Starting phenix.real_space_refine on Mon Jul 22 06:25:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szl_40920/07_2024/8szl_40920.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szl_40920/07_2024/8szl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szl_40920/07_2024/8szl_40920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szl_40920/07_2024/8szl_40920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szl_40920/07_2024/8szl_40920.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szl_40920/07_2024/8szl_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 Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 14.64, per 1000 atoms: 0.97 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 - 3.50 Amino acid : False - 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: 6.03 Conformation dependent library (CDL) restraints added in 5.0 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: 1.98 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: 4.49 Time building geometry restraints manager: 6.52 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: 99.35 - 106.29: 376 106.29 - 113.23: 8269 113.23 - 120.18: 5572 120.18 - 127.12: 6428 127.12 - 134.06: 149 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 2.440 nonbonded pdb=" OE2 GLU A 529 " pdb=" OH TYR D 517 " model vdw 2.084 2.440 nonbonded pdb=" ND2 ASN B 427 " pdb=" OD1 ASN C 465 " model vdw 2.121 2.520 nonbonded pdb=" OG1 THR A 211 " pdb=" OE2 GLU A 358 " model vdw 2.125 2.440 nonbonded pdb=" OH TYR B 517 " pdb=" OD1 ASP C 518 " model vdw 2.131 2.440 ... (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 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: 13.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.110 Set scattering table: 0.510 Process input model: 53.090 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.090 ------------------------------------------------------------------------------- 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= 0.241 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.663 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: 0.3342 time to fit residues: 116.1764 Evaluate side-chains 145 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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: 6.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 462 ASN A 524 HIS ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B 462 ASN B 468 HIS C 120 GLN B C 140 ASN C 408 HIS D 388 ASN D 404 GLN D 443 ASN D 445 HIS D 459 ASN ** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15382 Z= 0.242 Angle : 0.692 12.327 20794 Z= 0.354 Chirality : 0.043 0.210 2358 Planarity : 0.005 0.050 2681 Dihedral : 4.985 25.187 2100 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.92 % Allowed : 6.92 % Favored : 92.16 % 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: -0.54 (0.19), residues: 1940 helix: 0.01 (0.16), residues: 1002 sheet: -0.95 (0.45), residues: 120 loop : -0.56 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 194 HIS 0.006 0.001 HIS D 468 PHE 0.041 0.002 PHE D 505 TYR 0.034 0.002 TYR A 347 ARG 0.009 0.001 ARG D 503 *********************** 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 186 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 523 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.5069 (pp) REVERT: D 266 MET cc_start: 0.6155 (tpp) cc_final: 0.5732 (tpp) outliers start: 15 outliers final: 11 residues processed: 184 average time/residue: 0.2838 time to fit residues: 77.0099 Evaluate side-chains 150 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 366 THR 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 235 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 531 HIS C 252 ASN C 462 ASN D 408 HIS D 462 ASN D 531 HIS ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15382 Z= 0.319 Angle : 0.698 13.354 20794 Z= 0.361 Chirality : 0.043 0.228 2358 Planarity : 0.005 0.050 2681 Dihedral : 5.181 24.684 2100 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.78 % Allowed : 9.13 % Favored : 89.09 % 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: -0.53 (0.19), residues: 1940 helix: 0.01 (0.16), residues: 1019 sheet: -0.75 (0.43), residues: 118 loop : -0.58 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 194 HIS 0.008 0.001 HIS C 524 PHE 0.035 0.002 PHE A 77 TYR 0.017 0.002 TYR B 347 ARG 0.007 0.001 ARG D 109 *********************** 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 189 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 ASP cc_start: 0.6078 (t0) cc_final: 0.5811 (t0) outliers start: 29 outliers final: 24 residues processed: 179 average time/residue: 0.2773 time to fit residues: 73.3196 Evaluate side-chains 168 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 208 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 314 GLU 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 235 THR Chi-restraints excluded: chain C residue 245 GLU 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 459 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 50 optimal weight: 0.0070 overall best weight: 1.7804 ------------------------------------------------------------------------------- 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 140 ASN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15382 Z= 0.275 Angle : 0.666 14.050 20794 Z= 0.339 Chirality : 0.042 0.162 2358 Planarity : 0.004 0.054 2681 Dihedral : 5.031 25.009 2100 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.58 % Rotamer: Outliers : 1.41 % Allowed : 10.36 % Favored : 88.24 % 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: -0.38 (0.19), residues: 1940 helix: 0.14 (0.16), residues: 1025 sheet: -0.59 (0.45), residues: 118 loop : -0.54 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 194 HIS 0.007 0.001 HIS D 468 PHE 0.029 0.001 PHE D 505 TYR 0.015 0.002 TYR A 303 ARG 0.008 0.001 ARG B 117 *********************** 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 176 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6770 (t80) REVERT: D 266 MET cc_start: 0.6055 (tpp) cc_final: 0.5793 (tpp) outliers start: 23 outliers final: 16 residues processed: 170 average time/residue: 0.2739 time to fit residues: 69.2299 Evaluate side-chains 155 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 TYR 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 232 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 552 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 140 ASN C 573 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15382 Z= 0.171 Angle : 0.630 12.169 20794 Z= 0.315 Chirality : 0.041 0.165 2358 Planarity : 0.004 0.056 2681 Dihedral : 4.703 25.264 2100 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 1.10 % Allowed : 11.95 % Favored : 86.95 % 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: -0.08 (0.19), residues: 1940 helix: 0.34 (0.16), residues: 1022 sheet: -0.23 (0.45), residues: 120 loop : -0.39 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 194 HIS 0.009 0.001 HIS D 531 PHE 0.028 0.001 PHE D 505 TYR 0.016 0.001 TYR D 495 ARG 0.006 0.000 ARG D 551 *********************** 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 176 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6646 (t80) REVERT: D 529 GLU cc_start: 0.4294 (OUTLIER) cc_final: 0.3481 (tm-30) outliers start: 18 outliers final: 12 residues processed: 170 average time/residue: 0.2687 time to fit residues: 68.2169 Evaluate side-chains 155 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 GLN 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 459 ASN Chi-restraints excluded: chain D residue 529 GLU 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 63 optimal weight: 0.2980 chunk 169 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS C 140 ASN ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5822 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15382 Z= 0.179 Angle : 0.638 11.539 20794 Z= 0.319 Chirality : 0.041 0.162 2358 Planarity : 0.004 0.053 2681 Dihedral : 4.610 24.566 2100 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 1.10 % Allowed : 13.17 % Favored : 85.72 % 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: 0.45 (0.16), residues: 1022 sheet: -0.06 (0.45), residues: 120 loop : -0.25 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 194 HIS 0.011 0.001 HIS D 531 PHE 0.030 0.001 PHE A 168 TYR 0.017 0.001 TYR D 495 ARG 0.005 0.000 ARG D 551 *********************** 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 167 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 161 average time/residue: 0.2688 time to fit residues: 64.9894 Evaluate side-chains 157 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain B residue 108 LEU 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 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 140 ASN C 264 ASN C 459 ASN ** D 264 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15382 Z= 0.244 Angle : 0.652 11.268 20794 Z= 0.331 Chirality : 0.041 0.170 2358 Planarity : 0.004 0.053 2681 Dihedral : 4.767 23.963 2100 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 1.29 % Allowed : 14.09 % Favored : 84.62 % 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 (0.19), residues: 1940 helix: 0.34 (0.16), residues: 1027 sheet: -0.14 (0.45), residues: 119 loop : -0.26 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 194 HIS 0.006 0.001 HIS D 468 PHE 0.025 0.001 PHE D 505 TYR 0.016 0.001 TYR D 495 ARG 0.004 0.000 ARG C 205 *********************** 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 175 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 1.848 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: B 294 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.5874 (t80) outliers start: 21 outliers final: 16 residues processed: 169 average time/residue: 0.2665 time to fit residues: 67.9035 Evaluate side-chains 163 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain B residue 108 LEU 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 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 496 SER 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 116 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 0.0270 chunk 147 optimal weight: 8.9990 chunk 170 optimal weight: 0.0030 overall best weight: 0.5650 ------------------------------------------------------------------------------- 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 140 ASN C 443 ASN C 459 ASN ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15382 Z= 0.178 Angle : 0.643 11.243 20794 Z= 0.322 Chirality : 0.041 0.252 2358 Planarity : 0.004 0.054 2681 Dihedral : 4.575 24.622 2100 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 0.86 % Allowed : 14.71 % Favored : 84.44 % 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: 0.12 (0.20), residues: 1940 helix: 0.45 (0.17), residues: 1024 sheet: 0.01 (0.45), residues: 120 loop : -0.23 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 194 HIS 0.005 0.001 HIS D 468 PHE 0.029 0.001 PHE A 168 TYR 0.017 0.001 TYR D 495 ARG 0.004 0.000 ARG D 551 *********************** 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 172 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.799 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: B 294 TYR cc_start: 0.6474 (OUTLIER) cc_final: 0.5687 (t80) REVERT: D 341 MET cc_start: 0.4356 (mmm) cc_final: 0.4128 (mmm) outliers start: 14 outliers final: 12 residues processed: 167 average time/residue: 0.2834 time to fit residues: 70.4656 Evaluate side-chains 166 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 396 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 180 optimal weight: 2.9990 chunk 164 optimal weight: 0.0970 chunk 175 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 158 optimal weight: 0.2980 chunk 165 optimal weight: 0.2980 chunk 174 optimal weight: 0.9990 chunk 115 optimal weight: 0.0770 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 140 ASN ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15382 Z= 0.161 Angle : 0.636 11.583 20794 Z= 0.315 Chirality : 0.040 0.241 2358 Planarity : 0.004 0.050 2681 Dihedral : 4.382 24.227 2100 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.04 % Allowed : 14.89 % 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: 0.15 (0.19), residues: 1940 helix: 0.49 (0.16), residues: 1027 sheet: 0.14 (0.46), residues: 120 loop : -0.26 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 194 HIS 0.004 0.001 HIS D 468 PHE 0.024 0.001 PHE D 505 TYR 0.018 0.001 TYR D 495 ARG 0.013 0.000 ARG D 477 *********************** 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 177 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.852 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: C 294 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6602 (t80) REVERT: D 294 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6496 (t80) outliers start: 16 outliers final: 12 residues processed: 173 average time/residue: 0.2757 time to fit residues: 71.2056 Evaluate side-chains 165 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER 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 208 VAL Chi-restraints excluded: chain B residue 278 ILE 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 C residue 396 CYS Chi-restraints excluded: chain D residue 294 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 128 optimal weight: 0.0470 chunk 194 optimal weight: 0.0270 chunk 178 optimal weight: 6.9990 chunk 154 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 122 optimal weight: 0.6980 overall best weight: 0.1592 ------------------------------------------------------------------------------- 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 140 ASN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15382 Z= 0.165 Angle : 0.646 12.506 20794 Z= 0.319 Chirality : 0.041 0.237 2358 Planarity : 0.004 0.049 2681 Dihedral : 4.294 23.968 2100 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.98 % Allowed : 15.13 % Favored : 83.88 % 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: 0.19 (0.19), residues: 1940 helix: 0.52 (0.17), residues: 1020 sheet: 0.09 (0.47), residues: 120 loop : -0.22 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 194 HIS 0.004 0.001 HIS D 468 PHE 0.027 0.001 PHE A 168 TYR 0.019 0.001 TYR D 495 ARG 0.012 0.000 ARG D 477 ********************** 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 176 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.925 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 304 MET cc_start: 0.4375 (mtp) cc_final: 0.3967 (tpp) REVERT: C 294 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6635 (t80) REVERT: D 294 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6528 (t80) outliers start: 15 outliers final: 10 residues processed: 172 average time/residue: 0.2715 time to fit residues: 69.9506 Evaluate side-chains 164 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 278 ILE 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 C residue 396 CYS Chi-restraints excluded: chain D residue 294 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 0.0870 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 264 ASN ** 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 = 0.4141 r_free = 0.4141 target = 0.104512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.079086 restraints weight = 104685.032| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 6.54 r_work: 0.3398 rms_B_bonded: 6.34 restraints_weight: 2.0000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15382 Z= 0.174 Angle : 0.655 12.465 20794 Z= 0.322 Chirality : 0.040 0.151 2358 Planarity : 0.004 0.046 2681 Dihedral : 4.272 23.524 2100 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.92 % Allowed : 15.26 % Favored : 83.82 % 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: 0.28 (0.19), residues: 1940 helix: 0.56 (0.17), residues: 1018 sheet: 0.34 (0.47), residues: 120 loop : -0.17 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 194 HIS 0.004 0.001 HIS D 468 PHE 0.024 0.001 PHE D 505 TYR 0.020 0.001 TYR D 495 ARG 0.011 0.000 ARG D 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4078.61 seconds wall clock time: 74 minutes 13.78 seconds (4453.78 seconds total)