Starting phenix.real_space_refine on Fri Feb 6 14:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w90_65758/02_2026/9w90_65758.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w90_65758/02_2026/9w90_65758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w90_65758/02_2026/9w90_65758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w90_65758/02_2026/9w90_65758.map" model { file = "/net/cci-nas-00/data/ceres_data/9w90_65758/02_2026/9w90_65758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w90_65758/02_2026/9w90_65758.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 15171 2.51 5 N 4856 2.21 5 O 5017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25082 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3422 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 8, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 5469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 5469 Classifications: {'peptide': 1109} Incomplete info: {'truncation_to_alanine': 974} Link IDs: {'PTRANS': 40, 'TRANS': 1068} Chain breaks: 5 Unresolved chain link angles: 39 Unresolved non-hydrogen bonds: 3402 Unresolved non-hydrogen angles: 4369 Unresolved non-hydrogen dihedrals: 2779 Unresolved non-hydrogen chiralities: 350 Planarities with less than four sites: {'TYR:plan': 35, 'ASN:plan1': 52, 'GLN:plan1': 47, 'HIS:plan': 27, 'PHE:plan': 45, 'GLU:plan': 89, 'ASP:plan': 53, 'ARG:plan': 48, 'TRP:plan': 8} Unresolved non-hydrogen planarities: 1821 Chain: "C" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3448 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 8, 'TRANS': 421} Chain breaks: 1 Chain: "D" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 2610 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 478} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 501} Chain breaks: 2 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1816 Unresolved non-hydrogen angles: 2338 Unresolved non-hydrogen dihedrals: 1522 Unresolved non-hydrogen chiralities: 146 Planarities with less than four sites: {'ARG:plan': 43, 'GLN:plan1': 27, 'ASN:plan1': 27, 'HIS:plan': 20, 'GLU:plan': 31, 'TRP:plan': 4, 'PHE:plan': 40, 'ASP:plan': 28, 'TYR:plan': 19} Unresolved non-hydrogen planarities: 1121 Chain: "E" Number of atoms: 5449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 5449 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 970} Link IDs: {'PTRANS': 40, 'TRANS': 1064} Chain breaks: 5 Unresolved chain link angles: 39 Unresolved non-hydrogen bonds: 3387 Unresolved non-hydrogen angles: 4350 Unresolved non-hydrogen dihedrals: 2765 Unresolved non-hydrogen chiralities: 350 Planarities with less than four sites: {'TYR:plan': 34, 'GLN:plan1': 47, 'ASN:plan1': 51, 'HIS:plan': 27, 'PHE:plan': 45, 'GLU:plan': 89, 'ASP:plan': 53, 'ARG:plan': 48, 'TRP:plan': 8} Unresolved non-hydrogen planarities: 1811 Chain: "H" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 2677 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 491} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 514} Chain breaks: 1 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1863 Unresolved non-hydrogen angles: 2397 Unresolved non-hydrogen dihedrals: 1561 Unresolved non-hydrogen chiralities: 148 Planarities with less than four sites: {'ARG:plan': 45, 'GLN:plan1': 29, 'ASN:plan1': 28, 'HIS:plan': 20, 'GLU:plan': 31, 'TRP:plan': 4, 'PHE:plan': 41, 'ASP:plan': 29, 'TYR:plan': 19} Unresolved non-hydrogen planarities: 1151 Chain: "I" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 269 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "J" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 732 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 134} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 597 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 7, 'TYR:plan': 6, 'TRP:plan': 3, 'PHE:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 233 Chain: "K" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 727 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 133} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 596 Unresolved non-hydrogen dihedrals: 392 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 7, 'TYR:plan': 6, 'TRP:plan': 3, 'PHE:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 233 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 279 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 117 Time building chain proxies: 5.86, per 1000 atoms: 0.23 Number of scatterers: 25082 At special positions: 0 Unit cell: (241.53, 185.09, 131.97, 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 38 16.00 O 5017 8.00 N 4856 7.00 C 15171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8576 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 77 sheets defined 17.0% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 260 through 299 Processing helix chain 'A' and resid 347 through 363 Processing helix chain 'A' and resid 363 through 376 Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.652A pdb=" N THR A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.786A pdb=" N SER B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.670A pdb=" N GLY B 385 " --> pdb=" O PHE B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 760 removed outlier: 3.510A pdb=" N GLN B 759 " --> pdb=" O ALA B 756 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 760 " --> pdb=" O SER B 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 760' Processing helix chain 'B' and resid 1044 through 1062 removed outlier: 3.579A pdb=" N LEU B1050 " --> pdb=" O SER B1046 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B1060 " --> pdb=" O ASN B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1095 Processing helix chain 'B' and resid 1096 through 1100 Processing helix chain 'B' and resid 1106 through 1110 Processing helix chain 'B' and resid 1127 through 1137 Processing helix chain 'B' and resid 1138 through 1140 No H-bonds generated for 'chain 'B' and resid 1138 through 1140' Processing helix chain 'C' and resid 256 through 299 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 363 through 376 Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.662A pdb=" N THR C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 387 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 110 through 124 removed outlier: 3.780A pdb=" N ASN D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU D 122 " --> pdb=" O GLY D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 216 through 220 Processing helix chain 'D' and resid 263 through 272 Processing helix chain 'D' and resid 293 through 311 Processing helix chain 'D' and resid 312 through 327 removed outlier: 4.035A pdb=" N ASP D 324 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN D 325 " --> pdb=" O GLN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 353 Processing helix chain 'D' and resid 383 through 393 removed outlier: 3.716A pdb=" N LEU D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 399 Processing helix chain 'D' and resid 416 through 430 Processing helix chain 'D' and resid 437 through 448 removed outlier: 3.991A pdb=" N GLN D 447 " --> pdb=" O ARG D 443 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 255 Processing helix chain 'E' and resid 756 through 760 removed outlier: 3.592A pdb=" N GLN E 759 " --> pdb=" O ALA E 756 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 760 " --> pdb=" O SER E 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 756 through 760' Processing helix chain 'E' and resid 1044 through 1062 removed outlier: 3.701A pdb=" N LYS E1060 " --> pdb=" O ASN E1056 " (cutoff:3.500A) Processing helix chain 'E' and resid 1069 through 1073 Processing helix chain 'E' and resid 1090 through 1095 removed outlier: 3.830A pdb=" N ILE E1094 " --> pdb=" O ASP E1090 " (cutoff:3.500A) Processing helix chain 'E' and resid 1096 through 1100 Processing helix chain 'E' and resid 1106 through 1110 Processing helix chain 'E' and resid 1127 through 1137 Processing helix chain 'E' and resid 1138 through 1140 No H-bonds generated for 'chain 'E' and resid 1138 through 1140' Processing helix chain 'H' and resid 17 through 28 Processing helix chain 'H' and resid 34 through 41 Processing helix chain 'H' and resid 42 through 45 removed outlier: 3.628A pdb=" N ASN H 45 " --> pdb=" O PHE H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 42 through 45' Processing helix chain 'H' and resid 110 through 124 removed outlier: 4.886A pdb=" N PHE H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 174 removed outlier: 3.672A pdb=" N VAL H 173 " --> pdb=" O PRO H 169 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR H 174 " --> pdb=" O PHE H 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 169 through 174' Processing helix chain 'H' and resid 216 through 220 removed outlier: 3.544A pdb=" N ASN H 219 " --> pdb=" O LEU H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 272 Processing helix chain 'H' and resid 272 through 281 removed outlier: 3.600A pdb=" N GLN H 276 " --> pdb=" O PHE H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 289 Processing helix chain 'H' and resid 293 through 311 Processing helix chain 'H' and resid 312 through 329 removed outlier: 4.331A pdb=" N ASP H 324 " --> pdb=" O PHE H 320 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN H 325 " --> pdb=" O GLN H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 353 Processing helix chain 'H' and resid 383 through 393 removed outlier: 3.691A pdb=" N LEU H 387 " --> pdb=" O SER H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 399 Processing helix chain 'H' and resid 416 through 430 removed outlier: 3.550A pdb=" N GLN H 420 " --> pdb=" O ASN H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 448 removed outlier: 3.990A pdb=" N GLN H 447 " --> pdb=" O ARG H 443 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 61 Processing helix chain 'J' and resid 55 through 70 Processing helix chain 'J' and resid 152 through 166 Processing helix chain 'J' and resid 174 through 184 Processing helix chain 'J' and resid 184 through 199 Processing helix chain 'K' and resid 56 through 70 Processing helix chain 'K' and resid 152 through 166 Processing helix chain 'K' and resid 174 through 184 Processing helix chain 'K' and resid 184 through 199 Processing helix chain 'P' and resid 53 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 404 through 412 removed outlier: 5.487A pdb=" N VAL A 405 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 731 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU A 729 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 409 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 429 removed outlier: 4.000A pdb=" N GLY A 440 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.969A pdb=" N CYS A 475 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASP A 499 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG A 505 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 521 removed outlier: 4.117A pdb=" N LYS A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 558 through 563 removed outlier: 3.896A pdb=" N CYS A 579 " --> pdb=" O CYS A 575 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 607 removed outlier: 3.916A pdb=" N GLN A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASN A 626 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N CYS A 632 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 648 through 650 Processing sheet with id=AA8, first strand: chain 'B' and resid 1038 through 1042 removed outlier: 6.873A pdb=" N ASN B 4 " --> pdb=" O ILE B1089 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 21 removed outlier: 6.804A pdb=" N LEU B 39 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU B 54 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE B 41 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 67 removed outlier: 6.573A pdb=" N LEU B 80 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET B 64 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE B 78 " --> pdb=" O MET B 64 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU B 66 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU B 76 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA B 86 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N HIS B 105 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 99 " --> pdb=" O LYS B 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB3, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.575A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AB5, first strand: chain 'B' and resid 261 through 263 removed outlier: 7.617A pdb=" N LEU B 280 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU B 304 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N MET B 282 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 302 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 284 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 300 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU B 286 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 315 through 316 removed outlier: 6.701A pdb=" N SER B 331 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 352 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.819A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 396 through 403 removed outlier: 5.042A pdb=" N GLU B 398 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR B 703 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 410 through 413 Processing sheet with id=AC1, first strand: chain 'B' and resid 460 through 463 removed outlier: 3.815A pdb=" N GLN B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 476 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU B 489 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 478 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 498 through 503 removed outlier: 6.876A pdb=" N LEU B 516 " --> pdb=" O HIS B 531 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N HIS B 531 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR B 518 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 538 through 541 removed outlier: 4.079A pdb=" N CYS B 540 " --> pdb=" O GLY B 559 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 568 through 569 removed outlier: 3.711A pdb=" N ILE B 568 " --> pdb=" O HIS B 578 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS B 578 " --> pdb=" O ILE B 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 588 through 594 removed outlier: 4.431A pdb=" N ALA B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 637 through 642 removed outlier: 8.544A pdb=" N THR B 647 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N SER B 661 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 725 through 727 removed outlier: 3.505A pdb=" N CYS B 732 " --> pdb=" O GLN B 727 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 811 through 813 Processing sheet with id=AC9, first strand: chain 'B' and resid 817 through 819 removed outlier: 6.891A pdb=" N VAL B 850 " --> pdb=" O VAL B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 883 through 884 removed outlier: 5.898A pdb=" N GLU B 892 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR B 901 " --> pdb=" O GLU B 892 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 911 through 916 removed outlier: 7.156A pdb=" N VAL B 930 " --> pdb=" O ARG B 947 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG B 947 " --> pdb=" O VAL B 930 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 932 " --> pdb=" O ILE B 945 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 957 through 958 removed outlier: 3.596A pdb=" N GLU B 958 " --> pdb=" O LEU B 966 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 973 through 976 removed outlier: 4.249A pdb=" N PHE B 998 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 976 " --> pdb=" O GLY B 996 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 6.546A pdb=" N GLY B1031 " --> pdb=" O ASN B1005 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE B1007 " --> pdb=" O LEU B1029 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU B1029 " --> pdb=" O PHE B1007 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 404 through 412 removed outlier: 5.511A pdb=" N VAL C 405 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 731 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU C 729 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 409 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR C 724 " --> pdb=" O ASN C 720 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 424 through 429 removed outlier: 3.752A pdb=" N GLY C 440 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS C 444 " --> pdb=" O GLY C 440 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 478 removed outlier: 3.856A pdb=" N CYS C 475 " --> pdb=" O SER C 489 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP C 499 " --> pdb=" O ARG C 505 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG C 505 " --> pdb=" O ASP C 499 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 516 through 521 removed outlier: 4.121A pdb=" N LYS C 537 " --> pdb=" O SER C 533 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 558 through 563 removed outlier: 3.519A pdb=" N CYS C 579 " --> pdb=" O CYS C 575 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 602 through 607 removed outlier: 4.044A pdb=" N GLN C 621 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 634 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 648 through 650 Processing sheet with id=AE4, first strand: chain 'D' and resid 52 through 55 removed outlier: 5.771A pdb=" N VAL D 53 " --> pdb=" O PHE D 543 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE D 543 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 541 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 60 through 65 removed outlier: 7.167A pdb=" N ILE D 73 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE D 65 " --> pdb=" O TYR D 71 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR D 71 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER D 81 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU D 86 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU D 127 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 138 through 147 removed outlier: 5.877A pdb=" N GLY D 157 " --> pdb=" O ASN D 141 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N GLU D 143 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 11.083A pdb=" N ILE D 155 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N SER D 145 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 11.824A pdb=" N CYS D 153 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLU D 189 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LYS D 210 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR D 191 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR D 208 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU D 193 " --> pdb=" O THR D 206 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR D 206 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE D 195 " --> pdb=" O CYS D 204 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 222 through 225 removed outlier: 6.439A pdb=" N ILE D 239 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR D 255 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL D 241 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 330 through 335 removed outlier: 5.168A pdb=" N MET D 331 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR D 347 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASN D 369 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL D 375 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 466 through 467 removed outlier: 3.638A pdb=" N PHE D 499 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ALA D 491 " --> pdb=" O LEU D 497 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU D 497 " --> pdb=" O ALA D 491 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 6 through 8 removed outlier: 3.551A pdb=" N VAL E 7 " --> pdb=" O LEU E1039 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY E1038 " --> pdb=" O PHE E1030 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE E1030 " --> pdb=" O GLY E1038 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU E1029 " --> pdb=" O PHE E1007 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE E1007 " --> pdb=" O LEU E1029 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY E1031 " --> pdb=" O ASN E1005 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 17 through 21 removed outlier: 4.480A pdb=" N LYS E 53 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL E 43 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR E 45 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 63 through 67 removed outlier: 3.591A pdb=" N PHE E 67 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU E 76 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA E 86 " --> pdb=" O HIS E 105 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N HIS E 105 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE E 88 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP E 99 " --> pdb=" O LYS E 92 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AF5, first strand: chain 'E' and resid 164 through 169 removed outlier: 6.593A pdb=" N VAL E 181 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL E 167 " --> pdb=" O CYS E 179 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS E 179 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE E 169 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR E 177 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER E 196 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU E 201 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 216 through 221 removed outlier: 3.748A pdb=" N MET E 218 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS E 240 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 261 through 263 removed outlier: 6.709A pdb=" N LEU E 280 " --> pdb=" O LEU E 305 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP E 299 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU E 288 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU E 297 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 322 through 324 removed outlier: 5.517A pdb=" N LYS E 335 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA E 349 " --> pdb=" O LYS E 335 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 362 through 363 removed outlier: 3.919A pdb=" N LEU E 375 " --> pdb=" O ILE E 390 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 390 " --> pdb=" O LEU E 375 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 396 through 403 removed outlier: 4.280A pdb=" N GLU E 398 " --> pdb=" O THR E 703 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N THR E 703 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 410 through 413 Processing sheet with id=AG3, first strand: chain 'E' and resid 459 through 463 removed outlier: 4.151A pdb=" N PHE E 459 " --> pdb=" O ILE E 471 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN E 467 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER E 480 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 486 " --> pdb=" O SER E 480 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 500 through 502 removed outlier: 6.871A pdb=" N LEU E 516 " --> pdb=" O HIS E 531 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N HIS E 531 " --> pdb=" O LEU E 516 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR E 518 " --> pdb=" O ILE E 529 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 568 through 569 removed outlier: 3.813A pdb=" N HIS E 578 " --> pdb=" O ILE E 568 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 588 through 595 removed outlier: 4.395A pdb=" N ALA E 610 " --> pdb=" O LEU E 606 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 637 through 642 removed outlier: 8.008A pdb=" N THR E 647 " --> pdb=" O SER E 661 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER E 661 " --> pdb=" O THR E 647 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 725 through 727 removed outlier: 3.942A pdb=" N HIS E 803 " --> pdb=" O ILE E 793 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 811 through 812 Processing sheet with id=AH1, first strand: chain 'E' and resid 817 through 820 Processing sheet with id=AH2, first strand: chain 'E' and resid 870 through 872 removed outlier: 4.000A pdb=" N SER E 872 " --> pdb=" O SER E 883 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU E 892 " --> pdb=" O THR E 901 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR E 901 " --> pdb=" O GLU E 892 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 911 through 916 removed outlier: 3.530A pdb=" N TYR E 913 " --> pdb=" O GLY E 924 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA E 934 " --> pdb=" O GLU E 944 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU E 944 " --> pdb=" O ALA E 934 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 957 through 958 removed outlier: 3.592A pdb=" N GLU E 958 " --> pdb=" O LEU E 966 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 973 through 976 Processing sheet with id=AH6, first strand: chain 'E' and resid 1113 through 1114 removed outlier: 3.649A pdb=" N ARG E1122 " --> pdb=" O TYR E1114 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 52 through 55 removed outlier: 5.750A pdb=" N VAL H 53 " --> pdb=" O PHE H 543 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE H 543 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL H 541 " --> pdb=" O VAL H 55 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 60 through 65 removed outlier: 7.167A pdb=" N ILE H 73 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE H 65 " --> pdb=" O TYR H 71 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR H 71 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER H 81 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU H 82 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE H 130 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE H 84 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 138 through 147 removed outlier: 5.768A pdb=" N GLY H 157 " --> pdb=" O ASN H 141 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N GLU H 143 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N ILE H 155 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N SER H 145 " --> pdb=" O CYS H 153 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N CYS H 153 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLU H 189 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS H 210 " --> pdb=" O GLU H 189 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR H 191 " --> pdb=" O THR H 208 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR H 208 " --> pdb=" O TYR H 191 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU H 193 " --> pdb=" O THR H 206 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR H 206 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE H 195 " --> pdb=" O CYS H 204 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 222 through 225 removed outlier: 6.204A pdb=" N ILE H 239 " --> pdb=" O THR H 255 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR H 255 " --> pdb=" O ILE H 239 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL H 241 " --> pdb=" O VAL H 253 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR H 249 " --> pdb=" O THR H 245 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 330 through 338 removed outlier: 5.100A pdb=" N MET H 331 " --> pdb=" O THR H 347 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR H 347 " --> pdb=" O MET H 331 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N HIS H 341 " --> pdb=" O LEU H 337 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN H 369 " --> pdb=" O VAL H 375 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL H 375 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 466 through 467 removed outlier: 3.689A pdb=" N PHE H 499 " --> pdb=" O PHE H 489 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA H 491 " --> pdb=" O LEU H 497 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU H 497 " --> pdb=" O ALA H 491 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 75 through 79 Processing sheet with id=AI5, first strand: chain 'K' and resid 76 through 79 1256 hydrogen bonds defined for protein. 3423 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: 5.83 Time building geometry restraints manager: 3.03 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: 6023 1.33 - 1.45: 4861 1.45 - 1.58: 14264 1.58 - 1.70: 1 1.70 - 1.82: 50 Bond restraints: 25199 Sorted by residual: bond pdb=" CB MET A 299 " pdb=" CG MET A 299 " ideal model delta sigma weight residual 1.520 1.589 -0.069 3.00e-02 1.11e+03 5.33e+00 bond pdb=" C PHE A 392 " pdb=" N GLN A 393 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.27e-02 6.20e+03 2.94e+00 bond pdb=" CG GLU A 394 " pdb=" CD GLU A 394 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.37e+00 bond pdb=" CD1 PHE A 392 " pdb=" CE1 PHE A 392 " ideal model delta sigma weight residual 1.382 1.336 0.046 3.00e-02 1.11e+03 2.34e+00 bond pdb=" CD GLN A 393 " pdb=" OE1 GLN A 393 " ideal model delta sigma weight residual 1.231 1.206 0.025 1.90e-02 2.77e+03 1.73e+00 ... (remaining 25194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 34668 3.38 - 6.76: 76 6.76 - 10.14: 10 10.14 - 13.52: 3 13.52 - 16.90: 2 Bond angle restraints: 34759 Sorted by residual: angle pdb=" CA MET A 265 " pdb=" CB MET A 265 " pdb=" CG MET A 265 " ideal model delta sigma weight residual 114.10 127.24 -13.14 2.00e+00 2.50e-01 4.32e+01 angle pdb=" CB MET A 299 " pdb=" CG MET A 299 " pdb=" SD MET A 299 " ideal model delta sigma weight residual 112.70 129.60 -16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" CA GLU A 394 " pdb=" CB GLU A 394 " pdb=" CG GLU A 394 " ideal model delta sigma weight residual 114.10 124.25 -10.15 2.00e+00 2.50e-01 2.57e+01 angle pdb=" CB MET A 265 " pdb=" CG MET A 265 " pdb=" SD MET A 265 " ideal model delta sigma weight residual 112.70 127.62 -14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" C GLN A 393 " pdb=" N GLU A 394 " pdb=" CA GLU A 394 " ideal model delta sigma weight residual 120.72 112.87 7.85 1.67e+00 3.59e-01 2.21e+01 ... (remaining 34754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14258 17.80 - 35.61: 453 35.61 - 53.41: 101 53.41 - 71.21: 14 71.21 - 89.02: 4 Dihedral angle restraints: 14830 sinusoidal: 1698 harmonic: 13132 Sorted by residual: dihedral pdb=" CA LYS A 689 " pdb=" C LYS A 689 " pdb=" N ASP A 690 " pdb=" CA ASP A 690 " ideal model delta harmonic sigma weight residual -180.00 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA HIS A 363 " pdb=" C HIS A 363 " pdb=" N PHE A 364 " pdb=" CA PHE A 364 " ideal model delta harmonic sigma weight residual -180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TRP C 498 " pdb=" C TRP C 498 " pdb=" N ASP C 499 " pdb=" CA ASP C 499 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 14827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3373 0.047 - 0.095: 774 0.095 - 0.142: 344 0.142 - 0.189: 7 0.189 - 0.236: 4 Chirality restraints: 4502 Sorted by residual: chirality pdb=" CG LEU A 261 " pdb=" CB LEU A 261 " pdb=" CD1 LEU A 261 " pdb=" CD2 LEU A 261 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA MET A 265 " pdb=" N MET A 265 " pdb=" C MET A 265 " pdb=" CB MET A 265 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA GLU A 394 " pdb=" N GLU A 394 " pdb=" C GLU A 394 " pdb=" CB GLU A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 4499 not shown) Planarity restraints: 4871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 390 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ASP A 390 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP A 390 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 391 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 498 " -0.021 2.00e-02 2.50e+03 1.84e-02 8.50e+00 pdb=" CG TRP A 498 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 498 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 498 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 498 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 498 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 498 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 498 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 498 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 498 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 392 " -0.015 2.00e-02 2.50e+03 2.00e-02 6.97e+00 pdb=" CG PHE A 392 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 392 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 392 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 392 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 392 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 392 " -0.003 2.00e-02 2.50e+03 ... (remaining 4868 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 258 2.65 - 3.21: 22137 3.21 - 3.77: 35296 3.77 - 4.34: 42292 4.34 - 4.90: 71557 Nonbonded interactions: 171540 Sorted by model distance: nonbonded pdb=" OG SER A 659 " pdb=" OD1 ASN A 661 " model vdw 2.087 3.040 nonbonded pdb=" OH TYR C 418 " pdb=" O GLN H 325 " model vdw 2.114 3.040 nonbonded pdb=" O LYS A 398 " pdb=" OH TYR A 654 " model vdw 2.115 3.040 nonbonded pdb=" O LYS C 398 " pdb=" OH TYR C 654 " model vdw 2.152 3.040 nonbonded pdb=" O ASN C 484 " pdb=" N GLY C 500 " model vdw 2.198 3.120 ... (remaining 171535 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 260 through 299 or resid 347 through 731)) selection = (chain 'C' and resid 260 through 731) } ncs_group { reference = (chain 'B' and resid 5 through 1140) selection = chain 'E' } ncs_group { reference = (chain 'D' and ((resid 7 through 200 and (name N or name CA or name C or name O \ or name CB )) or resid 201 through 550)) selection = (chain 'H' and (resid 7 through 274 or resid 289 through 550)) } ncs_group { reference = (chain 'I' and (resid 3 through 19 or resid 32 through 64)) selection = (chain 'P' and resid 3 through 64) } ncs_group { reference = (chain 'J' and resid 55 through 201) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 23.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.820 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4786 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 : 0.002 0.069 25199 Z= 0.142 Angle : 0.609 16.899 34759 Z= 0.359 Chirality : 0.047 0.236 4502 Planarity : 0.002 0.046 4871 Dihedral : 10.426 89.017 6254 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 0.39 % Allowed : 26.07 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4487 helix: 2.03 (0.20), residues: 696 sheet: -0.23 (0.14), residues: 1434 loop : -1.59 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 706 TYR 0.018 0.001 TYR A 450 PHE 0.045 0.001 PHE A 392 TRP 0.048 0.002 TRP A 498 HIS 0.005 0.001 HIS C 598 Details of bonding type rmsd covalent geometry : bond 0.00250 (25199) covalent geometry : angle 0.60886 (34759) hydrogen bonds : bond 0.14241 ( 1256) hydrogen bonds : angle 6.45833 ( 3423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 MET cc_start: 0.7922 (ppp) cc_final: 0.7558 (pmm) REVERT: C 485 LEU cc_start: 0.8808 (tp) cc_final: 0.8445 (tp) REVERT: C 524 MET cc_start: 0.6594 (mmp) cc_final: 0.6385 (mmp) REVERT: C 665 TYR cc_start: 0.7672 (m-80) cc_final: 0.7308 (m-80) outliers start: 3 outliers final: 2 residues processed: 160 average time/residue: 0.1342 time to fit residues: 36.7470 Evaluate side-chains 157 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain C residue 371 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 7.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 644 ASN C 388 GLN C 419 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.146310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.129205 restraints weight = 190226.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.130873 restraints weight = 151784.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.130376 restraints weight = 121171.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.130596 restraints weight = 109426.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.130649 restraints weight = 99140.254| |-----------------------------------------------------------------------------| r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4887 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25199 Z= 0.196 Angle : 0.588 8.884 34759 Z= 0.342 Chirality : 0.047 0.173 4502 Planarity : 0.003 0.050 4871 Dihedral : 4.694 32.586 4601 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.11 % Rotamer: Outliers : 4.80 % Allowed : 19.71 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.12), residues: 4487 helix: 0.91 (0.19), residues: 718 sheet: -0.60 (0.14), residues: 1389 loop : -1.91 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 359 TYR 0.020 0.002 TYR C 509 PHE 0.017 0.002 PHE C 573 TRP 0.033 0.002 TRP A 625 HIS 0.007 0.002 HIS C 461 Details of bonding type rmsd covalent geometry : bond 0.00345 (25199) covalent geometry : angle 0.58812 (34759) hydrogen bonds : bond 0.04077 ( 1256) hydrogen bonds : angle 5.83568 ( 3423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6560 (mmtm) REVERT: A 467 MET cc_start: 0.7616 (mtm) cc_final: 0.7216 (mpp) REVERT: A 625 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7689 (m100) REVERT: C 434 ASP cc_start: 0.8723 (m-30) cc_final: 0.8153 (m-30) outliers start: 37 outliers final: 22 residues processed: 196 average time/residue: 0.1607 time to fit residues: 51.9811 Evaluate side-chains 182 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 625 TRP Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 730 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 181 optimal weight: 0.9990 chunk 317 optimal weight: 0.0670 chunk 423 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 405 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 312 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.147672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.130708 restraints weight = 189876.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.131776 restraints weight = 150102.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.132685 restraints weight = 123165.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.133059 restraints weight = 99157.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.132697 restraints weight = 81018.372| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4735 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25199 Z= 0.092 Angle : 0.457 8.023 34759 Z= 0.259 Chirality : 0.046 0.150 4502 Planarity : 0.002 0.034 4871 Dihedral : 3.683 20.538 4598 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 3.11 % Allowed : 21.40 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4487 helix: 1.75 (0.20), residues: 707 sheet: -0.42 (0.14), residues: 1399 loop : -1.71 (0.12), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 634 TYR 0.013 0.001 TYR A 667 PHE 0.022 0.001 PHE C 573 TRP 0.026 0.002 TRP C 625 HIS 0.003 0.001 HIS C 363 Details of bonding type rmsd covalent geometry : bond 0.00170 (25199) covalent geometry : angle 0.45655 (34759) hydrogen bonds : bond 0.03026 ( 1256) hydrogen bonds : angle 4.96882 ( 3423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6761 (tmm) cc_final: 0.6544 (tmm) REVERT: A 467 MET cc_start: 0.7573 (mtm) cc_final: 0.7240 (mpp) REVERT: C 434 ASP cc_start: 0.8713 (m-30) cc_final: 0.8254 (m-30) REVERT: C 467 MET cc_start: 0.7639 (mtm) cc_final: 0.7373 (mpp) REVERT: C 706 ARG cc_start: 0.5332 (ttt90) cc_final: 0.4702 (ttt90) REVERT: C 715 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.9074 (p) outliers start: 24 outliers final: 12 residues processed: 184 average time/residue: 0.1563 time to fit residues: 47.8915 Evaluate side-chains 169 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 625 TRP Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 715 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 88 optimal weight: 50.0000 chunk 105 optimal weight: 40.0000 chunk 278 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 306 optimal weight: 50.0000 chunk 390 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 93 optimal weight: 50.0000 chunk 116 optimal weight: 8.9990 overall best weight: 3.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.137407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.135944 restraints weight = 88379.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.135839 restraints weight = 19719.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.135806 restraints weight = 12351.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.135822 restraints weight = 9464.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.135822 restraints weight = 9146.349| |-----------------------------------------------------------------------------| r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3571 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 25199 Z= 0.264 Angle : 0.710 12.718 34759 Z= 0.415 Chirality : 0.049 0.190 4502 Planarity : 0.004 0.064 4871 Dihedral : 5.822 31.415 4598 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.41 % Favored : 88.50 % Rotamer: Outliers : 7.00 % Allowed : 20.62 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.12), residues: 4487 helix: -0.00 (0.19), residues: 705 sheet: -1.04 (0.14), residues: 1300 loop : -2.38 (0.11), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 691 TYR 0.032 0.002 TYR A 371 PHE 0.023 0.002 PHE A 521 TRP 0.027 0.002 TRP A 625 HIS 0.015 0.003 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00476 (25199) covalent geometry : angle 0.70994 (34759) hydrogen bonds : bond 0.04979 ( 1256) hydrogen bonds : angle 6.83094 ( 3423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8149 (m-80) cc_final: 0.7615 (m-80) REVERT: C 372 PHE cc_start: 0.8189 (m-80) cc_final: 0.7588 (m-80) REVERT: C 376 MET cc_start: 0.2959 (mmt) cc_final: 0.2105 (mpp) REVERT: C 434 ASP cc_start: 0.8502 (m-30) cc_final: 0.7828 (m-30) REVERT: C 485 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8753 (mm) REVERT: C 491 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7391 (p90) REVERT: C 614 VAL cc_start: 0.8697 (t) cc_final: 0.8324 (m) REVERT: C 651 ASN cc_start: 0.8877 (p0) cc_final: 0.8673 (p0) REVERT: C 654 TYR cc_start: 0.7371 (m-10) cc_final: 0.7042 (m-10) REVERT: C 660 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7281 (mt-10) REVERT: C 706 ARG cc_start: 0.6537 (ttt90) cc_final: 0.6149 (ttt90) outliers start: 54 outliers final: 35 residues processed: 209 average time/residue: 0.1621 time to fit residues: 55.7488 Evaluate side-chains 195 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 371 TYR Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 491 TYR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 730 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 115 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 71 optimal weight: 0.0040 chunk 73 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 294 optimal weight: 50.0000 chunk 346 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 140 optimal weight: 0.5980 overall best weight: 2.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN C 644 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.139197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.138538 restraints weight = 62436.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.138157 restraints weight = 1690.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.138151 restraints weight = 881.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.138151 restraints weight = 799.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.138151 restraints weight = 799.156| |-----------------------------------------------------------------------------| r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3594 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25199 Z= 0.185 Angle : 0.576 8.695 34759 Z= 0.332 Chirality : 0.047 0.197 4502 Planarity : 0.003 0.038 4871 Dihedral : 4.948 27.840 4598 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.25 % Favored : 91.71 % Rotamer: Outliers : 5.58 % Allowed : 23.48 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.12), residues: 4487 helix: 0.26 (0.19), residues: 707 sheet: -1.01 (0.15), residues: 1258 loop : -2.45 (0.11), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 359 TYR 0.018 0.002 TYR A 462 PHE 0.029 0.002 PHE C 573 TRP 0.033 0.002 TRP A 625 HIS 0.005 0.002 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00333 (25199) covalent geometry : angle 0.57561 (34759) hydrogen bonds : bond 0.03832 ( 1256) hydrogen bonds : angle 6.15017 ( 3423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 614 VAL cc_start: 0.8848 (t) cc_final: 0.8537 (m) REVERT: C 660 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7419 (mt-10) outliers start: 43 outliers final: 32 residues processed: 193 average time/residue: 0.1573 time to fit residues: 50.4046 Evaluate side-chains 183 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 371 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 730 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 71 optimal weight: 40.0000 chunk 147 optimal weight: 9.9990 chunk 303 optimal weight: 0.0010 chunk 4 optimal weight: 8.9990 chunk 327 optimal weight: 0.8980 chunk 259 optimal weight: 9.9990 chunk 443 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 overall best weight: 2.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.137353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.135749 restraints weight = 64839.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.135299 restraints weight = 13777.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.135304 restraints weight = 8039.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.135344 restraints weight = 7622.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.135342 restraints weight = 7179.523| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3574 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25199 Z= 0.177 Angle : 0.573 9.875 34759 Z= 0.328 Chirality : 0.047 0.254 4502 Planarity : 0.003 0.039 4871 Dihedral : 4.858 24.639 4598 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.01 % Favored : 88.95 % Rotamer: Outliers : 5.45 % Allowed : 24.12 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.12), residues: 4487 helix: 0.34 (0.19), residues: 712 sheet: -1.13 (0.14), residues: 1281 loop : -2.46 (0.11), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 568 TYR 0.022 0.002 TYR C 418 PHE 0.025 0.001 PHE C 573 TRP 0.038 0.002 TRP A 478 HIS 0.007 0.001 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00322 (25199) covalent geometry : angle 0.57293 (34759) hydrogen bonds : bond 0.03785 ( 1256) hydrogen bonds : angle 6.10508 ( 3423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8294 (m-80) cc_final: 0.7641 (m-80) REVERT: C 267 PHE cc_start: 0.7988 (t80) cc_final: 0.7327 (t80) REVERT: C 367 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7298 (mm) REVERT: C 562 LYS cc_start: 0.8098 (tptt) cc_final: 0.7796 (tptm) REVERT: C 614 VAL cc_start: 0.8835 (t) cc_final: 0.8509 (m) outliers start: 42 outliers final: 34 residues processed: 195 average time/residue: 0.1589 time to fit residues: 51.6686 Evaluate side-chains 194 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 730 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 399 optimal weight: 2.9990 chunk 85 optimal weight: 0.0030 chunk 226 optimal weight: 0.0030 chunk 287 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 179 optimal weight: 0.4980 chunk 285 optimal weight: 0.9990 chunk 389 optimal weight: 0.4980 chunk 114 optimal weight: 8.9990 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.142815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.125027 restraints weight = 190317.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.126150 restraints weight = 137096.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.126738 restraints weight = 106101.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.126882 restraints weight = 91136.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.126882 restraints weight = 85486.036| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4973 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25199 Z= 0.094 Angle : 0.493 11.023 34759 Z= 0.275 Chirality : 0.046 0.155 4502 Planarity : 0.002 0.035 4871 Dihedral : 4.037 20.415 4598 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 3.76 % Allowed : 26.46 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.12), residues: 4487 helix: 1.25 (0.20), residues: 701 sheet: -1.00 (0.14), residues: 1321 loop : -2.10 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 359 TYR 0.017 0.001 TYR A 583 PHE 0.024 0.001 PHE C 573 TRP 0.026 0.002 TRP A 478 HIS 0.004 0.001 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00179 (25199) covalent geometry : angle 0.49275 (34759) hydrogen bonds : bond 0.02939 ( 1256) hydrogen bonds : angle 5.31714 ( 3423) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7939 (t80) REVERT: A 485 LEU cc_start: 0.9229 (tp) cc_final: 0.8991 (mm) REVERT: C 265 MET cc_start: 0.8833 (ppp) cc_final: 0.8594 (pmm) REVERT: C 267 PHE cc_start: 0.8454 (t80) cc_final: 0.8176 (t80) REVERT: C 524 MET cc_start: 0.7271 (mmp) cc_final: 0.7054 (mmp) REVERT: C 612 GLU cc_start: 0.6422 (mm-30) cc_final: 0.6122 (mm-30) outliers start: 29 outliers final: 20 residues processed: 182 average time/residue: 0.1470 time to fit residues: 45.1476 Evaluate side-chains 177 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 371 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 715 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 223 optimal weight: 1.9990 chunk 434 optimal weight: 10.0000 chunk 392 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 411 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 185 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.138169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.119438 restraints weight = 193061.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.120506 restraints weight = 140614.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.120829 restraints weight = 113273.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.121327 restraints weight = 101250.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.121327 restraints weight = 92816.775| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5234 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25199 Z= 0.235 Angle : 0.672 10.495 34759 Z= 0.390 Chirality : 0.049 0.207 4502 Planarity : 0.004 0.049 4871 Dihedral : 5.538 24.705 4598 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.46 % Favored : 86.45 % Rotamer: Outliers : 5.06 % Allowed : 25.16 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.12), residues: 4487 helix: 0.10 (0.19), residues: 696 sheet: -1.25 (0.15), residues: 1194 loop : -2.53 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 356 TYR 0.024 0.002 TYR A 450 PHE 0.034 0.002 PHE A 372 TRP 0.028 0.002 TRP A 625 HIS 0.012 0.002 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00412 (25199) covalent geometry : angle 0.67186 (34759) hydrogen bonds : bond 0.04694 ( 1256) hydrogen bonds : angle 6.73563 ( 3423) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 ARG cc_start: 0.7301 (ttp-170) cc_final: 0.6717 (ttp-170) REVERT: C 485 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8817 (mm) REVERT: C 524 MET cc_start: 0.7395 (mmp) cc_final: 0.7187 (mmp) REVERT: C 614 VAL cc_start: 0.8790 (t) cc_final: 0.8576 (m) REVERT: C 660 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7559 (mt-10) outliers start: 39 outliers final: 34 residues processed: 185 average time/residue: 0.1599 time to fit residues: 49.1079 Evaluate side-chains 194 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 371 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 715 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 298 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 chunk 29 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 94 optimal weight: 50.0000 chunk 412 optimal weight: 0.9980 chunk 259 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 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 = 0.4635 r_free = 0.4635 target = 0.133894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.132835 restraints weight = 95256.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.132150 restraints weight = 23463.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.132174 restraints weight = 13179.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.132174 restraints weight = 12543.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.132174 restraints weight = 12543.455| |-----------------------------------------------------------------------------| r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3652 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25199 Z= 0.190 Angle : 0.609 16.317 34759 Z= 0.346 Chirality : 0.048 0.185 4502 Planarity : 0.003 0.045 4871 Dihedral : 5.101 22.942 4598 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.58 % Favored : 90.37 % Rotamer: Outliers : 4.67 % Allowed : 26.72 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.12), residues: 4487 helix: 0.04 (0.19), residues: 711 sheet: -1.33 (0.14), residues: 1213 loop : -2.58 (0.11), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 295 TYR 0.023 0.002 TYR A 450 PHE 0.045 0.002 PHE C 372 TRP 0.029 0.002 TRP A 625 HIS 0.006 0.001 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00342 (25199) covalent geometry : angle 0.60942 (34759) hydrogen bonds : bond 0.03906 ( 1256) hydrogen bonds : angle 6.41485 ( 3423) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8391 (mmtm) cc_final: 0.8069 (mmtm) REVERT: A 429 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7768 (t80) REVERT: C 388 GLN cc_start: 0.7636 (tt0) cc_final: 0.7327 (tt0) REVERT: C 524 MET cc_start: 0.7314 (mmp) cc_final: 0.7070 (mmp) REVERT: C 612 GLU cc_start: 0.5911 (mm-30) cc_final: 0.5653 (mm-30) REVERT: C 614 VAL cc_start: 0.8798 (t) cc_final: 0.8478 (m) REVERT: C 676 LEU cc_start: 0.8331 (mt) cc_final: 0.8102 (mt) outliers start: 36 outliers final: 32 residues processed: 189 average time/residue: 0.1571 time to fit residues: 49.2347 Evaluate side-chains 194 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 637 LYS Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 715 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 438 optimal weight: 10.0000 chunk 358 optimal weight: 8.9990 chunk 301 optimal weight: 50.0000 chunk 437 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 381 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 119 optimal weight: 0.1980 chunk 321 optimal weight: 0.0870 chunk 269 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 overall best weight: 2.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** 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 = 0.4631 r_free = 0.4631 target = 0.138009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.121016 restraints weight = 193851.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.121588 restraints weight = 148080.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.122230 restraints weight = 114576.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.122765 restraints weight = 98379.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.122854 restraints weight = 85689.649| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5067 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25199 Z= 0.180 Angle : 0.603 14.230 34759 Z= 0.342 Chirality : 0.048 0.181 4502 Planarity : 0.003 0.048 4871 Dihedral : 5.013 23.563 4598 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.42 % Favored : 86.54 % Rotamer: Outliers : 4.28 % Allowed : 27.63 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.12), residues: 4487 helix: 0.19 (0.19), residues: 704 sheet: -1.35 (0.15), residues: 1202 loop : -2.61 (0.11), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 691 TYR 0.035 0.002 TYR A 371 PHE 0.034 0.002 PHE C 372 TRP 0.039 0.002 TRP A 625 HIS 0.006 0.001 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00325 (25199) covalent geometry : angle 0.60267 (34759) hydrogen bonds : bond 0.03844 ( 1256) hydrogen bonds : angle 6.37989 ( 3423) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8974 Ramachandran restraints generated. 4487 Oldfield, 0 Emsley, 4487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7771 (t80) REVERT: C 485 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8934 (mm) REVERT: C 524 MET cc_start: 0.7437 (mmp) cc_final: 0.7170 (mmp) REVERT: C 612 GLU cc_start: 0.6576 (mm-30) cc_final: 0.6045 (mm-30) REVERT: C 614 VAL cc_start: 0.8837 (t) cc_final: 0.8603 (m) REVERT: C 660 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7438 (mt-10) outliers start: 33 outliers final: 28 residues processed: 185 average time/residue: 0.1608 time to fit residues: 49.0077 Evaluate side-chains 190 residues out of total 4049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 637 LYS Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 715 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 366 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 352 optimal weight: 10.0000 chunk 184 optimal weight: 0.4980 chunk 412 optimal weight: 20.0000 chunk 430 optimal weight: 10.0000 chunk 210 optimal weight: 50.0000 chunk 440 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** 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 = 0.4605 r_free = 0.4605 target = 0.136155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.119463 restraints weight = 193365.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.120674 restraints weight = 150402.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.120483 restraints weight = 123049.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.120966 restraints weight = 108852.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.121089 restraints weight = 90292.956| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5101 moved from start: 0.8009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25199 Z= 0.225 Angle : 0.679 14.309 34759 Z= 0.388 Chirality : 0.049 0.186 4502 Planarity : 0.004 0.047 4871 Dihedral : 5.613 24.651 4598 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.22 % Favored : 86.74 % Rotamer: Outliers : 5.32 % Allowed : 27.63 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.12), residues: 4487 helix: -0.32 (0.18), residues: 699 sheet: -1.55 (0.15), residues: 1177 loop : -2.75 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 691 TYR 0.028 0.002 TYR A 435 PHE 0.038 0.002 PHE C 372 TRP 0.039 0.002 TRP A 625 HIS 0.007 0.002 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00403 (25199) covalent geometry : angle 0.67906 (34759) hydrogen bonds : bond 0.04450 ( 1256) hydrogen bonds : angle 6.98934 ( 3423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7149.13 seconds wall clock time: 122 minutes 51.34 seconds (7371.34 seconds total)