Starting phenix.real_space_refine on Sat May 24 07:41:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsy_35008/05_2025/8hsy_35008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsy_35008/05_2025/8hsy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hsy_35008/05_2025/8hsy_35008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsy_35008/05_2025/8hsy_35008.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsy_35008/05_2025/8hsy_35008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsy_35008/05_2025/8hsy_35008.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.078 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.05, per 1000 atoms: 0.59 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: 5.92 Conformation dependent library (CDL) restraints added in 3.0 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: 3.16 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: 8.92 Time building geometry restraints manager: 6.98 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 2.490 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: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.280 Process input model: 55.130 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.570 ------------------------------------------------------------------------------- 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 : 7.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (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 TRP 0.011 0.001 TRP F 290 HIS 0.003 0.001 HIS F 45 PHE 0.011 0.001 PHE E 225 TYR 0.010 0.001 TYR C 148 ARG 0.005 0.000 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.16884 ( 918) hydrogen bonds : angle 7.11939 ( 2574) covalent geometry : bond 0.00397 (25890) covalent geometry : angle 0.70730 (35118) *********************** 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 : 2.874 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: 1.4553 time to fit residues: 430.7254 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 : 3.006 ------------------------------------------------------------------------------- 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 268 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 108 HIS C 189 HIS C 243 GLN C 368 ASN B 17 ASN B 243 GLN B 368 ASN D 108 HIS D 243 GLN D 368 ASN E 108 HIS E 243 GLN E 368 ASN F 17 ASN F 108 HIS F 189 HIS F 243 GLN F 368 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105869 restraints weight = 28323.339| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.56 r_work: 0.2967 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 25890 Z= 0.327 Angle : 0.755 8.134 35118 Z= 0.411 Chirality : 0.056 0.183 3978 Planarity : 0.006 0.053 4476 Dihedral : 6.032 49.657 3429 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.07 % Favored : 92.74 % Rotamer: Outliers : 3.62 % Allowed : 12.58 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3168 helix: 0.69 (0.16), residues: 1080 sheet: -0.71 (0.20), residues: 570 loop : -1.41 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 230 HIS 0.009 0.002 HIS F 45 PHE 0.018 0.003 PHE E 225 TYR 0.020 0.003 TYR C 318 ARG 0.006 0.001 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.06542 ( 918) hydrogen bonds : angle 5.53000 ( 2574) covalent geometry : bond 0.00804 (25890) covalent geometry : angle 0.75453 (35118) *********************** 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 303 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 203 time to evaluate : 2.794 Fit side-chains REVERT: A 337 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8613 (mt) REVERT: A 429 ASP cc_start: 0.8246 (m-30) cc_final: 0.8007 (m-30) REVERT: A 442 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.6037 (pm20) REVERT: A 453 VAL cc_start: 0.2590 (OUTLIER) cc_final: 0.2331 (p) REVERT: C 331 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.6281 (mp10) REVERT: C 453 VAL cc_start: 0.2673 (OUTLIER) cc_final: 0.2304 (p) REVERT: B 28 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: B 331 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6755 (mp10) REVERT: B 337 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8572 (mt) REVERT: B 429 ASP cc_start: 0.8241 (m-30) cc_final: 0.7907 (m-30) REVERT: B 453 VAL cc_start: 0.2916 (OUTLIER) cc_final: 0.2557 (p) REVERT: D 331 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: D 453 VAL cc_start: 0.2730 (OUTLIER) cc_final: 0.2384 (p) REVERT: E 331 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.6563 (mp10) REVERT: E 453 VAL cc_start: 0.2524 (OUTLIER) cc_final: 0.2252 (p) REVERT: F 305 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8547 (mttm) REVERT: F 331 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6338 (mp10) REVERT: F 342 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7437 (t0) REVERT: F 364 ASP cc_start: 0.8108 (p0) cc_final: 0.7833 (p0) REVERT: F 418 GLU cc_start: 0.7331 (pm20) cc_final: 0.7096 (pt0) REVERT: F 453 VAL cc_start: 0.2790 (OUTLIER) cc_final: 0.2431 (p) outliers start: 100 outliers final: 22 residues processed: 271 average time/residue: 1.2878 time to fit residues: 406.5932 Evaluate side-chains 227 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 2.706 ------------------------------------------------------------------------------- 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 362 ILE 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 259 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 322 GLU 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 163 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 331 GLN 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 305 LYS 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 453 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 204 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 295 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108340 restraints weight = 28243.802| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.82 r_work: 0.3098 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25890 Z= 0.123 Angle : 0.563 6.377 35118 Z= 0.304 Chirality : 0.047 0.148 3978 Planarity : 0.004 0.043 4476 Dihedral : 5.542 46.927 3429 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.50 % Favored : 93.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3168 helix: 1.10 (0.16), residues: 1080 sheet: -0.86 (0.18), residues: 660 loop : -1.33 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 290 HIS 0.003 0.001 HIS B 228 PHE 0.015 0.001 PHE E 225 TYR 0.009 0.001 TYR B 148 ARG 0.003 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 918) hydrogen bonds : angle 4.96069 ( 2574) covalent geometry : bond 0.00280 (25890) covalent geometry : angle 0.56330 (35118) *********************** 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 275 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 209 time to evaluate : 2.699 Fit side-chains REVERT: A 429 ASP cc_start: 0.8074 (m-30) cc_final: 0.7780 (m-30) REVERT: A 442 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5944 (pm20) REVERT: C 171 THR cc_start: 0.9443 (p) cc_final: 0.9241 (p) REVERT: B 331 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6564 (mp10) REVERT: B 429 ASP cc_start: 0.8164 (m-30) cc_final: 0.7756 (m-30) REVERT: D 331 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.6207 (mp10) REVERT: D 337 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (mt) REVERT: E 337 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8440 (mt) REVERT: F 171 THR cc_start: 0.9447 (p) cc_final: 0.9243 (p) REVERT: F 418 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7174 (pt0) outliers start: 66 outliers final: 20 residues processed: 253 average time/residue: 1.2750 time to fit residues: 375.9123 Evaluate side-chains 214 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET 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 314 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 86 ILE 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 E residue 86 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 232 LEU 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 418 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 269 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 312 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.150605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.108583 restraints weight = 28477.462| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.01 r_work: 0.3091 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25890 Z= 0.127 Angle : 0.556 6.524 35118 Z= 0.300 Chirality : 0.047 0.146 3978 Planarity : 0.004 0.043 4476 Dihedral : 5.316 32.114 3426 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.91 % Favored : 92.90 % Rotamer: Outliers : 2.89 % Allowed : 14.14 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3168 helix: 1.26 (0.16), residues: 1080 sheet: -0.61 (0.20), residues: 582 loop : -1.33 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 402 HIS 0.003 0.001 HIS D 45 PHE 0.014 0.001 PHE E 225 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 918) hydrogen bonds : angle 4.83717 ( 2574) covalent geometry : bond 0.00292 (25890) covalent geometry : angle 0.55648 (35118) *********************** 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 271 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 2.770 Fit side-chains REVERT: A 337 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 429 ASP cc_start: 0.8077 (m-30) cc_final: 0.7769 (m-30) REVERT: A 442 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5982 (pm20) REVERT: A 453 VAL cc_start: 0.2769 (OUTLIER) cc_final: 0.2552 (p) REVERT: C 171 THR cc_start: 0.9437 (p) cc_final: 0.9234 (p) REVERT: C 331 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6373 (mp10) REVERT: C 362 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8420 (tp) REVERT: C 453 VAL cc_start: 0.2849 (OUTLIER) cc_final: 0.2488 (p) REVERT: B 331 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6552 (mp10) REVERT: B 337 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8521 (mt) REVERT: B 429 ASP cc_start: 0.8067 (m-30) cc_final: 0.7699 (m-30) REVERT: B 453 VAL cc_start: 0.3098 (OUTLIER) cc_final: 0.2786 (p) REVERT: D 337 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8486 (mt) REVERT: D 418 GLU cc_start: 0.7022 (pt0) cc_final: 0.6803 (pm20) REVERT: D 453 VAL cc_start: 0.2564 (OUTLIER) cc_final: 0.2295 (p) REVERT: E 331 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6216 (mp10) REVERT: E 337 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8431 (mt) REVERT: E 453 VAL cc_start: 0.2895 (OUTLIER) cc_final: 0.2636 (p) REVERT: F 171 THR cc_start: 0.9445 (p) cc_final: 0.9242 (p) REVERT: F 331 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6472 (mp10) REVERT: F 418 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: F 442 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6282 (pm20) REVERT: F 453 VAL cc_start: 0.2826 (OUTLIER) cc_final: 0.2471 (p) outliers start: 80 outliers final: 26 residues processed: 249 average time/residue: 1.2267 time to fit residues: 359.0204 Evaluate side-chains 230 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 2.728 ------------------------------------------------------------------------------- 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 158 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 C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain B residue 197 MET 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 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 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 E residue 453 VAL 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 363 VAL Chi-restraints excluded: chain F residue 418 GLU 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 67 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 234 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.109963 restraints weight = 28574.841| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.83 r_work: 0.3102 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1762 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= 0.116 Angle : 0.540 6.363 35118 Z= 0.291 Chirality : 0.046 0.146 3978 Planarity : 0.004 0.041 4476 Dihedral : 5.200 29.426 3426 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.69 % Favored : 93.12 % Rotamer: Outliers : 2.93 % Allowed : 14.46 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3168 helix: 1.38 (0.16), residues: 1080 sheet: -0.66 (0.20), residues: 540 loop : -1.27 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 402 HIS 0.003 0.001 HIS D 45 PHE 0.013 0.001 PHE E 225 TYR 0.009 0.001 TYR E 245 ARG 0.002 0.000 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 918) hydrogen bonds : angle 4.72496 ( 2574) covalent geometry : bond 0.00262 (25890) covalent geometry : angle 0.53979 (35118) *********************** 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 274 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 193 time to evaluate : 2.907 Fit side-chains REVERT: A 337 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8494 (mt) REVERT: A 429 ASP cc_start: 0.8138 (m-30) cc_final: 0.7747 (m-30) REVERT: A 442 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.6028 (pm20) REVERT: A 453 VAL cc_start: 0.2754 (OUTLIER) cc_final: 0.2528 (p) REVERT: C 171 THR cc_start: 0.9413 (p) cc_final: 0.9202 (p) REVERT: C 362 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8431 (tp) REVERT: C 453 VAL cc_start: 0.2732 (OUTLIER) cc_final: 0.2374 (p) REVERT: B 331 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6528 (mp10) REVERT: B 337 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8513 (mt) REVERT: B 429 ASP cc_start: 0.8082 (m-30) cc_final: 0.7689 (m-30) REVERT: B 453 VAL cc_start: 0.3073 (OUTLIER) cc_final: 0.2756 (p) REVERT: D 337 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8441 (mt) REVERT: D 453 VAL cc_start: 0.2563 (OUTLIER) cc_final: 0.2281 (p) REVERT: E 119 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: E 331 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: E 337 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8397 (mt) REVERT: E 418 GLU cc_start: 0.7012 (pt0) cc_final: 0.6808 (pm20) REVERT: E 453 VAL cc_start: 0.2802 (OUTLIER) cc_final: 0.2553 (p) REVERT: F 171 THR cc_start: 0.9430 (p) cc_final: 0.9212 (p) REVERT: F 331 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6350 (mp10) REVERT: F 453 VAL cc_start: 0.2809 (OUTLIER) cc_final: 0.2454 (p) outliers start: 81 outliers final: 23 residues processed: 253 average time/residue: 1.2597 time to fit residues: 372.7323 Evaluate side-chains 231 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 2.808 ------------------------------------------------------------------------------- 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 158 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 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 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 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 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 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 363 VAL 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 186 optimal weight: 0.4980 chunk 48 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 246 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 269 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.152676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.110756 restraints weight = 28461.167| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.99 r_work: 0.3134 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1824 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 : 0.523 6.301 35118 Z= 0.280 Chirality : 0.046 0.148 3978 Planarity : 0.004 0.039 4476 Dihedral : 4.999 25.657 3426 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.99 % Rotamer: Outliers : 2.86 % Allowed : 14.71 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3168 helix: 1.51 (0.16), residues: 1080 sheet: -0.53 (0.21), residues: 516 loop : -1.18 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 290 HIS 0.003 0.001 HIS A 414 PHE 0.012 0.001 PHE E 225 TYR 0.008 0.001 TYR E 245 ARG 0.002 0.000 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 918) hydrogen bonds : angle 4.60038 ( 2574) covalent geometry : bond 0.00232 (25890) covalent geometry : angle 0.52342 (35118) *********************** 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 284 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 205 time to evaluate : 2.874 Fit side-chains REVERT: A 337 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8395 (mt) REVERT: A 429 ASP cc_start: 0.8074 (m-30) cc_final: 0.7731 (m-30) REVERT: A 442 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5975 (pm20) REVERT: A 453 VAL cc_start: 0.2769 (OUTLIER) cc_final: 0.2550 (p) REVERT: C 119 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: C 171 THR cc_start: 0.9383 (p) cc_final: 0.9140 (p) REVERT: C 453 VAL cc_start: 0.2712 (OUTLIER) cc_final: 0.2352 (p) REVERT: B 331 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6209 (mp10) REVERT: B 337 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8427 (mt) REVERT: B 429 ASP cc_start: 0.8049 (m-30) cc_final: 0.7666 (m-30) REVERT: B 453 VAL cc_start: 0.3011 (OUTLIER) cc_final: 0.2681 (p) REVERT: D 119 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: D 337 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8400 (mt) REVERT: D 453 VAL cc_start: 0.2507 (OUTLIER) cc_final: 0.2181 (p) REVERT: E 92 MET cc_start: 0.8826 (mtm) cc_final: 0.8541 (mtp) REVERT: E 331 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.5700 (mp10) REVERT: E 337 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8410 (mt) REVERT: E 418 GLU cc_start: 0.6947 (pt0) cc_final: 0.6699 (pm20) REVERT: F 171 THR cc_start: 0.9378 (p) cc_final: 0.9133 (p) REVERT: F 453 VAL cc_start: 0.2680 (OUTLIER) cc_final: 0.2328 (p) outliers start: 79 outliers final: 27 residues processed: 267 average time/residue: 1.2420 time to fit residues: 389.3261 Evaluate side-chains 235 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 2.959 ------------------------------------------------------------------------------- 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 A residue 474 VAL 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 158 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 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 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 163 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 238 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 312 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 237 optimal weight: 0.5980 chunk 180 optimal weight: 0.7980 chunk 313 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.158778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120400 restraints weight = 30670.036| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.55 r_work: 0.3234 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25890 Z= 0.116 Angle : 0.535 6.258 35118 Z= 0.287 Chirality : 0.046 0.156 3978 Planarity : 0.004 0.041 4476 Dihedral : 5.003 22.203 3426 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.01 % Favored : 92.80 % Rotamer: Outliers : 2.53 % Allowed : 15.22 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3168 helix: 1.52 (0.16), residues: 1080 sheet: -0.44 (0.21), residues: 528 loop : -1.18 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 402 HIS 0.003 0.001 HIS E 228 PHE 0.012 0.001 PHE C 225 TYR 0.009 0.001 TYR E 245 ARG 0.002 0.000 ARG F 211 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 918) hydrogen bonds : angle 4.61145 ( 2574) covalent geometry : bond 0.00263 (25890) covalent geometry : angle 0.53502 (35118) *********************** 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 265 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 195 time to evaluate : 3.084 Fit side-chains REVERT: A 337 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8430 (mt) REVERT: A 429 ASP cc_start: 0.8046 (m-30) cc_final: 0.7694 (m-30) REVERT: A 453 VAL cc_start: 0.2897 (OUTLIER) cc_final: 0.2669 (p) REVERT: A 461 MET cc_start: 0.3759 (pmt) cc_final: 0.2760 (mpp) REVERT: C 171 THR cc_start: 0.9421 (p) cc_final: 0.9202 (p) REVERT: C 453 VAL cc_start: 0.2924 (OUTLIER) cc_final: 0.2563 (p) REVERT: B 331 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6300 (mp10) REVERT: B 337 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8502 (mt) REVERT: B 429 ASP cc_start: 0.8138 (m-30) cc_final: 0.7739 (m-30) REVERT: B 453 VAL cc_start: 0.3311 (OUTLIER) cc_final: 0.3001 (p) REVERT: D 337 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8466 (mt) REVERT: D 453 VAL cc_start: 0.2860 (OUTLIER) cc_final: 0.2514 (p) REVERT: D 506 LEU cc_start: 0.3140 (OUTLIER) cc_final: 0.2708 (pp) REVERT: E 92 MET cc_start: 0.8926 (mtm) cc_final: 0.8643 (mtp) REVERT: E 331 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.5672 (mp10) REVERT: E 337 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8453 (mt) REVERT: E 453 VAL cc_start: 0.3026 (OUTLIER) cc_final: 0.2734 (p) REVERT: F 171 THR cc_start: 0.9432 (p) cc_final: 0.9216 (p) REVERT: F 362 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8347 (tp) REVERT: F 453 VAL cc_start: 0.2807 (OUTLIER) cc_final: 0.2457 (p) REVERT: F 518 THR cc_start: 0.4760 (OUTLIER) cc_final: 0.4128 (p) outliers start: 70 outliers final: 28 residues processed: 247 average time/residue: 1.3060 time to fit residues: 379.5041 Evaluate side-chains 233 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 3.158 ------------------------------------------------------------------------------- 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 453 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 158 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 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 438 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 518 THR 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 163 ASP 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 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 362 ILE Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 518 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 147 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 275 optimal weight: 0.0970 chunk 307 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 277 optimal weight: 0.0570 chunk 118 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.160852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123185 restraints weight = 30466.679| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.88 r_work: 0.3289 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25890 Z= 0.097 Angle : 0.514 6.160 35118 Z= 0.273 Chirality : 0.045 0.161 3978 Planarity : 0.004 0.039 4476 Dihedral : 4.815 20.724 3426 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.85 % Favored : 92.96 % Rotamer: Outliers : 2.21 % Allowed : 15.51 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3168 helix: 1.62 (0.16), residues: 1086 sheet: -0.46 (0.22), residues: 516 loop : -1.06 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 290 HIS 0.003 0.001 HIS B 414 PHE 0.011 0.001 PHE F 225 TYR 0.007 0.001 TYR E 148 ARG 0.002 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 918) hydrogen bonds : angle 4.48584 ( 2574) covalent geometry : bond 0.00210 (25890) covalent geometry : angle 0.51383 (35118) *********************** 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 267 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 2.735 Fit side-chains REVERT: A 337 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8396 (mt) REVERT: A 429 ASP cc_start: 0.8028 (m-30) cc_final: 0.7685 (m-30) REVERT: A 453 VAL cc_start: 0.2965 (OUTLIER) cc_final: 0.2749 (p) REVERT: A 461 MET cc_start: 0.3709 (pmt) cc_final: 0.2731 (mpp) REVERT: C 453 VAL cc_start: 0.3148 (OUTLIER) cc_final: 0.2770 (p) REVERT: B 337 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8432 (mt) REVERT: B 429 ASP cc_start: 0.8078 (m-30) cc_final: 0.7693 (m-30) REVERT: B 453 VAL cc_start: 0.3231 (OUTLIER) cc_final: 0.2918 (p) REVERT: B 506 LEU cc_start: 0.2912 (OUTLIER) cc_final: 0.2536 (pp) REVERT: D 92 MET cc_start: 0.8802 (mtm) cc_final: 0.8507 (mtp) REVERT: D 337 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8443 (mt) REVERT: D 506 LEU cc_start: 0.3135 (OUTLIER) cc_final: 0.2732 (pp) REVERT: E 92 MET cc_start: 0.8831 (mtm) cc_final: 0.8539 (mtp) REVERT: E 337 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8378 (mt) REVERT: E 418 GLU cc_start: 0.6968 (pt0) cc_final: 0.6704 (pm20) REVERT: E 453 VAL cc_start: 0.3069 (OUTLIER) cc_final: 0.2742 (p) REVERT: F 119 GLU cc_start: 0.7796 (pt0) cc_final: 0.7588 (pt0) REVERT: F 171 THR cc_start: 0.9384 (p) cc_final: 0.9135 (p) REVERT: F 362 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8346 (tp) outliers start: 61 outliers final: 27 residues processed: 256 average time/residue: 1.1946 time to fit residues: 360.0151 Evaluate side-chains 237 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 76 TYR Chi-restraints excluded: chain C residue 158 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 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 518 THR 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 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 28 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 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 506 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.156140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117317 restraints weight = 30389.880| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.54 r_work: 0.3170 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25890 Z= 0.184 Angle : 0.607 6.691 35118 Z= 0.327 Chirality : 0.049 0.210 3978 Planarity : 0.004 0.039 4476 Dihedral : 5.250 20.714 3426 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.42 % Favored : 92.39 % Rotamer: Outliers : 2.02 % Allowed : 15.65 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3168 helix: 1.37 (0.16), residues: 1080 sheet: -0.34 (0.21), residues: 558 loop : -1.23 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 466 HIS 0.005 0.001 HIS B 228 PHE 0.014 0.002 PHE E 225 TYR 0.012 0.002 TYR D 245 ARG 0.003 0.000 ARG F 211 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 918) hydrogen bonds : angle 4.82329 ( 2574) covalent geometry : bond 0.00448 (25890) covalent geometry : angle 0.60682 (35118) *********************** 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 251 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 195 time to evaluate : 2.757 Fit side-chains REVERT: A 337 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8540 (mt) REVERT: A 429 ASP cc_start: 0.8185 (m-30) cc_final: 0.7805 (m-30) REVERT: A 453 VAL cc_start: 0.2918 (OUTLIER) cc_final: 0.2676 (p) REVERT: A 461 MET cc_start: 0.3682 (pmt) cc_final: 0.2875 (mpp) REVERT: C 119 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: C 362 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8541 (tp) REVERT: C 453 VAL cc_start: 0.2865 (OUTLIER) cc_final: 0.2502 (p) REVERT: B 331 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6546 (mp10) REVERT: B 337 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8547 (mt) REVERT: B 429 ASP cc_start: 0.8148 (m-30) cc_final: 0.7764 (m-30) REVERT: B 453 VAL cc_start: 0.3245 (OUTLIER) cc_final: 0.2916 (p) REVERT: D 337 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8502 (mt) REVERT: D 506 LEU cc_start: 0.3021 (OUTLIER) cc_final: 0.2604 (pp) REVERT: E 337 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8509 (mt) REVERT: E 418 GLU cc_start: 0.7167 (pt0) cc_final: 0.6777 (pm20) REVERT: E 453 VAL cc_start: 0.3126 (OUTLIER) cc_final: 0.2882 (p) REVERT: F 119 GLU cc_start: 0.7989 (pt0) cc_final: 0.7780 (pt0) REVERT: F 331 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6096 (mp10) REVERT: F 362 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8476 (tp) REVERT: F 453 VAL cc_start: 0.2728 (OUTLIER) cc_final: 0.2369 (p) outliers start: 56 outliers final: 30 residues processed: 239 average time/residue: 1.2883 time to fit residues: 362.1133 Evaluate side-chains 234 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 158 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 438 VAL Chi-restraints excluded: chain B residue 453 VAL 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 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 506 LEU 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 362 ILE 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 86 ILE 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 362 ILE 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 169 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 232 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.158668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120018 restraints weight = 30499.779| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.90 r_work: 0.3256 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25890 Z= 0.114 Angle : 0.543 8.010 35118 Z= 0.290 Chirality : 0.046 0.203 3978 Planarity : 0.004 0.039 4476 Dihedral : 4.990 20.245 3426 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.69 % Favored : 93.12 % Rotamer: Outliers : 1.92 % Allowed : 15.76 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3168 helix: 1.50 (0.16), residues: 1080 sheet: -0.51 (0.22), residues: 516 loop : -1.16 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 230 HIS 0.003 0.001 HIS F 228 PHE 0.012 0.001 PHE E 225 TYR 0.009 0.001 TYR E 245 ARG 0.002 0.000 ARG F 211 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 918) hydrogen bonds : angle 4.60797 ( 2574) covalent geometry : bond 0.00257 (25890) covalent geometry : angle 0.54326 (35118) ********************** 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 245 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 2.811 Fit side-chains REVERT: A 337 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8424 (mt) REVERT: A 429 ASP cc_start: 0.8102 (m-30) cc_final: 0.7758 (m-30) REVERT: A 453 VAL cc_start: 0.2736 (OUTLIER) cc_final: 0.2501 (p) REVERT: A 461 MET cc_start: 0.3644 (pmt) cc_final: 0.2701 (mpp) REVERT: A 506 LEU cc_start: 0.2707 (OUTLIER) cc_final: 0.2458 (pp) REVERT: C 119 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: C 453 VAL cc_start: 0.2664 (OUTLIER) cc_final: 0.2295 (p) REVERT: B 331 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.6426 (mp10) REVERT: B 337 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8454 (mt) REVERT: B 429 ASP cc_start: 0.8062 (m-30) cc_final: 0.7704 (m-30) REVERT: B 453 VAL cc_start: 0.3040 (OUTLIER) cc_final: 0.2718 (p) REVERT: D 337 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8453 (mt) REVERT: D 453 VAL cc_start: 0.2744 (OUTLIER) cc_final: 0.2422 (p) REVERT: D 506 LEU cc_start: 0.3410 (OUTLIER) cc_final: 0.2934 (pp) REVERT: E 337 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8441 (mt) REVERT: E 418 GLU cc_start: 0.7022 (pt0) cc_final: 0.6691 (pm20) REVERT: E 453 VAL cc_start: 0.3014 (OUTLIER) cc_final: 0.2726 (p) REVERT: F 119 GLU cc_start: 0.7850 (pt0) cc_final: 0.7639 (pt0) REVERT: F 171 THR cc_start: 0.9407 (p) cc_final: 0.9183 (p) REVERT: F 362 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8391 (tp) REVERT: F 453 VAL cc_start: 0.2465 (OUTLIER) cc_final: 0.2115 (p) outliers start: 53 outliers final: 26 residues processed: 238 average time/residue: 1.2831 time to fit residues: 357.6459 Evaluate side-chains 231 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 76 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 158 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 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 438 VAL Chi-restraints excluded: chain B residue 453 VAL 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 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 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE 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 274 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.155073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116301 restraints weight = 30280.624| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.54 r_work: 0.3173 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25890 Z= 0.215 Angle : 0.639 9.073 35118 Z= 0.344 Chirality : 0.051 0.225 3978 Planarity : 0.005 0.042 4476 Dihedral : 5.370 21.116 3426 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.61 % Favored : 92.20 % Rotamer: Outliers : 1.95 % Allowed : 15.98 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3168 helix: 1.21 (0.16), residues: 1080 sheet: -0.38 (0.21), residues: 558 loop : -1.30 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 466 HIS 0.005 0.001 HIS E 45 PHE 0.014 0.002 PHE E 225 TYR 0.014 0.002 TYR A 318 ARG 0.003 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 918) hydrogen bonds : angle 4.90405 ( 2574) covalent geometry : bond 0.00528 (25890) covalent geometry : angle 0.63870 (35118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18417.45 seconds wall clock time: 320 minutes 22.08 seconds (19222.08 seconds total)