 GLN E 17 ASN E 243 GLN E 368 ASN F 17 ASN F 243 GLN F 368 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112149 restraints weight = 28672.334| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.92 r_work: 0.3140 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25890 Z= 0.118 Angle : 0.551 6.064 35118 Z= 0.294 Chirality : 0.046 0.155 3978 Planarity : 0.004 0.037 4476 Dihedral : 5.242 42.522 3429 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.28 % Rotamer: Outliers : 2.39 % Allowed : 13.88 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3168 helix: 1.28 (0.16), residues: 1074 sheet: -0.72 (0.20), residues: 570 loop : -1.10 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.008 0.001 TYR C 148 PHE 0.014 0.001 PHE E 225 TRP 0.006 0.001 TRP F 402 HIS 0.004 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00263 (25890) covalent geometry : angle 0.55103 (35118) hydrogen bonds : bond 0.04114 ( 918) hydrogen bonds : angle 5.07664 ( 2574) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 0.998 Fit side-chains REVERT: A 309 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7114 (tm-30) REVERT: A 429 ASP cc_start: 0.7924 (m-30) cc_final: 0.7697 (m-30) REVERT: A 442 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6083 (pt0) REVERT: C 331 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6242 (mp10) REVERT: C 362 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8371 (tp) REVERT: B 331 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6467 (mp10) REVERT: B 429 ASP cc_start: 0.7992 (m-30) cc_final: 0.7716 (m-30) REVERT: D 92 MET cc_start: 0.8845 (mtm) cc_final: 0.8487 (mtp) REVERT: D 119 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: D 331 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.5709 (mp10) REVERT: E 92 MET cc_start: 0.8893 (mtm) cc_final: 0.8562 (mtp) REVERT: E 331 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.5989 (mp10) REVERT: F 171 THR cc_start: 0.9432 (p) cc_final: 0.9166 (p) REVERT: F 331 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6301 (mp10) outliers start: 66 outliers final: 12 residues processed: 271 average time/residue: 0.6609 time to fit residues: 207.6274 Evaluate side-chains 227 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 316 optimal weight: 0.0070 chunk 123 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN D 108 HIS D 368 ASN E 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.149376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108083 restraints weight = 28492.596| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.87 r_work: 0.3061 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25890 Z= 0.198 Angle : 0.623 6.980 35118 Z= 0.339 Chirality : 0.050 0.154 3978 Planarity : 0.004 0.041 4476 Dihedral : 5.468 31.248 3426 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 3.00 % Allowed : 12.91 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.15), residues: 3168 helix: 1.14 (0.16), residues: 1080 sheet: -0.62 (0.20), residues: 570 loop : -1.26 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 211 TYR 0.013 0.002 TYR F 318 PHE 0.015 0.002 PHE E 225 TRP 0.008 0.002 TRP F 290 HIS 0.006 0.001 HIS F 45 Details of bonding type rmsd covalent geometry : bond 0.00479 (25890) covalent geometry : angle 0.62329 (35118) hydrogen bonds : bond 0.05032 ( 918) hydrogen bonds : angle 5.06743 ( 2574) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 202 time to evaluate : 0.984 Fit side-chains REVERT: A 337 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8500 (mt) REVERT: A 429 ASP cc_start: 0.8087 (m-30) cc_final: 0.7766 (m-30) REVERT: A 442 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.6053 (pm20) REVERT: A 453 VAL cc_start: 0.2839 (OUTLIER) cc_final: 0.2578 (p) REVERT: C 331 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.6073 (mp10) REVERT: C 453 VAL cc_start: 0.2897 (OUTLIER) cc_final: 0.2527 (p) REVERT: B 331 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: B 337 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8521 (mt) REVERT: B 429 ASP cc_start: 0.8013 (m-30) cc_final: 0.7662 (m-30) REVERT: B 453 VAL cc_start: 0.3064 (OUTLIER) cc_final: 0.2698 (p) REVERT: D 119 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7960 (pt0) REVERT: D 331 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6229 (mp10) REVERT: D 337 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8451 (mt) REVERT: D 453 VAL cc_start: 0.2624 (OUTLIER) cc_final: 0.2348 (p) REVERT: E 119 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: E 331 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.6317 (mp10) REVERT: E 337 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8433 (mt) REVERT: E 453 VAL cc_start: 0.2789 (OUTLIER) cc_final: 0.2528 (p) REVERT: F 42 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8546 (ttpt) REVERT: F 331 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.6143 (mp10) REVERT: F 453 VAL cc_start: 0.3216 (OUTLIER) cc_final: 0.2840 (p) outliers start: 83 outliers final: 23 residues processed: 262 average time/residue: 0.6453 time to fit residues: 196.2677 Evaluate side-chains 230 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 170 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 274 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 189 HIS D 189 HIS E 189 HIS F 189 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106564 restraints weight = 28192.286| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.71 r_work: 0.3060 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25890 Z= 0.194 Angle : 0.618 6.874 35118 Z= 0.337 Chirality : 0.050 0.164 3978 Planarity : 0.005 0.043 4476 Dihedral : 5.517 27.031 3426 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.66 % Favored : 93.15 % Rotamer: Outliers : 2.89 % Allowed : 14.03 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3168 helix: 1.14 (0.16), residues: 1080 sheet: -0.63 (0.20), residues: 570 loop : -1.36 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 130 TYR 0.013 0.002 TYR C 318 PHE 0.015 0.002 PHE D 225 TRP 0.010 0.002 TRP E 466 HIS 0.006 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00472 (25890) covalent geometry : angle 0.61825 (35118) hydrogen bonds : bond 0.04839 ( 918) hydrogen bonds : angle 5.00460 ( 2574) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 194 time to evaluate : 1.008 Fit side-chains REVERT: A 337 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8548 (mt) REVERT: A 429 ASP cc_start: 0.8166 (m-30) cc_final: 0.7843 (m-30) REVERT: A 442 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5988 (pm20) REVERT: A 453 VAL cc_start: 0.2567 (OUTLIER) cc_final: 0.2345 (p) REVERT: C 453 VAL cc_start: 0.2570 (OUTLIER) cc_final: 0.2220 (p) REVERT: B 331 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6589 (mp10) REVERT: B 337 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8547 (mt) REVERT: B 429 ASP cc_start: 0.8139 (m-30) cc_final: 0.7779 (m-30) REVERT: B 453 VAL cc_start: 0.2996 (OUTLIER) cc_final: 0.2667 (p) REVERT: D 119 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: D 331 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6276 (mp10) REVERT: D 337 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8428 (mt) REVERT: D 453 VAL cc_start: 0.2273 (OUTLIER) cc_final: 0.1996 (p) REVERT: E 119 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: E 337 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8428 (mt) REVERT: E 453 VAL cc_start: 0.2468 (OUTLIER) cc_final: 0.2249 (p) REVERT: F 42 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8561 (ttpt) REVERT: F 331 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6170 (mp10) REVERT: F 442 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6063 (pm20) REVERT: F 453 VAL cc_start: 0.2554 (OUTLIER) cc_final: 0.2205 (p) outliers start: 80 outliers final: 26 residues processed: 256 average time/residue: 0.6389 time to fit residues: 191.2054 Evaluate side-chains 228 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 263 optimal weight: 5.9990 chunk 294 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106960 restraints weight = 28308.518| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.41 r_work: 0.3067 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25890 Z= 0.163 Angle : 0.585 6.709 35118 Z= 0.318 Chirality : 0.048 0.150 3978 Planarity : 0.004 0.043 4476 Dihedral : 5.381 22.624 3426 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.04 % Favored : 92.77 % Rotamer: Outliers : 2.68 % Allowed : 14.61 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3168 helix: 1.22 (0.16), residues: 1080 sheet: -0.81 (0.19), residues: 606 loop : -1.33 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 211 TYR 0.012 0.002 TYR E 245 PHE 0.014 0.002 PHE E 225 TRP 0.008 0.002 TRP E 466 HIS 0.004 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00390 (25890) covalent geometry : angle 0.58542 (35118) hydrogen bonds : bond 0.04450 ( 918) hydrogen bonds : angle 4.88776 ( 2574) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 196 time to evaluate : 0.939 Fit side-chains REVERT: A 337 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8532 (mt) REVERT: A 429 ASP cc_start: 0.8203 (m-30) cc_final: 0.7795 (m-30) REVERT: A 453 VAL cc_start: 0.2684 (OUTLIER) cc_final: 0.2450 (p) REVERT: C 171 THR cc_start: 0.9462 (p) cc_final: 0.9250 (p) REVERT: C 362 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8556 (tp) REVERT: C 453 VAL cc_start: 0.2619 (OUTLIER) cc_final: 0.2259 (p) REVERT: B 331 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: B 337 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 429 ASP cc_start: 0.8196 (m-30) cc_final: 0.7825 (m-30) REVERT: B 453 VAL cc_start: 0.2984 (OUTLIER) cc_final: 0.2648 (p) REVERT: D 119 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: D 337 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8432 (mt) REVERT: D 453 VAL cc_start: 0.1962 (OUTLIER) cc_final: 0.1729 (p) REVERT: E 337 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8435 (mt) REVERT: E 453 VAL cc_start: 0.2484 (OUTLIER) cc_final: 0.2253 (p) REVERT: F 42 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8518 (ttpt) REVERT: F 442 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6150 (pm20) REVERT: F 453 VAL cc_start: 0.2619 (OUTLIER) cc_final: 0.2251 (p) outliers start: 74 outliers final: 30 residues processed: 254 average time/residue: 0.6480 time to fit residues: 191.3467 Evaluate side-chains 230 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 208 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 314 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108589 restraints weight = 28372.854| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.96 r_work: 0.3096 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25890 Z= 0.122 Angle : 0.550 6.463 35118 Z= 0.297 Chirality : 0.046 0.151 3978 Planarity : 0.004 0.041 4476 Dihedral : 5.206 21.823 3426 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.63 % Favored : 93.18 % Rotamer: Outliers : 2.60 % Allowed : 15.29 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3168 helix: 1.35 (0.16), residues: 1080 sheet: -0.80 (0.19), residues: 618 loop : -1.28 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 211 TYR 0.010 0.001 TYR D 245 PHE 0.013 0.001 PHE E 225 TRP 0.007 0.001 TRP F 402 HIS 0.003 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00276 (25890) covalent geometry : angle 0.54989 (35118) hydrogen bonds : bond 0.03860 ( 918) hydrogen bonds : angle 4.72916 ( 2574) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 193 time to evaluate : 1.057 Fit side-chains REVERT: A 119 GLU cc_start: 0.7788 (pt0) cc_final: 0.7571 (pt0) REVERT: A 337 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8472 (mt) REVERT: A 429 ASP cc_start: 0.8126 (m-30) cc_final: 0.7738 (m-30) REVERT: A 453 VAL cc_start: 0.2675 (OUTLIER) cc_final: 0.2442 (p) REVERT: A 461 MET cc_start: 0.3850 (pmt) cc_final: 0.2852 (mpp) REVERT: C 119 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7704 (pt0) REVERT: C 171 THR cc_start: 0.9438 (p) cc_final: 0.9207 (p) REVERT: C 362 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8460 (tp) REVERT: C 453 VAL cc_start: 0.2585 (OUTLIER) cc_final: 0.2234 (p) REVERT: B 331 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6455 (mp10) REVERT: B 337 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8543 (mt) REVERT: B 429 ASP cc_start: 0.8043 (m-30) cc_final: 0.7682 (m-30) REVERT: B 453 VAL cc_start: 0.2979 (OUTLIER) cc_final: 0.2640 (p) REVERT: D 331 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6113 (mp10) REVERT: D 337 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8407 (mt) REVERT: D 453 VAL cc_start: 0.2534 (OUTLIER) cc_final: 0.2222 (p) REVERT: E 92 MET cc_start: 0.8920 (mtm) cc_final: 0.8616 (mtp) REVERT: E 337 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8428 (mt) REVERT: E 453 VAL cc_start: 0.2845 (OUTLIER) cc_final: 0.2595 (p) REVERT: F 442 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6206 (pm20) REVERT: F 453 VAL cc_start: 0.2604 (OUTLIER) cc_final: 0.2242 (p) outliers start: 72 outliers final: 27 residues processed: 252 average time/residue: 0.6654 time to fit residues: 194.5467 Evaluate side-chains 231 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 147 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 274 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 228 optimal weight: 0.6980 chunk 296 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106308 restraints weight = 28235.129| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.15 r_work: 0.3075 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25890 Z= 0.156 Angle : 0.580 6.634 35118 Z= 0.313 Chirality : 0.048 0.156 3978 Planarity : 0.004 0.044 4476 Dihedral : 5.272 21.664 3426 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.26 % Favored : 92.55 % Rotamer: Outliers : 2.64 % Allowed : 15.22 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3168 helix: 1.30 (0.16), residues: 1080 sheet: -0.83 (0.19), residues: 618 loop : -1.29 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 211 TYR 0.012 0.002 TYR E 245 PHE 0.014 0.002 PHE E 225 TRP 0.007 0.001 TRP B 466 HIS 0.004 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00373 (25890) covalent geometry : angle 0.57958 (35118) hydrogen bonds : bond 0.04304 ( 918) hydrogen bonds : angle 4.80370 ( 2574) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 191 time to evaluate : 1.055 Fit side-chains REVERT: A 119 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: A 337 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8454 (mt) REVERT: A 429 ASP cc_start: 0.8165 (m-30) cc_final: 0.7758 (m-30) REVERT: A 453 VAL cc_start: 0.2681 (OUTLIER) cc_final: 0.2440 (p) REVERT: C 119 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: C 171 THR cc_start: 0.9461 (p) cc_final: 0.9246 (p) REVERT: C 362 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8497 (tp) REVERT: C 453 VAL cc_start: 0.2682 (OUTLIER) cc_final: 0.2317 (p) REVERT: B 331 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6513 (mp10) REVERT: B 337 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8545 (mt) REVERT: B 343 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: B 429 ASP cc_start: 0.8100 (m-30) cc_final: 0.7715 (m-30) REVERT: B 453 VAL cc_start: 0.2992 (OUTLIER) cc_final: 0.2645 (p) REVERT: D 331 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6164 (mp10) REVERT: D 337 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8419 (mt) REVERT: D 453 VAL cc_start: 0.2143 (OUTLIER) cc_final: 0.1891 (p) REVERT: E 331 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.6217 (mp10) REVERT: E 337 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8408 (mt) REVERT: F 42 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8537 (ttpt) REVERT: F 119 GLU cc_start: 0.7949 (pt0) cc_final: 0.7727 (pt0) REVERT: F 453 VAL cc_start: 0.2654 (OUTLIER) cc_final: 0.2277 (p) outliers start: 73 outliers final: 33 residues processed: 247 average time/residue: 0.6705 time to fit residues: 192.1819 Evaluate side-chains 235 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 282 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104879 restraints weight = 28235.426| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.12 r_work: 0.3045 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25890 Z= 0.230 Angle : 0.652 7.253 35118 Z= 0.354 Chirality : 0.051 0.167 3978 Planarity : 0.005 0.046 4476 Dihedral : 5.561 22.360 3426 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.48 % Favored : 92.33 % Rotamer: Outliers : 2.53 % Allowed : 15.51 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3168 helix: 1.09 (0.16), residues: 1080 sheet: -0.88 (0.19), residues: 606 loop : -1.35 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 211 TYR 0.014 0.002 TYR B 318 PHE 0.014 0.002 PHE E 225 TRP 0.013 0.002 TRP B 466 HIS 0.005 0.001 HIS F 213 Details of bonding type rmsd covalent geometry : bond 0.00566 (25890) covalent geometry : angle 0.65179 (35118) hydrogen bonds : bond 0.05169 ( 918) hydrogen bonds : angle 5.01307 ( 2574) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 181 time to evaluate : 1.014 Fit side-chains REVERT: A 337 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8503 (mt) REVERT: A 429 ASP cc_start: 0.8221 (m-30) cc_final: 0.7804 (m-30) REVERT: A 453 VAL cc_start: 0.2517 (OUTLIER) cc_final: 0.2283 (p) REVERT: A 461 MET cc_start: 0.3915 (pmt) cc_final: 0.3118 (mpp) REVERT: C 119 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7704 (pt0) REVERT: C 453 VAL cc_start: 0.2990 (OUTLIER) cc_final: 0.2619 (p) REVERT: B 260 GLN cc_start: 0.8475 (mm110) cc_final: 0.8261 (mm110) REVERT: B 331 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6661 (mp10) REVERT: B 337 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 343 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: B 429 ASP cc_start: 0.8196 (m-30) cc_final: 0.7781 (m-30) REVERT: B 453 VAL cc_start: 0.3018 (OUTLIER) cc_final: 0.2672 (p) REVERT: D 337 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8449 (mt) REVERT: D 453 VAL cc_start: 0.2256 (OUTLIER) cc_final: 0.2009 (p) REVERT: D 506 LEU cc_start: 0.3146 (OUTLIER) cc_final: 0.2757 (pp) REVERT: E 337 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8467 (mt) REVERT: F 453 VAL cc_start: 0.3076 (OUTLIER) cc_final: 0.2681 (p) outliers start: 70 outliers final: 33 residues processed: 240 average time/residue: 0.6450 time to fit residues: 180.3362 Evaluate side-chains 226 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 242 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 chunk 312 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106703 restraints weight = 28177.332| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.78 r_work: 0.3070 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25890 Z= 0.162 Angle : 0.599 6.632 35118 Z= 0.324 Chirality : 0.048 0.173 3978 Planarity : 0.004 0.045 4476 Dihedral : 5.422 22.148 3426 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.07 % Favored : 92.74 % Rotamer: Outliers : 2.24 % Allowed : 15.65 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3168 helix: 1.17 (0.16), residues: 1080 sheet: -0.68 (0.19), residues: 648 loop : -1.36 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 211 TYR 0.012 0.002 TYR E 245 PHE 0.014 0.002 PHE E 225 TRP 0.009 0.002 TRP E 466 HIS 0.004 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00388 (25890) covalent geometry : angle 0.59923 (35118) hydrogen bonds : bond 0.04461 ( 918) hydrogen bonds : angle 4.87612 ( 2574) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 1.107 Fit side-chains REVERT: A 337 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 429 ASP cc_start: 0.8191 (m-30) cc_final: 0.7787 (m-30) REVERT: A 453 VAL cc_start: 0.2651 (OUTLIER) cc_final: 0.2391 (p) REVERT: A 506 LEU cc_start: 0.2871 (OUTLIER) cc_final: 0.2524 (pp) REVERT: C 119 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: C 453 VAL cc_start: 0.2968 (OUTLIER) cc_final: 0.2596 (p) REVERT: B 331 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6536 (mp10) REVERT: B 337 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8539 (mt) REVERT: B 429 ASP cc_start: 0.8149 (m-30) cc_final: 0.7747 (m-30) REVERT: B 453 VAL cc_start: 0.3014 (OUTLIER) cc_final: 0.2635 (p) REVERT: B 506 LEU cc_start: 0.2914 (OUTLIER) cc_final: 0.2627 (pp) REVERT: D 337 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8431 (mt) REVERT: D 453 VAL cc_start: 0.2348 (OUTLIER) cc_final: 0.2094 (p) REVERT: D 506 LEU cc_start: 0.3175 (OUTLIER) cc_final: 0.2700 (pp) REVERT: E 337 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8439 (mt) REVERT: F 453 VAL cc_start: 0.2852 (OUTLIER) cc_final: 0.2452 (p) outliers start: 62 outliers final: 34 residues processed: 235 average time/residue: 0.6576 time to fit residues: 179.8725 Evaluate side-chains 223 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 506 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 171 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 278 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.148689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107054 restraints weight = 28329.034| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.75 r_work: 0.3058 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25890 Z= 0.166 Angle : 0.603 7.014 35118 Z= 0.324 Chirality : 0.048 0.186 3978 Planarity : 0.004 0.045 4476 Dihedral : 5.376 22.065 3426 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.26 % Favored : 92.55 % Rotamer: Outliers : 1.88 % Allowed : 16.20 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3168 helix: 1.19 (0.16), residues: 1080 sheet: -0.64 (0.19), residues: 648 loop : -1.37 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 211 TYR 0.013 0.002 TYR E 245 PHE 0.013 0.002 PHE E 225 TRP 0.011 0.002 TRP E 466 HIS 0.004 0.001 HIS F 213 Details of bonding type rmsd covalent geometry : bond 0.00399 (25890) covalent geometry : angle 0.60262 (35118) hydrogen bonds : bond 0.04437 ( 918) hydrogen bonds : angle 4.85162 ( 2574) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 1.018 Fit side-chains REVERT: A 337 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8491 (mt) REVERT: A 429 ASP cc_start: 0.8194 (m-30) cc_final: 0.7788 (m-30) REVERT: A 453 VAL cc_start: 0.2549 (OUTLIER) cc_final: 0.2294 (p) REVERT: A 506 LEU cc_start: 0.2672 (OUTLIER) cc_final: 0.2371 (pp) REVERT: C 119 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7742 (pt0) REVERT: C 453 VAL cc_start: 0.2946 (OUTLIER) cc_final: 0.2575 (p) REVERT: B 331 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6525 (mp10) REVERT: B 337 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8538 (mt) REVERT: B 429 ASP cc_start: 0.8043 (m-30) cc_final: 0.7659 (m-30) REVERT: B 453 VAL cc_start: 0.2882 (OUTLIER) cc_final: 0.2559 (p) REVERT: B 506 LEU cc_start: 0.2727 (OUTLIER) cc_final: 0.2473 (pp) REVERT: D 144 GLU cc_start: 0.6823 (pm20) cc_final: 0.6539 (pm20) REVERT: D 337 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8418 (mt) REVERT: D 453 VAL cc_start: 0.2348 (OUTLIER) cc_final: 0.2136 (p) REVERT: D 506 LEU cc_start: 0.3286 (OUTLIER) cc_final: 0.2841 (pp) REVERT: E 337 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8442 (mt) REVERT: F 453 VAL cc_start: 0.2915 (OUTLIER) cc_final: 0.2507 (p) outliers start: 52 outliers final: 35 residues processed: 229 average time/residue: 0.6268 time to fit residues: 166.5789 Evaluate side-chains 233 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 506 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 90 optimal weight: 2.9990 chunk 297 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 156 optimal weight: 0.0040 chunk 191 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110222 restraints weight = 28341.559| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.99 r_work: 0.3127 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25890 Z= 0.105 Angle : 0.541 8.399 35118 Z= 0.287 Chirality : 0.046 0.193 3978 Planarity : 0.004 0.042 4476 Dihedral : 5.020 21.759 3426 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.34 % Favored : 93.47 % Rotamer: Outliers : 1.92 % Allowed : 16.31 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3168 helix: 1.44 (0.16), residues: 1080 sheet: -0.36 (0.21), residues: 558 loop : -1.31 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.014 0.001 TYR F 361 PHE 0.012 0.001 PHE D 225 TRP 0.012 0.001 TRP E 290 HIS 0.003 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00231 (25890) covalent geometry : angle 0.54092 (35118) hydrogen bonds : bond 0.03387 ( 918) hydrogen bonds : angle 4.58636 ( 2574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9654.24 seconds wall clock time: 165 minutes 0.02 seconds (9900.02 seconds total)