Starting phenix.real_space_refine on Sun Jun 15 11:00:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szl_40920/06_2025/8szl_40920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szl_40920/06_2025/8szl_40920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8szl_40920/06_2025/8szl_40920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szl_40920/06_2025/8szl_40920.map" model { file = "/net/cci-nas-00/data/ceres_data/8szl_40920/06_2025/8szl_40920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szl_40920/06_2025/8szl_40920.cif" } resolution = 3.12 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2706 atoms to isotropic. 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 124 5.16 5 C 9573 2.51 5 N 2600 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15081 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3759 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 488, 3750 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 470} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Conformer: "B" Number of residues, atoms: 488, 3750 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 470} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 bond proxies already assigned to first conformer: 3813 Chain: "B" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3780 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 3771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 490, 3765 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 472} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Conformer: "B" Number of residues, atoms: 490, 3765 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 472} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 bond proxies already assigned to first conformer: 3832 Chain: "D" Number of atoms: 3771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 490, 3765 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 472} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Conformer: "B" Number of residues, atoms: 490, 3762 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 472} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 bond proxies already assigned to first conformer: 3828 Time building chain proxies: 17.22, per 1000 atoms: 1.14 Number of scatterers: 15081 At special positions: 0 Unit cell: (164.205, 171.585, 77.49, 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 124 16.00 O 2784 8.00 N 2600 7.00 C 9573 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: 4.27 Conformation dependent library (CDL) restraints added in 3.4 seconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 12 sheets defined 55.5% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.593A pdb=" N THR A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.532A pdb=" N VAL A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN A 120 " --> pdb=" O HIS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.960A pdb=" N PHE A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.538A pdb=" N GLN A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 Processing helix chain 'A' and resid 220 through 234 removed outlier: 4.415A pdb=" N LEU A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.612A pdb=" N HIS A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.537A pdb=" N ALA A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.628A pdb=" N VAL A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 444 through 459 removed outlier: 3.699A pdb=" N LEU A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 496 removed outlier: 3.581A pdb=" N ALA A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 removed outlier: 3.718A pdb=" N ARG A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 531 through 541 removed outlier: 3.554A pdb=" N PHE A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.530A pdb=" N ALA A 560 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.730A pdb=" N LYS A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.604A pdb=" N SER B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 115 " --> pdb=" O CYS B 111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL B 119 " --> pdb=" O MET B 115 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLN B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 removed outlier: 3.667A pdb=" N PHE B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.791A pdb=" N PHE B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 221 through 234 Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.665A pdb=" N PHE B 241 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.639A pdb=" N ALA B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 401 through 409 Processing helix chain 'B' and resid 445 through 459 removed outlier: 3.866A pdb=" N LEU B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 492 removed outlier: 3.798A pdb=" N VAL B 487 " --> pdb=" O ARG B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 508 removed outlier: 4.122A pdb=" N LEU B 502 " --> pdb=" O ASP B 498 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 528 Processing helix chain 'B' and resid 531 through 541 removed outlier: 3.916A pdb=" N VAL B 535 " --> pdb=" O HIS B 531 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 537 " --> pdb=" O GLU B 533 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.507A pdb=" N ASP B 559 " --> pdb=" O ILE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 removed outlier: 3.882A pdb=" N LYS B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU B 571 " --> pdb=" O GLU B 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 74 through 82 removed outlier: 3.890A pdb=" N TYR C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 98 removed outlier: 4.082A pdb=" N PHE C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 122 removed outlier: 3.659A pdb=" N VAL C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.565A pdb=" N LYS C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 156 through 174 removed outlier: 3.529A pdb=" N VAL C 164 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS C 172 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 removed outlier: 4.092A pdb=" N LEU C 224 " --> pdb=" O CYS C 220 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 267 through 278 removed outlier: 3.610A pdb=" N VAL C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 278 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 300 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.875A pdb=" N SER C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 331 Processing helix chain 'C' and resid 339 through 352 removed outlier: 3.590A pdb=" N PHE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 382 through 397 removed outlier: 3.512A pdb=" N VAL C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 400 No H-bonds generated for 'chain 'C' and resid 398 through 400' Processing helix chain 'C' and resid 401 through 409 Processing helix chain 'C' and resid 444 through 456 Processing helix chain 'C' and resid 486 through 497 removed outlier: 4.399A pdb=" N LEU C 490 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 508 removed outlier: 3.511A pdb=" N LEU C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 530 Processing helix chain 'C' and resid 531 through 542 Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.569A pdb=" N GLN C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 563 " --> pdb=" O ASP C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 574 Processing helix chain 'D' and resid 72 through 82 removed outlier: 3.672A pdb=" N LEU D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 105 through 107 No H-bonds generated for 'chain 'D' and resid 105 through 107' Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.550A pdb=" N VAL D 119 " --> pdb=" O MET D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 138 Processing helix chain 'D' and resid 140 through 149 removed outlier: 3.557A pdb=" N GLN D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 172 removed outlier: 3.644A pdb=" N GLY D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 164 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 233 removed outlier: 4.247A pdb=" N LEU D 224 " --> pdb=" O CYS D 220 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 267 through 278 removed outlier: 3.581A pdb=" N VAL D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 278 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 300 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.719A pdb=" N SER D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 331 removed outlier: 3.513A pdb=" N LYS D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'D' and resid 356 through 369 Processing helix chain 'D' and resid 382 through 397 removed outlier: 3.509A pdb=" N VAL D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 409 Processing helix chain 'D' and resid 444 through 456 removed outlier: 3.762A pdb=" N PHE D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 497 removed outlier: 4.175A pdb=" N LEU D 490 " --> pdb=" O THR D 486 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 491 " --> pdb=" O VAL D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 507 removed outlier: 3.551A pdb=" N LEU D 502 " --> pdb=" O ASP D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 530 removed outlier: 3.808A pdb=" N VAL D 525 " --> pdb=" O THR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 542 removed outlier: 3.604A pdb=" N CYS D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 564 Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.562A pdb=" N LYS D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 571 " --> pdb=" O GLU D 567 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 209 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.652A pdb=" N ILE B 87 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 128 " --> pdb=" O ILE B 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 205 through 209 Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 216 Processing sheet with id=AA7, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.748A pdb=" N ASN B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 205 through 209 Processing sheet with id=AA9, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 88 removed outlier: 4.253A pdb=" N ILE D 87 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 128 " --> pdb=" O ILE D 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 205 through 209 Processing sheet with id=AB3, first strand: chain 'D' and resid 215 through 216 696 hydrogen bonds defined for protein. 2026 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: 5.59 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3257 1.33 - 1.45: 3329 1.45 - 1.57: 8608 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 15382 Sorted by residual: bond pdb=" C ARG D 320 " pdb=" N ASN D 321 " ideal model delta sigma weight residual 1.335 1.303 0.031 1.36e-02 5.41e+03 5.30e+00 bond pdb=" C ARG D 320 " pdb=" O ARG D 320 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.19e-02 7.06e+03 5.13e+00 bond pdb=" CA ARG D 320 " pdb=" C ARG D 320 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.29e-02 6.01e+03 3.44e+00 bond pdb=" N LEU C 69 " pdb=" CA LEU C 69 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N LEU D 69 " pdb=" CA LEU D 69 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 15377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 19468 1.18 - 2.36: 1080 2.36 - 3.54: 164 3.54 - 4.72: 68 4.72 - 5.89: 14 Bond angle restraints: 20794 Sorted by residual: angle pdb=" C TYR B 399 " pdb=" CA TYR B 399 " pdb=" CB TYR B 399 " ideal model delta sigma weight residual 117.23 111.34 5.89 1.36e+00 5.41e-01 1.88e+01 angle pdb=" N ALA D 480 " pdb=" CA ALA D 480 " pdb=" C ALA D 480 " ideal model delta sigma weight residual 110.43 115.50 -5.07 1.31e+00 5.83e-01 1.50e+01 angle pdb=" CA GLY D 234 " pdb=" C GLY D 234 " pdb=" N THR D 235 " ideal model delta sigma weight residual 114.23 116.97 -2.74 8.80e-01 1.29e+00 9.71e+00 angle pdb=" N LYS B 297 " pdb=" CA LYS B 297 " pdb=" C LYS B 297 " ideal model delta sigma weight residual 113.12 109.30 3.82 1.25e+00 6.40e-01 9.35e+00 angle pdb=" N ALA B 364 " pdb=" CA ALA B 364 " pdb=" CB ALA B 364 " ideal model delta sigma weight residual 114.17 110.74 3.43 1.14e+00 7.69e-01 9.03e+00 ... (remaining 20789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 8408 17.54 - 35.08: 685 35.08 - 52.62: 111 52.62 - 70.16: 25 70.16 - 87.69: 11 Dihedral angle restraints: 9240 sinusoidal: 3572 harmonic: 5668 Sorted by residual: dihedral pdb=" CA LEU A 367 " pdb=" C LEU A 367 " pdb=" N ALA A 368 " pdb=" CA ALA A 368 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA TYR D 463 " pdb=" C TYR D 463 " pdb=" N ASP D 464 " pdb=" CA ASP D 464 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TYR C 463 " pdb=" C TYR C 463 " pdb=" N ASP C 464 " pdb=" CA ASP C 464 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2112 0.062 - 0.125: 229 0.125 - 0.187: 15 0.187 - 0.250: 1 0.250 - 0.312: 1 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CA ALA D 480 " pdb=" N ALA D 480 " pdb=" C ALA D 480 " pdb=" CB ALA D 480 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA VAL B 499 " pdb=" N VAL B 499 " pdb=" C VAL B 499 " pdb=" CB VAL B 499 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE A 555 " pdb=" N ILE A 555 " pdb=" C ILE A 555 " pdb=" CB ILE A 555 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 2355 not shown) Planarity restraints: 2681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 105 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO C 106 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 555 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 556 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 556 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 556 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 105 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO D 106 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 106 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 106 " -0.026 5.00e-02 4.00e+02 ... (remaining 2678 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 183 2.61 - 3.18: 14306 3.18 - 3.76: 22665 3.76 - 4.33: 32987 4.33 - 4.90: 52737 Nonbonded interactions: 122878 Sorted by model distance: nonbonded pdb=" O SER C 395 " pdb=" OG SER C 402 " model vdw 2.040 3.040 nonbonded pdb=" OE2 GLU A 529 " pdb=" OH TYR D 517 " model vdw 2.084 3.040 nonbonded pdb=" ND2 ASN B 427 " pdb=" OD1 ASN C 465 " model vdw 2.121 3.120 nonbonded pdb=" OG1 THR A 211 " pdb=" OE2 GLU A 358 " model vdw 2.125 3.040 nonbonded pdb=" OH TYR B 517 " pdb=" OD1 ASP C 518 " model vdw 2.131 3.040 ... (remaining 122873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 69 through 119 or resid 121 through 378 or resid 380 throu \ gh 576)) selection = (chain 'B' and (resid 69 through 119 or resid 121 through 173 or resid 192 throu \ gh 378 or resid 380 through 576)) selection = (chain 'C' and (resid 69 through 119 or resid 121 through 173 or resid 192 throu \ gh 378 or resid 380 through 576)) selection = (chain 'D' and (resid 69 through 119 or resid 121 through 173 or resid 192 throu \ gh 378 or resid 380 through 576)) } 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=0.06 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: 19.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.830 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 48.620 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 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 0.035 15382 Z= 0.164 Angle : 0.650 5.894 20794 Z= 0.363 Chirality : 0.040 0.312 2358 Planarity : 0.005 0.056 2681 Dihedral : 13.639 87.695 5584 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 1940 helix: -0.36 (0.17), residues: 948 sheet: -1.04 (0.46), residues: 117 loop : -0.74 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 552 HIS 0.007 0.002 HIS B 461 PHE 0.017 0.002 PHE D 152 TYR 0.015 0.001 TYR A 303 ARG 0.006 0.001 ARG D 476 Details of bonding type rmsd hydrogen bonds : bond 0.27323 ( 696) hydrogen bonds : angle 8.57076 ( 2026) covalent geometry : bond 0.00367 (15382) covalent geometry : angle 0.65028 (20794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3655 time to fit residues: 128.1226 Evaluate side-chains 145 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS A 321 ASN ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 HIS ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN B 468 HIS D 404 GLN D 443 ASN D 445 HIS D 459 ASN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.106451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.081743 restraints weight = 81854.329| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 5.58 r_work: 0.3508 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15382 Z= 0.148 Angle : 0.697 11.881 20794 Z= 0.358 Chirality : 0.043 0.231 2358 Planarity : 0.005 0.052 2681 Dihedral : 4.925 25.127 2100 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.92 % Allowed : 6.74 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 1940 helix: 0.09 (0.16), residues: 988 sheet: -0.97 (0.45), residues: 122 loop : -0.53 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 194 HIS 0.005 0.001 HIS D 468 PHE 0.041 0.002 PHE D 505 TYR 0.033 0.002 TYR A 347 ARG 0.010 0.001 ARG D 503 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 696) hydrogen bonds : angle 5.67738 ( 2026) covalent geometry : bond 0.00327 (15382) covalent geometry : angle 0.69686 (20794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8384 (mp) cc_final: 0.8133 (mp) REVERT: A 78 TYR cc_start: 0.8678 (m-80) cc_final: 0.8417 (m-80) REVERT: A 507 LEU cc_start: 0.9065 (tp) cc_final: 0.8798 (mp) REVERT: B 266 MET cc_start: 0.8941 (mmt) cc_final: 0.8296 (mmm) REVERT: B 478 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6954 (tm-30) REVERT: C 115 MET cc_start: 0.8333 (tpp) cc_final: 0.8064 (tpp) REVERT: C 495 TYR cc_start: 0.9012 (t80) cc_final: 0.8755 (t80) REVERT: C 523 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8191 (pp) outliers start: 15 outliers final: 10 residues processed: 193 average time/residue: 0.2695 time to fit residues: 78.0396 Evaluate side-chains 152 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 249 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 134 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B 531 HIS C 120 GLN B C 408 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS D 462 ASN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.099161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.074056 restraints weight = 85696.259| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 5.75 r_work: 0.3287 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15382 Z= 0.280 Angle : 0.776 14.730 20794 Z= 0.403 Chirality : 0.046 0.198 2358 Planarity : 0.005 0.071 2681 Dihedral : 5.518 24.048 2100 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.02 % Allowed : 9.19 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1940 helix: -0.19 (0.16), residues: 1016 sheet: -0.70 (0.44), residues: 118 loop : -0.70 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 194 HIS 0.009 0.002 HIS D 468 PHE 0.032 0.002 PHE D 505 TYR 0.018 0.002 TYR D 78 ARG 0.008 0.001 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 696) hydrogen bonds : angle 5.61441 ( 2026) covalent geometry : bond 0.00636 (15382) covalent geometry : angle 0.77584 (20794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8671 (m-80) cc_final: 0.8336 (m-80) REVERT: A 110 ASP cc_start: 0.8989 (p0) cc_final: 0.8729 (p0) REVERT: A 200 THR cc_start: 0.8915 (m) cc_final: 0.8705 (p) REVERT: A 432 MET cc_start: 0.8456 (ttm) cc_final: 0.8168 (tpp) REVERT: A 515 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8443 (ttmt) REVERT: A 573 GLN cc_start: 0.9306 (tp-100) cc_final: 0.8965 (mm-40) REVERT: B 200 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 266 MET cc_start: 0.9072 (mmt) cc_final: 0.8455 (mmm) REVERT: B 393 MET cc_start: 0.9099 (mtm) cc_final: 0.8844 (mtm) outliers start: 33 outliers final: 28 residues processed: 180 average time/residue: 0.2933 time to fit residues: 78.1658 Evaluate side-chains 173 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 100 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 129 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 ASN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS D 573 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.102726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.076580 restraints weight = 116417.822| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 6.92 r_work: 0.3335 rms_B_bonded: 6.53 restraints_weight: 2.0000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15382 Z= 0.125 Angle : 0.653 13.065 20794 Z= 0.329 Chirality : 0.041 0.158 2358 Planarity : 0.004 0.058 2681 Dihedral : 4.900 25.081 2100 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.04 % Allowed : 11.03 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1940 helix: 0.17 (0.16), residues: 1017 sheet: -0.66 (0.43), residues: 123 loop : -0.45 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 194 HIS 0.005 0.001 HIS D 468 PHE 0.029 0.001 PHE D 505 TYR 0.017 0.001 TYR D 237 ARG 0.006 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 696) hydrogen bonds : angle 5.16946 ( 2026) covalent geometry : bond 0.00279 (15382) covalent geometry : angle 0.65276 (20794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8433 (mp) cc_final: 0.8216 (mp) REVERT: A 78 TYR cc_start: 0.8634 (m-80) cc_final: 0.8332 (m-80) REVERT: A 200 THR cc_start: 0.8876 (m) cc_final: 0.8594 (p) REVERT: A 573 GLN cc_start: 0.9313 (tp-100) cc_final: 0.8962 (mm-40) REVERT: B 294 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8183 (t80) REVERT: B 432 MET cc_start: 0.8429 (ttm) cc_final: 0.7886 (tpp) REVERT: C 505 PHE cc_start: 0.9152 (m-80) cc_final: 0.8945 (m-80) REVERT: C 573 GLN cc_start: 0.9347 (mm110) cc_final: 0.9080 (mm110) REVERT: D 112 MET cc_start: 0.9035 (mmp) cc_final: 0.8759 (mmm) REVERT: D 340 MET cc_start: 0.8376 (tmm) cc_final: 0.8063 (tmm) REVERT: D 510 MET cc_start: 0.5924 (ppp) cc_final: 0.5677 (ppp) REVERT: D 529 GLU cc_start: 0.8652 (tp30) cc_final: 0.8043 (tm-30) outliers start: 17 outliers final: 10 residues processed: 169 average time/residue: 0.2709 time to fit residues: 68.5373 Evaluate side-chains 155 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 401 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 0.1980 chunk 163 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 158 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.099386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073536 restraints weight = 104411.026| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 6.44 r_work: 0.3270 rms_B_bonded: 6.11 restraints_weight: 2.0000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15382 Z= 0.224 Angle : 0.703 12.353 20794 Z= 0.359 Chirality : 0.043 0.156 2358 Planarity : 0.005 0.061 2681 Dihedral : 5.109 23.636 2100 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.78 % Allowed : 11.52 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 1940 helix: 0.02 (0.16), residues: 1034 sheet: -0.54 (0.45), residues: 124 loop : -0.51 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 194 HIS 0.007 0.001 HIS D 468 PHE 0.026 0.002 PHE D 505 TYR 0.028 0.002 TYR A 347 ARG 0.005 0.000 ARG C 205 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 696) hydrogen bonds : angle 5.28321 ( 2026) covalent geometry : bond 0.00510 (15382) covalent geometry : angle 0.70256 (20794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8476 (mp) cc_final: 0.8236 (mp) REVERT: A 78 TYR cc_start: 0.8689 (m-80) cc_final: 0.8410 (m-80) REVERT: A 200 THR cc_start: 0.8912 (m) cc_final: 0.8667 (p) REVERT: A 573 GLN cc_start: 0.9460 (tp-100) cc_final: 0.8997 (mm-40) REVERT: B 200 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8596 (p) REVERT: B 294 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8161 (t80) REVERT: B 432 MET cc_start: 0.8449 (ttm) cc_final: 0.7880 (tpp) REVERT: C 573 GLN cc_start: 0.9411 (mm110) cc_final: 0.9146 (mm110) REVERT: D 112 MET cc_start: 0.9167 (mmp) cc_final: 0.8880 (mmm) REVERT: D 510 MET cc_start: 0.5882 (ppp) cc_final: 0.5588 (ppp) REVERT: D 523 LEU cc_start: 0.9449 (tt) cc_final: 0.9082 (mp) outliers start: 28 outliers final: 23 residues processed: 169 average time/residue: 0.2700 time to fit residues: 69.3704 Evaluate side-chains 175 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 401 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 517 TYR Chi-restraints excluded: chain D residue 552 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 187 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 183 optimal weight: 0.0170 chunk 43 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.101289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.075915 restraints weight = 94536.175| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 6.16 r_work: 0.3327 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15382 Z= 0.133 Angle : 0.645 13.260 20794 Z= 0.325 Chirality : 0.041 0.166 2358 Planarity : 0.004 0.057 2681 Dihedral : 4.808 24.807 2100 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.47 % Allowed : 12.75 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.19), residues: 1940 helix: 0.23 (0.16), residues: 1023 sheet: -0.44 (0.45), residues: 122 loop : -0.43 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 194 HIS 0.005 0.001 HIS D 468 PHE 0.025 0.001 PHE D 505 TYR 0.030 0.002 TYR A 347 ARG 0.005 0.000 ARG C 205 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 696) hydrogen bonds : angle 5.08541 ( 2026) covalent geometry : bond 0.00305 (15382) covalent geometry : angle 0.64547 (20794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8431 (mp) cc_final: 0.8205 (mp) REVERT: A 78 TYR cc_start: 0.8651 (m-80) cc_final: 0.8364 (m-80) REVERT: A 200 THR cc_start: 0.8901 (m) cc_final: 0.8625 (p) REVERT: A 573 GLN cc_start: 0.9422 (tp-100) cc_final: 0.9023 (mm-40) REVERT: B 200 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8547 (p) REVERT: B 294 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8164 (t80) REVERT: B 432 MET cc_start: 0.8346 (ttm) cc_final: 0.7718 (tpp) REVERT: C 505 PHE cc_start: 0.9156 (m-80) cc_final: 0.8928 (m-80) REVERT: C 573 GLN cc_start: 0.9397 (mm110) cc_final: 0.9072 (mm110) REVERT: D 112 MET cc_start: 0.9103 (mmp) cc_final: 0.8811 (mmm) REVERT: D 340 MET cc_start: 0.8333 (tmm) cc_final: 0.8063 (tmm) REVERT: D 523 LEU cc_start: 0.9433 (tt) cc_final: 0.9052 (mp) REVERT: D 529 GLU cc_start: 0.8694 (tp30) cc_final: 0.8132 (tm-30) outliers start: 23 outliers final: 16 residues processed: 180 average time/residue: 0.2838 time to fit residues: 76.5561 Evaluate side-chains 170 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 401 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 517 TYR Chi-restraints excluded: chain D residue 552 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 165 optimal weight: 0.0050 chunk 113 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 155 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 185 optimal weight: 0.0770 chunk 135 optimal weight: 5.9990 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.102841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.077023 restraints weight = 102722.674| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 6.51 r_work: 0.3358 rms_B_bonded: 6.19 restraints_weight: 2.0000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15382 Z= 0.115 Angle : 0.640 13.167 20794 Z= 0.320 Chirality : 0.041 0.211 2358 Planarity : 0.004 0.054 2681 Dihedral : 4.583 24.336 2100 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.10 % Allowed : 13.36 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1940 helix: 0.27 (0.16), residues: 1027 sheet: -0.20 (0.46), residues: 123 loop : -0.30 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 194 HIS 0.004 0.001 HIS D 468 PHE 0.029 0.001 PHE A 168 TYR 0.019 0.001 TYR C 237 ARG 0.004 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 696) hydrogen bonds : angle 4.98121 ( 2026) covalent geometry : bond 0.00258 (15382) covalent geometry : angle 0.63983 (20794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8409 (mp) cc_final: 0.8172 (mp) REVERT: A 78 TYR cc_start: 0.8629 (m-80) cc_final: 0.8328 (m-80) REVERT: A 91 LYS cc_start: 0.9653 (OUTLIER) cc_final: 0.9080 (mptt) REVERT: A 200 THR cc_start: 0.8882 (m) cc_final: 0.8576 (p) REVERT: A 398 MET cc_start: 0.8347 (mmm) cc_final: 0.7672 (mmm) REVERT: A 573 GLN cc_start: 0.9434 (tp-100) cc_final: 0.9034 (mm-40) REVERT: B 200 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 294 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7961 (t80) REVERT: B 320 ARG cc_start: 0.8835 (mpp80) cc_final: 0.8589 (mtm-85) REVERT: B 432 MET cc_start: 0.8262 (ttm) cc_final: 0.7762 (tpp) REVERT: B 507 LEU cc_start: 0.9260 (mt) cc_final: 0.9058 (mp) REVERT: C 505 PHE cc_start: 0.9144 (m-80) cc_final: 0.8924 (m-80) REVERT: C 573 GLN cc_start: 0.9372 (mm110) cc_final: 0.9058 (mm110) REVERT: D 112 MET cc_start: 0.9060 (mmp) cc_final: 0.8805 (mmm) REVERT: D 340 MET cc_start: 0.8335 (tmm) cc_final: 0.8083 (tmm) REVERT: D 510 MET cc_start: 0.5989 (ppp) cc_final: 0.5787 (ppp) REVERT: D 523 LEU cc_start: 0.9429 (tt) cc_final: 0.9047 (mp) outliers start: 17 outliers final: 12 residues processed: 179 average time/residue: 0.2770 time to fit residues: 74.8023 Evaluate side-chains 170 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 401 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 552 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 46 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.101889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.076696 restraints weight = 81550.918| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 5.68 r_work: 0.3361 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15382 Z= 0.130 Angle : 0.657 14.470 20794 Z= 0.328 Chirality : 0.041 0.207 2358 Planarity : 0.004 0.051 2681 Dihedral : 4.574 23.925 2100 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.16 % Allowed : 14.52 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.19), residues: 1940 helix: 0.33 (0.16), residues: 1019 sheet: -0.13 (0.46), residues: 123 loop : -0.23 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 194 HIS 0.004 0.001 HIS D 468 PHE 0.024 0.001 PHE D 505 TYR 0.021 0.001 TYR C 237 ARG 0.004 0.000 ARG C 205 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 696) hydrogen bonds : angle 4.96349 ( 2026) covalent geometry : bond 0.00300 (15382) covalent geometry : angle 0.65731 (20794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8417 (mp) cc_final: 0.8153 (mp) REVERT: A 78 TYR cc_start: 0.8588 (m-80) cc_final: 0.8317 (m-80) REVERT: A 91 LYS cc_start: 0.9638 (OUTLIER) cc_final: 0.9023 (mptt) REVERT: A 200 THR cc_start: 0.8874 (m) cc_final: 0.8606 (p) REVERT: A 398 MET cc_start: 0.8292 (mmm) cc_final: 0.7560 (mmm) REVERT: A 573 GLN cc_start: 0.9451 (tp-100) cc_final: 0.9046 (mm-40) REVERT: B 200 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8533 (p) REVERT: B 294 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7922 (t80) REVERT: B 320 ARG cc_start: 0.8827 (mpp80) cc_final: 0.8558 (mtm-85) REVERT: B 432 MET cc_start: 0.8289 (ttm) cc_final: 0.7748 (tpp) REVERT: C 280 MET cc_start: 0.9074 (pmm) cc_final: 0.8674 (pmm) REVERT: C 505 PHE cc_start: 0.9161 (m-80) cc_final: 0.8926 (m-80) REVERT: C 540 GLU cc_start: 0.9447 (tm-30) cc_final: 0.9217 (pp20) REVERT: C 573 GLN cc_start: 0.9354 (mm110) cc_final: 0.9005 (mm110) REVERT: D 112 MET cc_start: 0.9053 (mmp) cc_final: 0.8807 (mmm) REVERT: D 340 MET cc_start: 0.8333 (tmm) cc_final: 0.8058 (tmm) REVERT: D 341 MET cc_start: 0.7097 (mmm) cc_final: 0.6839 (mmm) REVERT: D 510 MET cc_start: 0.5901 (ppp) cc_final: 0.5692 (ppp) REVERT: D 523 LEU cc_start: 0.9432 (tt) cc_final: 0.9051 (mp) outliers start: 18 outliers final: 12 residues processed: 168 average time/residue: 0.2823 time to fit residues: 73.3598 Evaluate side-chains 169 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 401 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 552 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 40 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 194 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 HIS ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.100845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.075726 restraints weight = 92002.685| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 5.99 r_work: 0.3324 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15382 Z= 0.146 Angle : 0.667 14.137 20794 Z= 0.335 Chirality : 0.041 0.174 2358 Planarity : 0.004 0.051 2681 Dihedral : 4.625 23.554 2100 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.98 % Allowed : 14.95 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1940 helix: 0.30 (0.16), residues: 1017 sheet: -0.10 (0.47), residues: 123 loop : -0.16 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 194 HIS 0.005 0.001 HIS D 468 PHE 0.027 0.001 PHE A 168 TYR 0.020 0.001 TYR C 237 ARG 0.003 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 696) hydrogen bonds : angle 4.97303 ( 2026) covalent geometry : bond 0.00337 (15382) covalent geometry : angle 0.66663 (20794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8434 (mp) cc_final: 0.8164 (mp) REVERT: A 78 TYR cc_start: 0.8617 (m-80) cc_final: 0.8339 (m-80) REVERT: A 91 LYS cc_start: 0.9621 (OUTLIER) cc_final: 0.9002 (mptt) REVERT: A 200 THR cc_start: 0.8884 (m) cc_final: 0.8621 (p) REVERT: A 398 MET cc_start: 0.8388 (mmm) cc_final: 0.7540 (mmm) REVERT: A 573 GLN cc_start: 0.9498 (tp-100) cc_final: 0.9068 (mm-40) REVERT: B 200 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8569 (p) REVERT: B 294 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8075 (t80) REVERT: C 505 PHE cc_start: 0.9152 (m-80) cc_final: 0.8908 (m-80) REVERT: C 540 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9249 (pp20) REVERT: C 573 GLN cc_start: 0.9369 (mm110) cc_final: 0.9024 (mm110) REVERT: D 112 MET cc_start: 0.9090 (mmp) cc_final: 0.8817 (mmm) REVERT: D 340 MET cc_start: 0.8407 (tmm) cc_final: 0.8120 (tmm) REVERT: D 341 MET cc_start: 0.7148 (mmm) cc_final: 0.6940 (mmm) REVERT: D 510 MET cc_start: 0.5953 (ppp) cc_final: 0.5699 (ppp) REVERT: D 523 LEU cc_start: 0.9444 (tt) cc_final: 0.9074 (mp) REVERT: D 533 GLU cc_start: 0.9432 (pm20) cc_final: 0.9204 (pm20) outliers start: 15 outliers final: 10 residues processed: 165 average time/residue: 0.2848 time to fit residues: 71.8621 Evaluate side-chains 168 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 401 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 169 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 134 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.101848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.076915 restraints weight = 78780.471| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 5.60 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15382 Z= 0.125 Angle : 0.657 14.204 20794 Z= 0.329 Chirality : 0.041 0.177 2358 Planarity : 0.004 0.052 2681 Dihedral : 4.556 23.979 2100 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.92 % Allowed : 15.13 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1940 helix: 0.31 (0.16), residues: 1019 sheet: -0.03 (0.47), residues: 123 loop : -0.19 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 194 HIS 0.004 0.001 HIS D 468 PHE 0.024 0.001 PHE D 505 TYR 0.021 0.001 TYR C 237 ARG 0.003 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 696) hydrogen bonds : angle 4.93925 ( 2026) covalent geometry : bond 0.00288 (15382) covalent geometry : angle 0.65717 (20794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8338 (mp) cc_final: 0.8095 (mp) REVERT: A 91 LYS cc_start: 0.9654 (OUTLIER) cc_final: 0.9007 (mptt) REVERT: A 200 THR cc_start: 0.8757 (m) cc_final: 0.8532 (p) REVERT: A 398 MET cc_start: 0.8141 (mmm) cc_final: 0.7343 (mmm) REVERT: A 573 GLN cc_start: 0.9507 (tp-100) cc_final: 0.9063 (mm-40) REVERT: B 294 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7720 (t80) REVERT: B 320 ARG cc_start: 0.8402 (mpp80) cc_final: 0.8159 (mtm-85) REVERT: C 280 MET cc_start: 0.9049 (pmm) cc_final: 0.8699 (pmm) REVERT: C 294 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.6318 (t80) REVERT: C 505 PHE cc_start: 0.9178 (m-80) cc_final: 0.8943 (m-80) REVERT: C 573 GLN cc_start: 0.9338 (mm110) cc_final: 0.8940 (mm110) REVERT: D 112 MET cc_start: 0.9006 (mmp) cc_final: 0.8801 (mmm) REVERT: D 340 MET cc_start: 0.8295 (tmm) cc_final: 0.8093 (tmm) REVERT: D 341 MET cc_start: 0.6894 (mmm) cc_final: 0.6627 (mmm) REVERT: D 510 MET cc_start: 0.5711 (ppp) cc_final: 0.5383 (ppp) REVERT: D 523 LEU cc_start: 0.9440 (tt) cc_final: 0.9091 (mp) REVERT: D 529 GLU cc_start: 0.8662 (tp30) cc_final: 0.8164 (tm-30) outliers start: 14 outliers final: 10 residues processed: 171 average time/residue: 0.2648 time to fit residues: 68.3005 Evaluate side-chains 167 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 401 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 56 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 76 optimal weight: 0.1980 chunk 138 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.100259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.074171 restraints weight = 115038.440| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 6.83 r_work: 0.3297 rms_B_bonded: 6.42 restraints_weight: 2.0000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15382 Z= 0.160 Angle : 0.694 13.984 20794 Z= 0.349 Chirality : 0.042 0.214 2358 Planarity : 0.004 0.054 2681 Dihedral : 4.664 23.395 2100 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.10 % Allowed : 15.44 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1940 helix: 0.24 (0.16), residues: 1024 sheet: 0.07 (0.47), residues: 118 loop : -0.22 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 194 HIS 0.005 0.001 HIS D 468 PHE 0.029 0.001 PHE A 168 TYR 0.044 0.002 TYR A 78 ARG 0.003 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 696) hydrogen bonds : angle 5.00866 ( 2026) covalent geometry : bond 0.00370 (15382) covalent geometry : angle 0.69418 (20794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13300.54 seconds wall clock time: 230 minutes 32.31 seconds (13832.31 seconds total)