Starting phenix.real_space_refine on Thu Mar 21 13:57:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxh_29533/03_2024/8fxh_29533_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxh_29533/03_2024/8fxh_29533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxh_29533/03_2024/8fxh_29533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxh_29533/03_2024/8fxh_29533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxh_29533/03_2024/8fxh_29533_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxh_29533/03_2024/8fxh_29533_neut.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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 84 5.16 5 C 19284 2.51 5 N 5070 2.21 5 O 5790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C GLU 563": "OE1" <-> "OE2" Residue "C GLU 582": "OE1" <-> "OE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 482": "OE1" <-> "OE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D GLU 563": "OE1" <-> "OE2" Residue "D GLU 582": "OE1" <-> "OE2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "E GLU 482": "OE1" <-> "OE2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "E GLU 565": "OE1" <-> "OE2" Residue "E GLU 582": "OE1" <-> "OE2" Residue "E GLU 621": "OE1" <-> "OE2" Residue "E GLU 631": "OE1" <-> "OE2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F GLU 449": "OE1" <-> "OE2" Residue "F GLU 482": "OE1" <-> "OE2" Residue "F GLU 614": "OE1" <-> "OE2" Residue "F GLU 631": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30228 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "B" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "C" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "D" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "E" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "F" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Time building chain proxies: 15.08, per 1000 atoms: 0.50 Number of scatterers: 30228 At special positions: 0 Unit cell: (152.55, 188.325, 162.675, 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 84 16.00 O 5790 8.00 N 5070 7.00 C 19284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.04 Conformation dependent library (CDL) restraints added in 5.4 seconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7128 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 34 sheets defined 35.1% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 removed outlier: 4.090A pdb=" N TYR A 58 " --> pdb=" O PRO A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.669A pdb=" N TYR A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.742A pdb=" N LEU A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 134 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.716A pdb=" N SER A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 362 through 373 removed outlier: 3.590A pdb=" N HIS A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 407 removed outlier: 4.186A pdb=" N VAL A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 408 through 420 Processing helix chain 'A' and resid 470 through 479 removed outlier: 4.020A pdb=" N PHE A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.620A pdb=" N ALA A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A 486 " --> pdb=" O LYS A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'A' and resid 496 through 509 Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.946A pdb=" N ASN A 540 " --> pdb=" O HIS A 536 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 583 through 589 removed outlier: 3.644A pdb=" N LEU A 587 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 589 " --> pdb=" O ILE A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.692A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 630 " --> pdb=" O GLN A 626 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 removed outlier: 3.848A pdb=" N TYR B 58 " --> pdb=" O PRO B 54 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.782A pdb=" N LEU B 69 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 66 through 70' Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.646A pdb=" N LEU B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 136 Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.548A pdb=" N ASN B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.860A pdb=" N ALA B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.709A pdb=" N SER B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.820A pdb=" N LEU B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.604A pdb=" N LYS B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 334 through 345 removed outlier: 3.652A pdb=" N SER B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 408 through 420 Processing helix chain 'B' and resid 469 through 479 removed outlier: 4.181A pdb=" N ARG B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE B 478 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 removed outlier: 3.936A pdb=" N ARG B 486 " --> pdb=" O LYS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 509 removed outlier: 3.590A pdb=" N MET B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 547 removed outlier: 3.561A pdb=" N ASN B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 565 Processing helix chain 'B' and resid 583 through 589 Processing helix chain 'B' and resid 624 through 629 removed outlier: 3.602A pdb=" N TYR B 628 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 629 " --> pdb=" O GLU B 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 624 through 629' Processing helix chain 'C' and resid 54 through 64 removed outlier: 4.207A pdb=" N TYR C 58 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.989A pdb=" N LYS C 70 " --> pdb=" O TYR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.579A pdb=" N LEU C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 137 removed outlier: 3.725A pdb=" N GLN C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 Processing helix chain 'C' and resid 161 through 174 removed outlier: 3.857A pdb=" N ALA C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.729A pdb=" N GLN C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.790A pdb=" N SER C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 226 Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.687A pdb=" N VAL C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 removed outlier: 3.609A pdb=" N ALA C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 removed outlier: 3.546A pdb=" N SER C 345 " --> pdb=" O LYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 373 removed outlier: 3.786A pdb=" N HIS C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 407 removed outlier: 4.256A pdb=" N VAL C 407 " --> pdb=" O THR C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 407' Processing helix chain 'C' and resid 408 through 420 Processing helix chain 'C' and resid 469 through 477 removed outlier: 4.151A pdb=" N ARG C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 486 removed outlier: 3.964A pdb=" N ARG C 486 " --> pdb=" O LYS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 509 removed outlier: 3.594A pdb=" N LEU C 500 " --> pdb=" O SER C 496 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C 502 " --> pdb=" O ARG C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 547 removed outlier: 4.080A pdb=" N ASN C 540 " --> pdb=" O HIS C 536 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 541 " --> pdb=" O TYR C 537 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 542 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 565 Processing helix chain 'C' and resid 583 through 589 Processing helix chain 'C' and resid 624 through 629 Processing helix chain 'D' and resid 54 through 64 removed outlier: 4.207A pdb=" N TYR D 58 " --> pdb=" O PRO D 54 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 removed outlier: 3.988A pdb=" N LYS D 70 " --> pdb=" O TYR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.578A pdb=" N LEU D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 137 removed outlier: 3.725A pdb=" N GLN D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 Processing helix chain 'D' and resid 161 through 174 removed outlier: 3.857A pdb=" N ALA D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 removed outlier: 3.731A pdb=" N GLN D 195 " --> pdb=" O GLY D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.789A pdb=" N SER D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 226 Processing helix chain 'D' and resid 241 through 250 removed outlier: 3.686A pdb=" N VAL D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.609A pdb=" N ALA D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 removed outlier: 3.547A pdb=" N SER D 345 " --> pdb=" O LYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 373 removed outlier: 3.786A pdb=" N HIS D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 407 removed outlier: 4.256A pdb=" N VAL D 407 " --> pdb=" O THR D 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 407' Processing helix chain 'D' and resid 408 through 420 Processing helix chain 'D' and resid 469 through 477 removed outlier: 4.151A pdb=" N ARG D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 477 " --> pdb=" O ARG D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 486 removed outlier: 3.964A pdb=" N ARG D 486 " --> pdb=" O LYS D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 509 removed outlier: 3.594A pdb=" N LEU D 500 " --> pdb=" O SER D 496 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN D 501 " --> pdb=" O ILE D 497 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 502 " --> pdb=" O ARG D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 547 removed outlier: 4.080A pdb=" N ASN D 540 " --> pdb=" O HIS D 536 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL D 541 " --> pdb=" O TYR D 537 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 542 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 565 Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'E' and resid 54 through 64 removed outlier: 3.848A pdb=" N TYR E 58 " --> pdb=" O PRO E 54 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.781A pdb=" N LEU E 69 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS E 70 " --> pdb=" O PRO E 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 66 through 70' Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.647A pdb=" N LEU E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 136 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.548A pdb=" N ASN E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 174 removed outlier: 3.860A pdb=" N ALA E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.708A pdb=" N SER E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 227 removed outlier: 3.820A pdb=" N LEU E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 250 removed outlier: 3.604A pdb=" N LYS E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU E 249 " --> pdb=" O GLU E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 334 through 345 removed outlier: 3.652A pdb=" N SER E 345 " --> pdb=" O LYS E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 408 through 420 Processing helix chain 'E' and resid 469 through 479 removed outlier: 4.181A pdb=" N ARG E 473 " --> pdb=" O ASP E 469 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE E 478 " --> pdb=" O ILE E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 486 removed outlier: 3.936A pdb=" N ARG E 486 " --> pdb=" O LYS E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 509 removed outlier: 3.591A pdb=" N MET E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 547 removed outlier: 3.561A pdb=" N ASN E 547 " --> pdb=" O ASN E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 565 Processing helix chain 'E' and resid 583 through 589 Processing helix chain 'E' and resid 624 through 629 removed outlier: 3.601A pdb=" N TYR E 628 " --> pdb=" O ILE E 624 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 629 " --> pdb=" O GLU E 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 624 through 629' Processing helix chain 'F' and resid 54 through 61 removed outlier: 4.089A pdb=" N TYR F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.670A pdb=" N TYR F 74 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 89 removed outlier: 3.742A pdb=" N LEU F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 134 Processing helix chain 'F' and resid 143 through 156 Processing helix chain 'F' and resid 161 through 174 Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.717A pdb=" N SER F 211 " --> pdb=" O SER F 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 336 through 344 Processing helix chain 'F' and resid 362 through 373 removed outlier: 3.590A pdb=" N HIS F 366 " --> pdb=" O ASP F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 407 removed outlier: 4.186A pdb=" N VAL F 407 " --> pdb=" O THR F 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 404 through 407' Processing helix chain 'F' and resid 408 through 420 Processing helix chain 'F' and resid 470 through 479 removed outlier: 4.020A pdb=" N PHE F 478 " --> pdb=" O ILE F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 486 removed outlier: 3.621A pdb=" N ALA F 485 " --> pdb=" O GLU F 482 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG F 486 " --> pdb=" O LYS F 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 482 through 486' Processing helix chain 'F' and resid 496 through 509 Processing helix chain 'F' and resid 536 through 547 removed outlier: 3.946A pdb=" N ASN F 540 " --> pdb=" O HIS F 536 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 541 " --> pdb=" O TYR F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 565 Processing helix chain 'F' and resid 583 through 589 removed outlier: 3.643A pdb=" N LEU F 587 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 589 " --> pdb=" O ILE F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 632 removed outlier: 3.692A pdb=" N VAL F 627 " --> pdb=" O LEU F 623 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS F 630 " --> pdb=" O GLN F 626 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU F 631 " --> pdb=" O VAL F 627 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28 removed outlier: 5.980A pdb=" N ASN A 24 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP A 43 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 402 removed outlier: 3.841A pdb=" N LEU A 310 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA A 319 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG A 308 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU A 321 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP A 306 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 449 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 432 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE A 447 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 530 removed outlier: 6.295A pdb=" N ILE A 490 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 597 " --> pdb=" O LYS A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 28 removed outlier: 5.420A pdb=" N ILE B 22 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 45 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASN B 24 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP B 43 " --> pdb=" O ASN B 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 109 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 105 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.584A pdb=" N LEU B 186 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.511A pdb=" N ASP B 270 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 254 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 399 through 402 removed outlier: 5.388A pdb=" N PHE B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 312 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA B 318 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 310 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP B 306 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 449 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE B 432 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE B 447 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AB2, first strand: chain 'B' and resid 524 through 526 removed outlier: 3.621A pdb=" N GLU B 556 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE B 490 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 574 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 21 through 28 removed outlier: 4.268A pdb=" N VAL C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C 41 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN C 27 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA C 39 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 178 through 180 Processing sheet with id=AB5, first strand: chain 'C' and resid 234 through 236 Processing sheet with id=AB6, first strand: chain 'C' and resid 399 through 402 removed outlier: 6.908A pdb=" N LEU C 310 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA C 319 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG C 308 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU C 321 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP C 306 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 449 " --> pdb=" O ASP C 430 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE C 432 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE C 447 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 326 through 327 Processing sheet with id=AB8, first strand: chain 'C' and resid 529 through 530 removed outlier: 3.707A pdb=" N GLU C 556 " --> pdb=" O VAL C 519 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE C 490 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 574 " --> pdb=" O ILE C 489 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 21 through 28 removed outlier: 4.268A pdb=" N VAL D 25 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 41 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN D 27 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA D 39 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 178 through 180 Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 236 Processing sheet with id=AC3, first strand: chain 'D' and resid 399 through 402 removed outlier: 6.909A pdb=" N LEU D 310 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA D 319 " --> pdb=" O ARG D 308 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG D 308 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU D 321 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP D 306 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 449 " --> pdb=" O ASP D 430 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE D 432 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE D 447 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 326 through 327 Processing sheet with id=AC5, first strand: chain 'D' and resid 529 through 530 removed outlier: 3.706A pdb=" N GLU D 556 " --> pdb=" O VAL D 519 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 490 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 574 " --> pdb=" O ILE D 489 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 20 through 28 removed outlier: 5.420A pdb=" N ILE E 22 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA E 45 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASN E 24 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP E 43 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN E 109 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 105 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 178 through 181 removed outlier: 3.585A pdb=" N LEU E 186 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 269 through 270 removed outlier: 3.511A pdb=" N ASP E 270 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL E 254 " --> pdb=" O ASP E 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 399 through 402 removed outlier: 5.389A pdb=" N PHE E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL E 312 " --> pdb=" O PHE E 316 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA E 318 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 310 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP E 306 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 449 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE E 432 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE E 447 " --> pdb=" O ILE E 432 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 326 through 328 Processing sheet with id=AD2, first strand: chain 'E' and resid 524 through 526 removed outlier: 3.621A pdb=" N GLU E 556 " --> pdb=" O VAL E 519 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE E 490 " --> pdb=" O ALA E 555 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 574 " --> pdb=" O ILE E 489 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 23 through 28 removed outlier: 5.980A pdb=" N ASN F 24 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP F 43 " --> pdb=" O ASN F 24 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 179 through 181 Processing sheet with id=AD5, first strand: chain 'F' and resid 399 through 402 removed outlier: 3.840A pdb=" N LEU F 310 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA F 319 " --> pdb=" O ARG F 308 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG F 308 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU F 321 " --> pdb=" O ASP F 306 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP F 306 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 449 " --> pdb=" O ASP F 430 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE F 432 " --> pdb=" O ILE F 447 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE F 447 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 326 through 327 Processing sheet with id=AD7, first strand: chain 'F' and resid 529 through 530 removed outlier: 6.295A pdb=" N ILE F 490 " --> pdb=" O ALA F 555 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL F 597 " --> pdb=" O LYS F 608 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3084 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: 10.63 Time building geometry restraints manager: 11.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5353 1.32 - 1.44: 7776 1.44 - 1.56: 17571 1.56 - 1.69: 8 1.69 - 1.81: 132 Bond restraints: 30840 Sorted by residual: bond pdb=" C PHE A 132 " pdb=" N GLU A 133 " ideal model delta sigma weight residual 1.335 1.205 0.130 1.31e-02 5.83e+03 9.80e+01 bond pdb=" C PHE F 132 " pdb=" N GLU F 133 " ideal model delta sigma weight residual 1.335 1.206 0.129 1.31e-02 5.83e+03 9.74e+01 bond pdb=" C ILE A 335 " pdb=" N ALA A 336 " ideal model delta sigma weight residual 1.332 1.198 0.135 1.40e-02 5.10e+03 9.26e+01 bond pdb=" N PRO A 253 " pdb=" CD PRO A 253 " ideal model delta sigma weight residual 1.473 1.608 -0.135 1.40e-02 5.10e+03 9.23e+01 bond pdb=" N PRO F 253 " pdb=" CD PRO F 253 " ideal model delta sigma weight residual 1.473 1.607 -0.134 1.40e-02 5.10e+03 9.22e+01 ... (remaining 30835 not shown) Histogram of bond angle deviations from ideal: 85.64 - 103.79: 442 103.79 - 121.94: 34743 121.94 - 140.09: 6677 140.09 - 158.24: 4 158.24 - 176.39: 2 Bond angle restraints: 41868 Sorted by residual: angle pdb=" N GLY A 264 " pdb=" CA GLY A 264 " pdb=" C GLY A 264 " ideal model delta sigma weight residual 111.14 176.39 -65.25 1.46e+00 4.69e-01 2.00e+03 angle pdb=" N GLY F 264 " pdb=" CA GLY F 264 " pdb=" C GLY F 264 " ideal model delta sigma weight residual 111.14 176.29 -65.15 1.46e+00 4.69e-01 1.99e+03 angle pdb=" N VAL A 298 " pdb=" CA VAL A 298 " pdb=" C VAL A 298 " ideal model delta sigma weight residual 111.09 152.23 -41.14 1.25e+00 6.40e-01 1.08e+03 angle pdb=" N VAL F 298 " pdb=" CA VAL F 298 " pdb=" C VAL F 298 " ideal model delta sigma weight residual 111.09 152.23 -41.14 1.25e+00 6.40e-01 1.08e+03 angle pdb=" C LYS E 263 " pdb=" CA LYS E 263 " pdb=" CB LYS E 263 " ideal model delta sigma weight residual 116.63 147.89 -31.26 1.16e+00 7.43e-01 7.26e+02 ... (remaining 41863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 16029 17.60 - 35.20: 1779 35.20 - 52.79: 564 52.79 - 70.39: 140 70.39 - 87.99: 52 Dihedral angle restraints: 18564 sinusoidal: 7500 harmonic: 11064 Sorted by residual: dihedral pdb=" C HIS A 262 " pdb=" N HIS A 262 " pdb=" CA HIS A 262 " pdb=" CB HIS A 262 " ideal model delta harmonic sigma weight residual -122.60 -178.51 55.91 0 2.50e+00 1.60e-01 5.00e+02 dihedral pdb=" C HIS F 262 " pdb=" N HIS F 262 " pdb=" CA HIS F 262 " pdb=" CB HIS F 262 " ideal model delta harmonic sigma weight residual -122.60 -178.49 55.89 0 2.50e+00 1.60e-01 5.00e+02 dihedral pdb=" N HIS A 262 " pdb=" C HIS A 262 " pdb=" CA HIS A 262 " pdb=" CB HIS A 262 " ideal model delta harmonic sigma weight residual 122.80 177.97 -55.17 0 2.50e+00 1.60e-01 4.87e+02 ... (remaining 18561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.488: 4714 0.488 - 0.976: 18 0.976 - 1.464: 4 1.464 - 1.952: 2 1.952 - 2.440: 2 Chirality restraints: 4740 Sorted by residual: chirality pdb=" CA HIS A 262 " pdb=" N HIS A 262 " pdb=" C HIS A 262 " pdb=" CB HIS A 262 " both_signs ideal model delta sigma weight residual False 2.51 0.07 2.44 2.00e-01 2.50e+01 1.49e+02 chirality pdb=" CA HIS F 262 " pdb=" N HIS F 262 " pdb=" C HIS F 262 " pdb=" CB HIS F 262 " both_signs ideal model delta sigma weight residual False 2.51 0.07 2.44 2.00e-01 2.50e+01 1.49e+02 chirality pdb=" CA VAL A 298 " pdb=" N VAL A 298 " pdb=" C VAL A 298 " pdb=" CB VAL A 298 " both_signs ideal model delta sigma weight residual False 2.44 0.93 1.51 2.00e-01 2.50e+01 5.72e+01 ... (remaining 4737 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR F 252 " 0.137 5.00e-02 4.00e+02 1.93e-01 5.96e+01 pdb=" N PRO F 253 " -0.333 5.00e-02 4.00e+02 pdb=" CA PRO F 253 " 0.111 5.00e-02 4.00e+02 pdb=" CD PRO F 253 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 252 " -0.137 5.00e-02 4.00e+02 1.93e-01 5.95e+01 pdb=" N PRO A 253 " 0.333 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.111 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 264 " -0.033 2.00e-02 2.50e+03 6.67e-02 4.45e+01 pdb=" C GLY F 264 " 0.115 2.00e-02 2.50e+03 pdb=" O GLY F 264 " -0.042 2.00e-02 2.50e+03 pdb=" N ILE F 265 " -0.040 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5354 2.77 - 3.30: 27106 3.30 - 3.83: 44645 3.83 - 4.37: 50843 4.37 - 4.90: 92142 Nonbonded interactions: 220090 Sorted by model distance: nonbonded pdb=" OH TYR A 537 " pdb=" O GLU A 556 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR F 537 " pdb=" O GLU F 556 " model vdw 2.236 2.440 nonbonded pdb=" O LEU B 69 " pdb=" OH TYR B 74 " model vdw 2.244 2.440 nonbonded pdb=" O LEU E 69 " pdb=" OH TYR E 74 " model vdw 2.244 2.440 nonbonded pdb=" N SER A 333 " pdb=" O SER A 333 " model vdw 2.291 2.496 ... (remaining 220085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 28.920 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 75.840 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:14.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1821 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 : 0.006 0.135 30840 Z= 0.364 Angle : 1.370 65.253 41868 Z= 0.894 Chirality : 0.100 2.440 4740 Planarity : 0.008 0.193 5448 Dihedral : 17.250 87.988 11436 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.82 % Favored : 91.81 % Rotamer: Outliers : 1.19 % Allowed : 31.11 % Favored : 67.70 % Cbeta Deviations : 1.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3774 helix: 0.80 (0.16), residues: 1162 sheet: 0.75 (0.23), residues: 640 loop : -2.22 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 182 HIS 0.003 0.001 HIS F 262 PHE 0.021 0.001 PHE F 20 TYR 0.040 0.002 TYR A 74 ARG 0.013 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 319 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.2341 (OUTLIER) cc_final: 0.1701 (pt) REVERT: A 216 GLN cc_start: 0.2485 (mm110) cc_final: 0.2149 (mm-40) REVERT: A 238 PHE cc_start: 0.6446 (t80) cc_final: 0.6069 (t80) REVERT: A 327 VAL cc_start: 0.1824 (p) cc_final: 0.1356 (m) REVERT: A 365 MET cc_start: 0.6229 (ttt) cc_final: 0.5544 (tpt) REVERT: A 435 ASP cc_start: 0.4120 (t0) cc_final: 0.3865 (t0) REVERT: A 482 GLU cc_start: 0.4263 (tp30) cc_final: 0.3457 (mm-30) REVERT: A 603 ARG cc_start: 0.7634 (tpp80) cc_final: 0.7276 (tpt-90) REVERT: A 631 GLU cc_start: 0.4568 (mm-30) cc_final: 0.3564 (mt-10) REVERT: B 46 PHE cc_start: 0.0111 (OUTLIER) cc_final: -0.0658 (m-80) REVERT: B 134 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.4432 (m-80) REVERT: B 308 ARG cc_start: 0.2939 (OUTLIER) cc_final: 0.1834 (ttm110) REVERT: B 547 ASN cc_start: 0.3248 (t0) cc_final: 0.2478 (m-40) REVERT: C 188 GLN cc_start: 0.4176 (tt0) cc_final: 0.2723 (tt0) REVERT: C 194 GLN cc_start: 0.5313 (mt0) cc_final: 0.4645 (mm-40) REVERT: C 252 TYR cc_start: 0.4338 (OUTLIER) cc_final: 0.4135 (t80) REVERT: D 188 GLN cc_start: 0.4043 (tt0) cc_final: 0.3561 (tt0) REVERT: D 194 GLN cc_start: 0.5473 (mt0) cc_final: 0.5059 (mp10) REVERT: D 252 TYR cc_start: 0.4920 (OUTLIER) cc_final: 0.4506 (t80) REVERT: D 315 ARG cc_start: 0.3637 (mtt90) cc_final: 0.2838 (mtm180) REVERT: D 356 MET cc_start: 0.2407 (ptt) cc_final: 0.1083 (mpm) REVERT: D 585 MET cc_start: 0.2635 (mmt) cc_final: 0.2352 (tpp) REVERT: E 110 ARG cc_start: 0.4012 (mtt180) cc_final: 0.2702 (ppp-140) REVERT: E 122 LYS cc_start: 0.4052 (ttmt) cc_final: 0.3465 (ptpt) REVERT: E 308 ARG cc_start: 0.1481 (OUTLIER) cc_final: 0.0472 (mpp-170) REVERT: E 498 ARG cc_start: 0.4348 (mmm-85) cc_final: 0.4002 (tmm160) REVERT: E 505 ASP cc_start: 0.5024 (m-30) cc_final: 0.4414 (p0) REVERT: F 173 GLU cc_start: 0.6162 (mt-10) cc_final: 0.5945 (pp20) REVERT: F 360 ARG cc_start: 0.5319 (mmm-85) cc_final: 0.4143 (tmt170) REVERT: F 622 GLU cc_start: 0.2106 (tt0) cc_final: 0.1572 (mm-30) REVERT: F 631 GLU cc_start: 0.5390 (mm-30) cc_final: 0.5022 (mt-10) outliers start: 39 outliers final: 4 residues processed: 347 average time/residue: 1.2672 time to fit residues: 523.8773 Evaluate side-chains 189 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 252 TYR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain F residue 305 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.3980 chunk 286 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 296 optimal weight: 0.0270 chunk 114 optimal weight: 1.9990 chunk 180 optimal weight: 0.1980 chunk 220 optimal weight: 0.0970 chunk 343 optimal weight: 40.0000 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN B 366 HIS B 416 GLN C 225 GLN C 416 GLN D 225 GLN D 416 GLN D 421 HIS E 416 GLN ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 HIS F 343 ASN F 493 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2449 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 30840 Z= 0.225 Angle : 0.653 10.859 41868 Z= 0.342 Chirality : 0.047 0.247 4740 Planarity : 0.006 0.156 5448 Dihedral : 5.235 53.574 4161 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.71 % Favored : 91.94 % Rotamer: Outliers : 4.66 % Allowed : 28.31 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3774 helix: 0.79 (0.16), residues: 1180 sheet: 0.91 (0.23), residues: 648 loop : -2.16 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 129 HIS 0.013 0.001 HIS D 366 PHE 0.016 0.001 PHE A 179 TYR 0.030 0.002 TYR E 281 ARG 0.007 0.001 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 236 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.2803 (mmm) cc_final: 0.1120 (mpm) REVERT: A 194 GLN cc_start: 0.3923 (OUTLIER) cc_final: 0.3648 (mp10) REVERT: A 238 PHE cc_start: 0.6418 (t80) cc_final: 0.5948 (t80) REVERT: A 297 ILE cc_start: 0.3596 (OUTLIER) cc_final: 0.3049 (tp) REVERT: A 365 MET cc_start: 0.6277 (ttt) cc_final: 0.5502 (tpt) REVERT: A 482 GLU cc_start: 0.4501 (tp30) cc_final: 0.3805 (mm-30) REVERT: A 505 ASP cc_start: 0.5325 (t0) cc_final: 0.5023 (t0) REVERT: A 585 MET cc_start: 0.3461 (mmp) cc_final: 0.3181 (mmt) REVERT: A 603 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7464 (tpt-90) REVERT: A 631 GLU cc_start: 0.4534 (mm-30) cc_final: 0.3472 (mt-10) REVERT: B 46 PHE cc_start: 0.0250 (OUTLIER) cc_final: -0.0994 (m-80) REVERT: B 102 VAL cc_start: 0.3000 (OUTLIER) cc_final: 0.2338 (t) REVERT: B 365 MET cc_start: 0.0269 (OUTLIER) cc_final: -0.0605 (mmm) REVERT: B 498 ARG cc_start: 0.5291 (ptm-80) cc_final: 0.4337 (tmm160) REVERT: B 505 ASP cc_start: 0.5654 (OUTLIER) cc_final: 0.5381 (t70) REVERT: B 585 MET cc_start: 0.3709 (tpp) cc_final: 0.3371 (tpt) REVERT: C 194 GLN cc_start: 0.6086 (mt0) cc_final: 0.5608 (mm110) REVERT: C 252 TYR cc_start: 0.4349 (OUTLIER) cc_final: 0.4045 (t80) REVERT: C 356 MET cc_start: 0.3952 (OUTLIER) cc_final: 0.0006 (mpm) REVERT: C 480 GLU cc_start: 0.6178 (tt0) cc_final: 0.5851 (tp30) REVERT: C 592 PHE cc_start: 0.4364 (m-80) cc_final: 0.4132 (m-10) REVERT: D 194 GLN cc_start: 0.6201 (mt0) cc_final: 0.5777 (mm110) REVERT: D 227 LEU cc_start: 0.1922 (OUTLIER) cc_final: 0.1282 (tp) REVERT: D 252 TYR cc_start: 0.4833 (OUTLIER) cc_final: 0.4392 (t80) REVERT: D 480 GLU cc_start: 0.5698 (tt0) cc_final: 0.5369 (pt0) REVERT: D 585 MET cc_start: 0.2826 (mmt) cc_final: 0.2474 (ttt) REVERT: E 102 VAL cc_start: 0.0949 (OUTLIER) cc_final: 0.0068 (t) REVERT: E 122 LYS cc_start: 0.4174 (ttmt) cc_final: 0.3252 (mmtt) REVERT: E 240 LEU cc_start: 0.5115 (OUTLIER) cc_final: 0.4681 (tm) REVERT: E 244 LYS cc_start: 0.3989 (ptpt) cc_final: 0.3401 (tptp) REVERT: E 434 ASN cc_start: 0.1918 (p0) cc_final: 0.1542 (m-40) REVERT: E 475 LEU cc_start: 0.2084 (OUTLIER) cc_final: 0.1458 (tp) REVERT: E 498 ARG cc_start: 0.4430 (mmm-85) cc_final: 0.4118 (ttp-110) REVERT: E 505 ASP cc_start: 0.5219 (m-30) cc_final: 0.4721 (p0) REVERT: E 591 VAL cc_start: 0.1200 (OUTLIER) cc_final: 0.0584 (t) REVERT: E 616 TYR cc_start: 0.3823 (p90) cc_final: 0.3508 (p90) REVERT: F 11 ARG cc_start: 0.1627 (OUTLIER) cc_final: -0.1065 (mmp80) REVERT: F 170 THR cc_start: 0.3187 (OUTLIER) cc_final: 0.2881 (p) REVERT: F 187 MET cc_start: 0.2883 (mmm) cc_final: 0.0993 (ptp) REVERT: F 194 GLN cc_start: 0.3647 (OUTLIER) cc_final: 0.3225 (mp10) REVERT: F 238 PHE cc_start: 0.4511 (t80) cc_final: 0.4095 (t80) REVERT: F 360 ARG cc_start: 0.5583 (mmm-85) cc_final: 0.4215 (tmt170) REVERT: F 608 LYS cc_start: 0.3899 (tttt) cc_final: 0.3461 (mppt) REVERT: F 622 GLU cc_start: 0.1898 (tt0) cc_final: 0.1649 (mm-30) outliers start: 153 outliers final: 38 residues processed: 356 average time/residue: 1.1352 time to fit residues: 493.1710 Evaluate side-chains 236 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 181 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 TYR Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 585 MET Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 343 optimal weight: 0.0270 chunk 371 optimal weight: 8.9990 chunk 306 optimal weight: 0.7980 chunk 341 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 172 ASN A 175 HIS A 225 GLN A 233 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN B 37 GLN B 57 ASN B 421 HIS B 499 GLN B 538 ASN B 547 ASN C 305 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS D 484 ASN E 37 GLN E 421 HIS E 459 HIS F 175 HIS F 194 GLN F 343 ASN F 536 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4916 moved from start: 0.8371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.259 30840 Z= 0.444 Angle : 1.025 24.914 41868 Z= 0.534 Chirality : 0.060 0.619 4740 Planarity : 0.008 0.145 5448 Dihedral : 6.206 53.360 4142 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.14 % Favored : 90.46 % Rotamer: Outliers : 7.62 % Allowed : 25.53 % Favored : 66.85 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.13), residues: 3774 helix: -0.69 (0.14), residues: 1144 sheet: 0.26 (0.22), residues: 634 loop : -2.56 (0.12), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP E 440 HIS 0.020 0.002 HIS D 366 PHE 0.035 0.003 PHE E 154 TYR 0.049 0.003 TYR C 77 ARG 0.021 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 310 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 MET cc_start: 0.5845 (ttt) cc_final: 0.5081 (ttt) REVERT: A 482 GLU cc_start: 0.6063 (tp30) cc_final: 0.5829 (mm-30) REVERT: A 631 GLU cc_start: 0.5073 (mm-30) cc_final: 0.4080 (mt-10) REVERT: B 184 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6311 (tt0) REVERT: B 210 ASP cc_start: 0.2167 (m-30) cc_final: 0.1934 (m-30) REVERT: B 411 ASN cc_start: 0.2771 (OUTLIER) cc_final: 0.1587 (t0) REVERT: B 464 ILE cc_start: 0.3561 (OUTLIER) cc_final: 0.3325 (tt) REVERT: B 482 GLU cc_start: 0.5981 (tt0) cc_final: 0.5628 (tt0) REVERT: B 505 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6315 (m-30) REVERT: B 604 GLU cc_start: 0.5551 (mt-10) cc_final: 0.5220 (tt0) REVERT: C 24 ASN cc_start: -0.1010 (OUTLIER) cc_final: -0.1251 (t0) REVERT: C 37 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6628 (mm-40) REVERT: C 87 GLU cc_start: 0.6290 (tp30) cc_final: 0.5973 (tp30) REVERT: C 218 ASP cc_start: 0.5639 (m-30) cc_final: 0.5157 (m-30) REVERT: C 449 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6269 (tt0) REVERT: C 476 GLU cc_start: 0.6039 (mt-10) cc_final: 0.5817 (mt-10) REVERT: C 532 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6650 (mm) REVERT: C 556 GLU cc_start: 0.7183 (pt0) cc_final: 0.6536 (pp20) REVERT: C 559 GLU cc_start: 0.6790 (tt0) cc_final: 0.6240 (tm-30) REVERT: C 585 MET cc_start: 0.1876 (tpp) cc_final: 0.1569 (ppp) REVERT: C 604 GLU cc_start: 0.4287 (mt-10) cc_final: 0.4071 (tp30) REVERT: D 105 ILE cc_start: 0.3050 (OUTLIER) cc_final: 0.2249 (mp) REVERT: D 218 ASP cc_start: 0.5768 (m-30) cc_final: 0.5228 (m-30) REVERT: D 222 LYS cc_start: 0.5907 (OUTLIER) cc_final: 0.5663 (mtpp) REVERT: D 449 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6143 (tt0) REVERT: D 476 GLU cc_start: 0.6120 (mt-10) cc_final: 0.5849 (mt-10) REVERT: D 480 GLU cc_start: 0.7390 (tt0) cc_final: 0.6635 (mp0) REVERT: D 556 GLU cc_start: 0.7180 (pt0) cc_final: 0.6562 (pp20) REVERT: D 604 GLU cc_start: 0.4989 (mt-10) cc_final: 0.4586 (tp30) REVERT: D 610 LYS cc_start: 0.7515 (mtpt) cc_final: 0.7288 (mttm) REVERT: E 122 LYS cc_start: 0.4236 (ttmt) cc_final: 0.3782 (tppt) REVERT: E 302 ILE cc_start: 0.1826 (OUTLIER) cc_final: 0.1201 (mp) REVERT: E 471 THR cc_start: 0.4546 (OUTLIER) cc_final: 0.4296 (p) REVERT: E 483 LYS cc_start: 0.6740 (tttm) cc_final: 0.5924 (mmmt) REVERT: E 505 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.5500 (t0) REVERT: E 552 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7235 (tm) REVERT: E 604 GLU cc_start: 0.5036 (mt-10) cc_final: 0.4738 (tt0) REVERT: F 64 ASP cc_start: 0.3806 (OUTLIER) cc_final: 0.3254 (t0) REVERT: F 129 TRP cc_start: 0.2339 (t60) cc_final: 0.1991 (t60) REVERT: F 359 ILE cc_start: 0.5989 (mp) cc_final: 0.5758 (mm) REVERT: F 360 ARG cc_start: 0.5612 (mmm-85) cc_final: 0.4330 (tmt170) REVERT: F 365 MET cc_start: 0.4431 (mmp) cc_final: 0.4210 (tpt) REVERT: F 374 LEU cc_start: 0.3279 (OUTLIER) cc_final: 0.2221 (tp) REVERT: F 482 GLU cc_start: 0.5855 (tp30) cc_final: 0.5413 (tp30) REVERT: F 608 LYS cc_start: 0.4343 (tttt) cc_final: 0.3893 (mppt) outliers start: 250 outliers final: 52 residues processed: 515 average time/residue: 1.2479 time to fit residues: 766.5134 Evaluate side-chains 256 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 187 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 389 ARG Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 20.0000 chunk 258 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 164 optimal weight: 0.0060 chunk 230 optimal weight: 2.9990 chunk 345 optimal weight: 0.6980 chunk 365 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 327 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 411 ASN A 626 GLN B 32 ASN B 37 GLN B 57 ASN B 117 HIS C 57 ASN C 172 ASN C 188 GLN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN C 547 ASN D 37 GLN D 172 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 HIS D 434 ASN D 547 ASN E 411 ASN E 538 ASN F 146 GLN F 208 HIS F 451 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.9617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 30840 Z= 0.271 Angle : 0.717 15.529 41868 Z= 0.373 Chirality : 0.051 0.363 4740 Planarity : 0.006 0.147 5448 Dihedral : 5.147 52.368 4138 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.02 % Favored : 92.63 % Rotamer: Outliers : 4.30 % Allowed : 29.13 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3774 helix: 0.22 (0.15), residues: 1154 sheet: 0.42 (0.22), residues: 634 loop : -2.45 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 131 HIS 0.015 0.002 HIS D 366 PHE 0.033 0.002 PHE B 213 TYR 0.025 0.002 TYR E 281 ARG 0.014 0.001 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 241 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ILE cc_start: 0.3550 (OUTLIER) cc_final: 0.2911 (tp) REVERT: A 356 MET cc_start: 0.1752 (tpp) cc_final: 0.0877 (tmt) REVERT: A 429 ILE cc_start: 0.4162 (OUTLIER) cc_final: 0.3734 (mm) REVERT: A 537 TYR cc_start: 0.4349 (t80) cc_final: 0.3401 (t80) REVERT: B 193 LYS cc_start: 0.7546 (pttp) cc_final: 0.7265 (pttp) REVERT: B 204 ASP cc_start: 0.5794 (p0) cc_final: 0.5552 (p0) REVERT: B 356 MET cc_start: -0.0029 (mmp) cc_final: -0.0296 (mmt) REVERT: B 483 LYS cc_start: 0.6706 (tttm) cc_final: 0.5790 (tptt) REVERT: B 497 ILE cc_start: 0.5592 (mm) cc_final: 0.5026 (mm) REVERT: B 505 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.6169 (m-30) REVERT: B 604 GLU cc_start: 0.5861 (mt-10) cc_final: 0.5495 (tt0) REVERT: C 559 GLU cc_start: 0.7128 (tt0) cc_final: 0.5660 (mp0) REVERT: C 579 ASP cc_start: 0.6799 (p0) cc_final: 0.6593 (m-30) REVERT: C 585 MET cc_start: 0.1917 (tpp) cc_final: 0.1555 (ppp) REVERT: D 218 ASP cc_start: 0.5890 (m-30) cc_final: 0.5355 (m-30) REVERT: D 240 LEU cc_start: 0.4740 (OUTLIER) cc_final: 0.4529 (mm) REVERT: D 449 GLU cc_start: 0.6807 (tt0) cc_final: 0.6370 (tt0) REVERT: D 480 GLU cc_start: 0.7491 (tt0) cc_final: 0.6620 (mp0) REVERT: D 498 ARG cc_start: 0.5482 (mmm-85) cc_final: 0.4751 (mpp-170) REVERT: D 509 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.4900 (mpp) REVERT: D 590 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6317 (m-30) REVERT: D 604 GLU cc_start: 0.6033 (mt-10) cc_final: 0.5477 (mm-30) REVERT: E 193 LYS cc_start: 0.7767 (pttp) cc_final: 0.7421 (pttm) REVERT: E 302 ILE cc_start: 0.1914 (OUTLIER) cc_final: 0.1259 (mp) REVERT: E 483 LYS cc_start: 0.6526 (tttm) cc_final: 0.5654 (mmmt) REVERT: E 505 ASP cc_start: 0.6375 (m-30) cc_final: 0.5935 (m-30) REVERT: E 567 MET cc_start: 0.1910 (ptm) cc_final: 0.1464 (ptm) REVERT: E 594 ASP cc_start: 0.7376 (m-30) cc_final: 0.7160 (m-30) REVERT: E 604 GLU cc_start: 0.5649 (mt-10) cc_final: 0.5287 (tt0) REVERT: F 204 ASP cc_start: 0.4652 (t0) cc_final: 0.4444 (t70) REVERT: F 360 ARG cc_start: 0.5805 (mmm-85) cc_final: 0.4469 (mtt180) REVERT: F 440 TRP cc_start: 0.2440 (p-90) cc_final: 0.1732 (p90) REVERT: F 458 MET cc_start: 0.4611 (pmt) cc_final: 0.4378 (ptt) REVERT: F 482 GLU cc_start: 0.6238 (tp30) cc_final: 0.5897 (tp30) REVERT: F 536 HIS cc_start: 0.4839 (t70) cc_final: 0.4600 (t70) REVERT: F 568 PHE cc_start: 0.5173 (t80) cc_final: 0.4961 (t80) outliers start: 141 outliers final: 47 residues processed: 363 average time/residue: 1.2594 time to fit residues: 549.2106 Evaluate side-chains 233 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 179 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 593 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 0.6980 chunk 327 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN A 408 HIS A 411 ASN B 32 ASN B 57 ASN B 194 GLN B 195 GLN B 420 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN C 233 GLN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 HIS D 626 GLN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS F 408 HIS F 536 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 1.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 30840 Z= 0.492 Angle : 1.024 23.677 41868 Z= 0.539 Chirality : 0.061 0.402 4740 Planarity : 0.008 0.135 5448 Dihedral : 6.061 51.804 4138 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.70 % Favored : 89.88 % Rotamer: Outliers : 5.85 % Allowed : 27.12 % Favored : 67.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.13), residues: 3774 helix: -0.38 (0.14), residues: 1128 sheet: -0.20 (0.22), residues: 616 loop : -2.84 (0.12), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 182 HIS 0.012 0.002 HIS F 408 PHE 0.031 0.004 PHE D 23 TYR 0.139 0.003 TYR C 281 ARG 0.014 0.001 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 285 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.1594 (tpp) cc_final: 0.0866 (ptm) REVERT: A 449 GLU cc_start: 0.5472 (mm-30) cc_final: 0.5098 (mt-10) REVERT: A 451 ASN cc_start: 0.5185 (m-40) cc_final: 0.4927 (p0) REVERT: A 509 MET cc_start: 0.6054 (tpt) cc_final: 0.5327 (ttm) REVERT: B 98 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6466 (ptpp) REVERT: B 183 ASP cc_start: 0.5894 (m-30) cc_final: 0.5634 (m-30) REVERT: B 302 ILE cc_start: 0.3133 (OUTLIER) cc_final: 0.2787 (mt) REVERT: B 356 MET cc_start: 0.1213 (mmp) cc_final: 0.0770 (mmt) REVERT: B 449 GLU cc_start: 0.5342 (mt-10) cc_final: 0.5133 (mm-30) REVERT: B 461 LYS cc_start: 0.6726 (mmtp) cc_final: 0.5429 (mtmp) REVERT: B 464 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6189 (tp) REVERT: B 466 GLU cc_start: 0.6386 (mm-30) cc_final: 0.5561 (pm20) REVERT: B 476 GLU cc_start: 0.5626 (pt0) cc_final: 0.5395 (mt-10) REVERT: B 483 LYS cc_start: 0.7038 (tttm) cc_final: 0.6147 (tptt) REVERT: B 505 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5648 (m-30) REVERT: B 530 GLU cc_start: 0.7724 (tt0) cc_final: 0.7268 (tp30) REVERT: B 594 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.6181 (p0) REVERT: B 604 GLU cc_start: 0.6342 (mt-10) cc_final: 0.5700 (tm-30) REVERT: B 614 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.5548 (mp0) REVERT: B 634 THR cc_start: 0.6834 (m) cc_final: 0.6367 (p) REVERT: C 26 LYS cc_start: 0.7820 (mtmm) cc_final: 0.6646 (mmmt) REVERT: C 184 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: C 194 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7429 (mm-40) REVERT: C 217 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4246 (mttt) REVERT: C 222 LYS cc_start: 0.6417 (OUTLIER) cc_final: 0.6160 (mmmt) REVERT: C 480 GLU cc_start: 0.7376 (tt0) cc_final: 0.6361 (mp0) REVERT: C 483 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6967 (mmtp) REVERT: C 498 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6244 (mtp180) REVERT: C 535 ARG cc_start: 0.7072 (mtm-85) cc_final: 0.6804 (ptm-80) REVERT: C 556 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: C 585 MET cc_start: 0.2536 (tpp) cc_final: 0.1951 (tpp) REVERT: C 590 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6580 (m-30) REVERT: C 604 GLU cc_start: 0.5770 (mt-10) cc_final: 0.5004 (mm-30) REVERT: C 610 LYS cc_start: 0.7331 (mtpt) cc_final: 0.6902 (mttm) REVERT: C 617 GLU cc_start: 0.7534 (tt0) cc_final: 0.7256 (tp30) REVERT: D 79 GLU cc_start: 0.5702 (OUTLIER) cc_final: 0.3700 (tm-30) REVERT: D 184 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: D 194 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7419 (mm-40) REVERT: D 252 TYR cc_start: 0.4430 (OUTLIER) cc_final: 0.4176 (t80) REVERT: D 449 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6843 (tt0) REVERT: D 498 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6265 (mtp180) REVERT: D 535 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6813 (ptm-80) REVERT: D 556 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7245 (pp20) REVERT: D 558 ASP cc_start: 0.6628 (p0) cc_final: 0.6379 (p0) REVERT: D 560 ASP cc_start: 0.6161 (m-30) cc_final: 0.5934 (m-30) REVERT: D 582 GLU cc_start: 0.6970 (mp0) cc_final: 0.6628 (tm-30) REVERT: D 590 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6424 (m-30) REVERT: D 604 GLU cc_start: 0.5721 (mt-10) cc_final: 0.4993 (mm-30) REVERT: D 610 LYS cc_start: 0.7190 (mtpt) cc_final: 0.6792 (mttm) REVERT: E 93 MET cc_start: 0.2069 (mmp) cc_final: 0.1850 (mmm) REVERT: E 97 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5870 (pp) REVERT: E 356 MET cc_start: 0.0295 (OUTLIER) cc_final: -0.0363 (mtt) REVERT: E 431 ILE cc_start: 0.5746 (tt) cc_final: 0.5527 (tt) REVERT: E 483 LYS cc_start: 0.6859 (tttm) cc_final: 0.5997 (tptt) REVERT: E 505 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5696 (m-30) REVERT: E 584 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6686 (mp0) REVERT: E 604 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5499 (tp30) REVERT: E 619 GLU cc_start: 0.5914 (mm-30) cc_final: 0.5677 (tp30) REVERT: E 634 THR cc_start: 0.6892 (m) cc_final: 0.6411 (p) REVERT: F 44 PHE cc_start: 0.5230 (OUTLIER) cc_final: 0.4608 (m-10) REVERT: F 194 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6519 (mm-40) REVERT: F 199 ILE cc_start: 0.5497 (OUTLIER) cc_final: 0.5191 (tp) REVERT: F 307 TYR cc_start: 0.3489 (m-80) cc_final: 0.3087 (m-80) REVERT: F 509 MET cc_start: 0.6098 (tpt) cc_final: 0.5470 (ttm) REVERT: F 556 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.3974 (mp0) REVERT: F 626 GLN cc_start: 0.6107 (tp-100) cc_final: 0.5576 (mp10) outliers start: 192 outliers final: 61 residues processed: 432 average time/residue: 1.4189 time to fit residues: 715.3829 Evaluate side-chains 300 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 209 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 23 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 365 optimal weight: 4.9990 chunk 303 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN D 225 GLN D 366 HIS D 484 ASN E 27 GLN ** E 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 1.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 30840 Z= 0.262 Angle : 0.697 10.953 41868 Z= 0.368 Chirality : 0.050 0.279 4740 Planarity : 0.006 0.129 5448 Dihedral : 5.191 52.772 4138 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.34 % Favored : 92.34 % Rotamer: Outliers : 4.30 % Allowed : 29.13 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 3774 helix: 0.41 (0.15), residues: 1146 sheet: 0.03 (0.22), residues: 672 loop : -2.69 (0.12), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 440 HIS 0.009 0.001 HIS E 408 PHE 0.019 0.002 PHE B 478 TYR 0.026 0.002 TYR E 165 ARG 0.008 0.001 ARG E 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 211 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.4714 (mp) cc_final: 0.4461 (mp) REVERT: A 356 MET cc_start: 0.1861 (tpp) cc_final: 0.1315 (ptm) REVERT: A 371 GLU cc_start: 0.9464 (tt0) cc_final: 0.9179 (mt-10) REVERT: A 451 ASN cc_start: 0.5192 (m-40) cc_final: 0.4521 (p0) REVERT: A 509 MET cc_start: 0.5899 (tpt) cc_final: 0.5144 (mtp) REVERT: A 630 LYS cc_start: 0.7300 (mtpp) cc_final: 0.7034 (pttp) REVERT: B 183 ASP cc_start: 0.5910 (m-30) cc_final: 0.5664 (m-30) REVERT: B 302 ILE cc_start: 0.3140 (OUTLIER) cc_final: 0.2783 (mt) REVERT: B 356 MET cc_start: 0.1291 (mmp) cc_final: 0.0913 (mmt) REVERT: B 449 GLU cc_start: 0.6003 (mt-10) cc_final: 0.5769 (mp0) REVERT: B 461 LYS cc_start: 0.6813 (mmtp) cc_final: 0.5297 (ptpp) REVERT: B 464 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6112 (tp) REVERT: B 466 GLU cc_start: 0.6597 (mm-30) cc_final: 0.5646 (pm20) REVERT: B 476 GLU cc_start: 0.5727 (pt0) cc_final: 0.5469 (mt-10) REVERT: B 483 LYS cc_start: 0.7021 (tttm) cc_final: 0.6109 (tptt) REVERT: B 505 ASP cc_start: 0.6301 (m-30) cc_final: 0.5769 (m-30) REVERT: B 594 ASP cc_start: 0.6516 (OUTLIER) cc_final: 0.5979 (p0) REVERT: B 604 GLU cc_start: 0.6489 (mt-10) cc_final: 0.5720 (tm-30) REVERT: B 614 GLU cc_start: 0.6989 (tt0) cc_final: 0.5503 (mp0) REVERT: B 634 THR cc_start: 0.6815 (m) cc_final: 0.6377 (p) REVERT: C 187 MET cc_start: 0.8152 (mmt) cc_final: 0.7671 (tpp) REVERT: C 222 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.6002 (mmmt) REVERT: C 458 MET cc_start: 0.6481 (mtp) cc_final: 0.6252 (ptm) REVERT: C 480 GLU cc_start: 0.7438 (tt0) cc_final: 0.6434 (mp0) REVERT: C 498 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5827 (mtp180) REVERT: C 535 ARG cc_start: 0.6867 (mtm-85) cc_final: 0.6601 (ptm-80) REVERT: C 556 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7369 (pp20) REVERT: C 590 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6402 (m-30) REVERT: C 604 GLU cc_start: 0.6105 (mt-10) cc_final: 0.5229 (mm-30) REVERT: C 610 LYS cc_start: 0.7492 (mtpt) cc_final: 0.7016 (mttm) REVERT: C 631 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: D 483 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6929 (mmtp) REVERT: D 498 ARG cc_start: 0.6268 (mmm-85) cc_final: 0.5950 (mtp180) REVERT: D 535 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.6548 (ptm-80) REVERT: D 556 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: D 582 GLU cc_start: 0.7017 (mp0) cc_final: 0.6778 (mm-30) REVERT: D 590 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6314 (m-30) REVERT: D 604 GLU cc_start: 0.6058 (mt-10) cc_final: 0.5261 (mm-30) REVERT: D 610 LYS cc_start: 0.7427 (mtpt) cc_final: 0.6994 (mttm) REVERT: E 97 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.6127 (pp) REVERT: E 184 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6840 (mt-10) REVERT: E 306 ASP cc_start: 0.6812 (m-30) cc_final: 0.6555 (m-30) REVERT: E 356 MET cc_start: 0.0790 (mpp) cc_final: 0.0379 (mtt) REVERT: E 483 LYS cc_start: 0.6893 (tttm) cc_final: 0.6017 (tptt) REVERT: E 501 GLN cc_start: 0.5597 (mt0) cc_final: 0.5365 (mt0) REVERT: E 505 ASP cc_start: 0.6256 (m-30) cc_final: 0.5740 (m-30) REVERT: E 604 GLU cc_start: 0.6376 (mt-10) cc_final: 0.5642 (tp30) REVERT: E 634 THR cc_start: 0.6872 (m) cc_final: 0.6457 (p) REVERT: F 44 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4399 (m-10) REVERT: F 119 ARG cc_start: 0.5202 (ttp80) cc_final: 0.4607 (ttp-170) REVERT: F 199 ILE cc_start: 0.5565 (OUTLIER) cc_final: 0.5317 (tp) REVERT: F 421 HIS cc_start: 0.6141 (OUTLIER) cc_final: 0.4105 (t70) REVERT: F 449 GLU cc_start: 0.4629 (mm-30) cc_final: 0.4018 (mt-10) REVERT: F 509 MET cc_start: 0.5932 (tpt) cc_final: 0.5402 (mtp) outliers start: 141 outliers final: 57 residues processed: 325 average time/residue: 1.3336 time to fit residues: 511.7459 Evaluate side-chains 253 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 180 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 GLN Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 484 ASN Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 572 SER Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 267 optimal weight: 0.0870 chunk 206 optimal weight: 0.5980 chunk 307 optimal weight: 8.9990 chunk 204 optimal weight: 0.3980 chunk 364 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 146 GLN A 172 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 1.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 30840 Z= 0.172 Angle : 0.580 8.655 41868 Z= 0.307 Chirality : 0.046 0.201 4740 Planarity : 0.005 0.124 5448 Dihedral : 4.716 53.643 4138 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.37 % Favored : 92.32 % Rotamer: Outliers : 2.56 % Allowed : 31.11 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3774 helix: 0.84 (0.16), residues: 1148 sheet: 0.25 (0.22), residues: 680 loop : -2.50 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 129 HIS 0.051 0.001 HIS D 366 PHE 0.019 0.001 PHE D 23 TYR 0.024 0.001 TYR E 281 ARG 0.019 0.000 ARG E 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 202 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.1875 (tpp) cc_final: 0.1442 (ptm) REVERT: A 371 GLU cc_start: 0.9473 (tt0) cc_final: 0.9209 (mt-10) REVERT: A 509 MET cc_start: 0.5928 (tpt) cc_final: 0.5213 (mtp) REVERT: A 530 GLU cc_start: 0.7270 (mp0) cc_final: 0.6662 (mt-10) REVERT: A 603 ARG cc_start: 0.7980 (tpp80) cc_final: 0.7596 (tpp80) REVERT: A 630 LYS cc_start: 0.7333 (mtpp) cc_final: 0.7064 (pttp) REVERT: B 183 ASP cc_start: 0.5603 (m-30) cc_final: 0.5350 (m-30) REVERT: B 194 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.6798 (mm-40) REVERT: B 302 ILE cc_start: 0.3172 (OUTLIER) cc_final: 0.2814 (mt) REVERT: B 356 MET cc_start: 0.1590 (mmp) cc_final: 0.1249 (mmt) REVERT: B 449 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5872 (mt-10) REVERT: B 461 LYS cc_start: 0.6926 (mmtp) cc_final: 0.5494 (mtmt) REVERT: B 464 ILE cc_start: 0.6647 (OUTLIER) cc_final: 0.6085 (tp) REVERT: B 466 GLU cc_start: 0.6742 (mm-30) cc_final: 0.5746 (pm20) REVERT: B 476 GLU cc_start: 0.5697 (pt0) cc_final: 0.5471 (mt-10) REVERT: B 483 LYS cc_start: 0.6901 (tttm) cc_final: 0.5900 (tptt) REVERT: B 505 ASP cc_start: 0.6345 (m-30) cc_final: 0.5778 (m-30) REVERT: B 594 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.5973 (p0) REVERT: B 604 GLU cc_start: 0.6481 (mt-10) cc_final: 0.5718 (mm-30) REVERT: B 614 GLU cc_start: 0.6892 (tt0) cc_final: 0.5358 (mp0) REVERT: B 634 THR cc_start: 0.6625 (m) cc_final: 0.6188 (p) REVERT: C 187 MET cc_start: 0.8080 (mmt) cc_final: 0.7769 (tpp) REVERT: C 194 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6953 (mm-40) REVERT: C 480 GLU cc_start: 0.7421 (tt0) cc_final: 0.6426 (mp0) REVERT: C 498 ARG cc_start: 0.5894 (mmm-85) cc_final: 0.5668 (mtp180) REVERT: C 535 ARG cc_start: 0.6713 (mtm-85) cc_final: 0.6477 (ptm-80) REVERT: C 590 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6369 (m-30) REVERT: C 601 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.6054 (mt0) REVERT: C 604 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5220 (mm-30) REVERT: C 610 LYS cc_start: 0.7446 (mtpt) cc_final: 0.6969 (mttm) REVERT: C 631 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: D 187 MET cc_start: 0.8121 (mmt) cc_final: 0.7825 (tpp) REVERT: D 194 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.6967 (mm-40) REVERT: D 497 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6996 (mm) REVERT: D 498 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5449 (mmt-90) REVERT: D 535 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.6413 (ptm-80) REVERT: D 582 GLU cc_start: 0.6965 (mp0) cc_final: 0.6754 (mm-30) REVERT: D 590 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6263 (m-30) REVERT: D 604 GLU cc_start: 0.6087 (mt-10) cc_final: 0.5231 (mm-30) REVERT: D 610 LYS cc_start: 0.7275 (mtpt) cc_final: 0.6833 (mttm) REVERT: E 119 ARG cc_start: 0.6154 (tmm-80) cc_final: 0.5939 (tmt170) REVERT: E 306 ASP cc_start: 0.6836 (m-30) cc_final: 0.6539 (m-30) REVERT: E 365 MET cc_start: 0.2174 (mmt) cc_final: 0.1210 (mpt) REVERT: E 483 LYS cc_start: 0.6846 (tttm) cc_final: 0.5867 (tptt) REVERT: E 501 GLN cc_start: 0.5597 (mt0) cc_final: 0.5359 (mt0) REVERT: E 505 ASP cc_start: 0.6294 (m-30) cc_final: 0.5757 (m-30) REVERT: E 530 GLU cc_start: 0.7787 (tt0) cc_final: 0.7352 (tm-30) REVERT: E 604 GLU cc_start: 0.6456 (mt-10) cc_final: 0.5666 (tm-30) REVERT: E 634 THR cc_start: 0.6837 (m) cc_final: 0.6436 (p) REVERT: F 44 PHE cc_start: 0.5143 (OUTLIER) cc_final: 0.4348 (m-10) REVERT: F 119 ARG cc_start: 0.5152 (ttp80) cc_final: 0.4596 (ttp-170) REVERT: F 199 ILE cc_start: 0.5494 (OUTLIER) cc_final: 0.5263 (tp) REVERT: F 449 GLU cc_start: 0.4577 (mm-30) cc_final: 0.4017 (mt-10) REVERT: F 483 LYS cc_start: 0.7695 (mmtp) cc_final: 0.6661 (ptmt) REVERT: F 509 MET cc_start: 0.5802 (tpt) cc_final: 0.5321 (mtp) outliers start: 84 outliers final: 34 residues processed: 270 average time/residue: 1.3554 time to fit residues: 433.6685 Evaluate side-chains 236 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 GLN Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 585 MET Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 109 optimal weight: 0.0010 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 248 optimal weight: 0.2980 chunk 180 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN B 151 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN D 225 GLN D 366 HIS ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS F 451 ASN F 501 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 1.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 30840 Z= 0.173 Angle : 0.580 11.479 41868 Z= 0.305 Chirality : 0.046 0.190 4740 Planarity : 0.005 0.120 5448 Dihedral : 4.518 53.825 4138 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.94 % Favored : 92.69 % Rotamer: Outliers : 2.62 % Allowed : 30.93 % Favored : 66.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3774 helix: 1.03 (0.16), residues: 1154 sheet: 0.38 (0.22), residues: 684 loop : -2.42 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 129 HIS 0.006 0.001 HIS D 366 PHE 0.016 0.001 PHE F 42 TYR 0.023 0.001 TYR E 281 ARG 0.006 0.000 ARG B 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 189 time to evaluate : 4.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.2159 (OUTLIER) cc_final: 0.1776 (tp) REVERT: A 102 VAL cc_start: 0.4216 (OUTLIER) cc_final: 0.3960 (t) REVERT: A 315 ARG cc_start: 0.4442 (mmt90) cc_final: 0.3881 (mmm160) REVERT: A 356 MET cc_start: 0.1902 (tpp) cc_final: 0.1547 (ptm) REVERT: A 371 GLU cc_start: 0.9480 (tt0) cc_final: 0.9247 (mt-10) REVERT: A 509 MET cc_start: 0.5875 (tpt) cc_final: 0.5180 (mtp) REVERT: A 530 GLU cc_start: 0.7252 (mp0) cc_final: 0.6743 (mt-10) REVERT: A 603 ARG cc_start: 0.7962 (tpp80) cc_final: 0.7602 (tpp80) REVERT: A 630 LYS cc_start: 0.7386 (mtpp) cc_final: 0.7114 (pttp) REVERT: B 302 ILE cc_start: 0.3195 (OUTLIER) cc_final: 0.2855 (mt) REVERT: B 356 MET cc_start: 0.1888 (mmp) cc_final: 0.1566 (mmt) REVERT: B 449 GLU cc_start: 0.6241 (mt-10) cc_final: 0.5986 (mt-10) REVERT: B 461 LYS cc_start: 0.7104 (mmtp) cc_final: 0.5883 (mppt) REVERT: B 466 GLU cc_start: 0.6825 (mm-30) cc_final: 0.5783 (pm20) REVERT: B 476 GLU cc_start: 0.5715 (pt0) cc_final: 0.5485 (mt-10) REVERT: B 483 LYS cc_start: 0.6920 (tttm) cc_final: 0.5931 (tptt) REVERT: B 505 ASP cc_start: 0.6359 (m-30) cc_final: 0.5806 (m-30) REVERT: B 594 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.6003 (p0) REVERT: B 604 GLU cc_start: 0.6461 (mt-10) cc_final: 0.5668 (mm-30) REVERT: B 614 GLU cc_start: 0.6897 (tt0) cc_final: 0.5328 (mp0) REVERT: B 634 THR cc_start: 0.6593 (m) cc_final: 0.6170 (p) REVERT: C 187 MET cc_start: 0.8085 (mmt) cc_final: 0.7776 (tpp) REVERT: C 194 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7005 (mm-40) REVERT: C 480 GLU cc_start: 0.7406 (tt0) cc_final: 0.6385 (mp0) REVERT: C 556 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7335 (pp20) REVERT: C 590 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6359 (m-30) REVERT: C 601 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5957 (mt0) REVERT: C 604 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5241 (mm-30) REVERT: C 610 LYS cc_start: 0.7474 (mtpt) cc_final: 0.7167 (mtmm) REVERT: C 631 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: D 187 MET cc_start: 0.8074 (mmt) cc_final: 0.7785 (tpp) REVERT: D 497 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6990 (mm) REVERT: D 498 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5456 (mmt-90) REVERT: D 535 ARG cc_start: 0.6583 (mtm-85) cc_final: 0.6353 (ptm-80) REVERT: D 556 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7224 (pp20) REVERT: D 582 GLU cc_start: 0.6891 (mp0) cc_final: 0.6687 (mm-30) REVERT: D 590 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6283 (m-30) REVERT: D 604 GLU cc_start: 0.6107 (mt-10) cc_final: 0.5214 (mm-30) REVERT: D 610 LYS cc_start: 0.7358 (mtpt) cc_final: 0.6896 (mttm) REVERT: E 184 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: E 194 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7222 (mm-40) REVERT: E 306 ASP cc_start: 0.6958 (m-30) cc_final: 0.6738 (m-30) REVERT: E 483 LYS cc_start: 0.6855 (tttm) cc_final: 0.5908 (tptt) REVERT: E 501 GLN cc_start: 0.5717 (mt0) cc_final: 0.5488 (mt0) REVERT: E 505 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.5784 (m-30) REVERT: E 535 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5844 (pmm150) REVERT: E 594 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6244 (p0) REVERT: E 604 GLU cc_start: 0.6460 (mt-10) cc_final: 0.5688 (mm-30) REVERT: E 634 THR cc_start: 0.6690 (m) cc_final: 0.6309 (p) REVERT: F 44 PHE cc_start: 0.5193 (OUTLIER) cc_final: 0.4549 (m-80) REVERT: F 119 ARG cc_start: 0.5210 (ttp80) cc_final: 0.4658 (ttp80) REVERT: F 199 ILE cc_start: 0.5493 (OUTLIER) cc_final: 0.5276 (tp) REVERT: F 421 HIS cc_start: 0.6079 (OUTLIER) cc_final: 0.4157 (t70) REVERT: F 483 LYS cc_start: 0.7624 (mmtp) cc_final: 0.6600 (ptmt) REVERT: F 509 MET cc_start: 0.5738 (tpt) cc_final: 0.5315 (mtp) outliers start: 86 outliers final: 28 residues processed: 256 average time/residue: 1.5049 time to fit residues: 451.0478 Evaluate side-chains 228 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 179 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 GLN Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 535 ARG Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 3.9990 chunk 349 optimal weight: 20.0000 chunk 318 optimal weight: 0.9980 chunk 339 optimal weight: 9.9990 chunk 348 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN B 151 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN D 366 HIS E 411 ASN ** E 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 1.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 30840 Z= 0.289 Angle : 0.744 24.613 41868 Z= 0.387 Chirality : 0.051 0.309 4740 Planarity : 0.006 0.117 5448 Dihedral : 5.046 53.691 4138 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.85 % Favored : 90.83 % Rotamer: Outliers : 2.74 % Allowed : 31.02 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3774 helix: 0.75 (0.16), residues: 1148 sheet: 0.34 (0.22), residues: 688 loop : -2.46 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 440 HIS 0.010 0.001 HIS E 208 PHE 0.021 0.002 PHE E 568 TYR 0.033 0.002 TYR B 457 ARG 0.009 0.001 ARG E 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 193 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 VAL cc_start: 0.4433 (OUTLIER) cc_final: 0.4130 (t) REVERT: A 108 ILE cc_start: 0.4122 (OUTLIER) cc_final: 0.3238 (tp) REVERT: A 315 ARG cc_start: 0.4590 (mmt90) cc_final: 0.3978 (mmm160) REVERT: A 356 MET cc_start: 0.2187 (tpp) cc_final: 0.1807 (ptm) REVERT: A 371 GLU cc_start: 0.9501 (tt0) cc_final: 0.9263 (mt-10) REVERT: A 509 MET cc_start: 0.5951 (tpt) cc_final: 0.5408 (mtp) REVERT: A 525 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6920 (mp) REVERT: A 603 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7686 (tpp80) REVERT: A 630 LYS cc_start: 0.7465 (mtpp) cc_final: 0.7059 (pttm) REVERT: B 92 GLU cc_start: 0.6958 (tp30) cc_final: 0.6613 (tt0) REVERT: B 302 ILE cc_start: 0.3212 (OUTLIER) cc_final: 0.2857 (mt) REVERT: B 356 MET cc_start: 0.2286 (mmp) cc_final: 0.1777 (mmt) REVERT: B 449 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6545 (mt-10) REVERT: B 461 LYS cc_start: 0.6830 (mmtp) cc_final: 0.5784 (mtpt) REVERT: B 466 GLU cc_start: 0.6781 (mm-30) cc_final: 0.5681 (pm20) REVERT: B 476 GLU cc_start: 0.5684 (pt0) cc_final: 0.5418 (mt-10) REVERT: B 483 LYS cc_start: 0.7128 (tttm) cc_final: 0.6109 (tptt) REVERT: B 505 ASP cc_start: 0.6331 (m-30) cc_final: 0.5744 (m-30) REVERT: B 594 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.6113 (p0) REVERT: B 604 GLU cc_start: 0.6396 (mt-10) cc_final: 0.5608 (mm-30) REVERT: B 614 GLU cc_start: 0.6995 (tt0) cc_final: 0.5487 (mp0) REVERT: C 194 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7190 (mm-40) REVERT: C 222 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5980 (mmmt) REVERT: C 480 GLU cc_start: 0.7429 (tt0) cc_final: 0.6445 (mp0) REVERT: C 556 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7392 (pp20) REVERT: C 582 GLU cc_start: 0.7278 (pm20) cc_final: 0.6491 (tp30) REVERT: C 601 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.6178 (mt0) REVERT: C 604 GLU cc_start: 0.6155 (mt-10) cc_final: 0.5240 (mm-30) REVERT: C 610 LYS cc_start: 0.7477 (mtpt) cc_final: 0.7161 (mtmm) REVERT: C 631 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6232 (mp0) REVERT: D 497 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7047 (mm) REVERT: D 498 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5566 (mmt-90) REVERT: D 535 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6501 (ptm-80) REVERT: D 556 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7282 (pp20) REVERT: D 590 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6275 (m-30) REVERT: D 604 GLU cc_start: 0.6139 (mt-10) cc_final: 0.5259 (mm-30) REVERT: D 610 LYS cc_start: 0.7467 (mtpt) cc_final: 0.6994 (mttm) REVERT: E 306 ASP cc_start: 0.7475 (m-30) cc_final: 0.6894 (m-30) REVERT: E 461 LYS cc_start: 0.6854 (mmtp) cc_final: 0.5680 (mtpt) REVERT: E 483 LYS cc_start: 0.7047 (tttm) cc_final: 0.6076 (tptt) REVERT: E 501 GLN cc_start: 0.5793 (mt0) cc_final: 0.5508 (mt0) REVERT: E 505 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5762 (m-30) REVERT: E 530 GLU cc_start: 0.7827 (tt0) cc_final: 0.7226 (tm-30) REVERT: E 604 GLU cc_start: 0.6304 (mt-10) cc_final: 0.5573 (mm-30) REVERT: F 119 ARG cc_start: 0.5587 (ttp80) cc_final: 0.4930 (ttp-170) REVERT: F 199 ILE cc_start: 0.5611 (OUTLIER) cc_final: 0.5268 (tp) REVERT: F 483 LYS cc_start: 0.7621 (mmtp) cc_final: 0.6548 (ptmt) REVERT: F 509 MET cc_start: 0.5925 (tpt) cc_final: 0.5497 (mtp) REVERT: F 630 LYS cc_start: 0.7579 (tppt) cc_final: 0.7367 (pmtt) outliers start: 90 outliers final: 39 residues processed: 264 average time/residue: 1.5110 time to fit residues: 466.3713 Evaluate side-chains 234 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 178 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 GLN Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 chunk 359 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 249 optimal weight: 0.7980 chunk 376 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 146 GLN A 175 HIS ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN D 366 HIS ** E 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 1.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 30840 Z= 0.219 Angle : 0.635 18.978 41868 Z= 0.332 Chirality : 0.049 0.512 4740 Planarity : 0.005 0.114 5448 Dihedral : 4.735 54.359 4138 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.05 % Favored : 92.63 % Rotamer: Outliers : 1.98 % Allowed : 31.57 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3774 helix: 0.96 (0.16), residues: 1140 sheet: 0.27 (0.22), residues: 708 loop : -2.37 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 129 HIS 0.022 0.001 HIS D 366 PHE 0.020 0.002 PHE F 42 TYR 0.040 0.002 TYR B 457 ARG 0.011 0.000 ARG E 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 196 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 VAL cc_start: 0.4480 (OUTLIER) cc_final: 0.4150 (t) REVERT: A 108 ILE cc_start: 0.4691 (OUTLIER) cc_final: 0.3575 (tp) REVERT: A 315 ARG cc_start: 0.4516 (mmt90) cc_final: 0.3880 (mmm160) REVERT: A 356 MET cc_start: 0.2217 (tpp) cc_final: 0.1971 (ptm) REVERT: A 371 GLU cc_start: 0.9494 (tt0) cc_final: 0.9275 (mt-10) REVERT: A 509 MET cc_start: 0.5960 (tpt) cc_final: 0.5527 (mtp) REVERT: A 586 ILE cc_start: 0.6626 (tp) cc_final: 0.6221 (pp) REVERT: A 626 GLN cc_start: 0.6033 (tp-100) cc_final: 0.5388 (mp10) REVERT: B 92 GLU cc_start: 0.7075 (tp30) cc_final: 0.6817 (tt0) REVERT: B 302 ILE cc_start: 0.3130 (OUTLIER) cc_final: 0.2643 (mt) REVERT: B 356 MET cc_start: 0.2462 (mmp) cc_final: 0.1916 (mmt) REVERT: B 449 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6537 (mt-10) REVERT: B 461 LYS cc_start: 0.7035 (mmtp) cc_final: 0.5956 (mtpt) REVERT: B 466 GLU cc_start: 0.6965 (mm-30) cc_final: 0.5821 (pm20) REVERT: B 476 GLU cc_start: 0.5672 (pt0) cc_final: 0.5443 (mt-10) REVERT: B 483 LYS cc_start: 0.6949 (tttm) cc_final: 0.5919 (tptt) REVERT: B 505 ASP cc_start: 0.6401 (m-30) cc_final: 0.5802 (m-30) REVERT: B 594 ASP cc_start: 0.6559 (OUTLIER) cc_final: 0.6055 (p0) REVERT: B 604 GLU cc_start: 0.6374 (mt-10) cc_final: 0.5644 (mm-30) REVERT: B 614 GLU cc_start: 0.6931 (tt0) cc_final: 0.5406 (mp0) REVERT: C 187 MET cc_start: 0.8190 (mmt) cc_final: 0.7787 (tpp) REVERT: C 194 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7058 (mm-40) REVERT: C 222 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5966 (mmmt) REVERT: C 480 GLU cc_start: 0.7428 (tt0) cc_final: 0.6431 (mp0) REVERT: C 556 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7405 (pp20) REVERT: C 582 GLU cc_start: 0.7318 (pm20) cc_final: 0.6706 (tp30) REVERT: C 590 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6284 (m-30) REVERT: C 601 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.6052 (mt0) REVERT: C 604 GLU cc_start: 0.6122 (mt-10) cc_final: 0.5235 (mm-30) REVERT: C 610 LYS cc_start: 0.7459 (mtpt) cc_final: 0.7149 (mtmm) REVERT: C 631 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: D 187 MET cc_start: 0.8146 (mmt) cc_final: 0.7741 (tpp) REVERT: D 497 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6952 (mm) REVERT: D 498 ARG cc_start: 0.6200 (OUTLIER) cc_final: 0.5437 (mmt-90) REVERT: D 556 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7276 (pp20) REVERT: D 590 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6226 (m-30) REVERT: D 604 GLU cc_start: 0.6136 (mt-10) cc_final: 0.5243 (mm-30) REVERT: D 610 LYS cc_start: 0.7434 (mtpt) cc_final: 0.6952 (mttm) REVERT: E 306 ASP cc_start: 0.7335 (m-30) cc_final: 0.6900 (m-30) REVERT: E 356 MET cc_start: 0.1532 (mpt) cc_final: 0.1034 (mtt) REVERT: E 483 LYS cc_start: 0.6892 (tttm) cc_final: 0.5968 (tptt) REVERT: E 501 GLN cc_start: 0.5862 (mt0) cc_final: 0.5594 (mt0) REVERT: E 505 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.5781 (m-30) REVERT: E 594 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6380 (p0) REVERT: E 604 GLU cc_start: 0.6391 (mt-10) cc_final: 0.5632 (mm-30) REVERT: F 119 ARG cc_start: 0.5546 (ttp80) cc_final: 0.4898 (ttp-170) REVERT: F 199 ILE cc_start: 0.5592 (OUTLIER) cc_final: 0.5299 (tp) REVERT: F 315 ARG cc_start: 0.4643 (mpt-90) cc_final: 0.3904 (mmm160) REVERT: F 483 LYS cc_start: 0.7630 (mmtp) cc_final: 0.6529 (ptmt) REVERT: F 509 MET cc_start: 0.5858 (tpt) cc_final: 0.5468 (mtp) REVERT: F 630 LYS cc_start: 0.7731 (tppt) cc_final: 0.7218 (pmtt) outliers start: 65 outliers final: 34 residues processed: 244 average time/residue: 1.4615 time to fit residues: 415.3992 Evaluate side-chains 231 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 180 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 GLN Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.0470 chunk 238 optimal weight: 0.2980 chunk 319 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 300 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 146 GLN A 156 ASN A 172 ASN A 175 HIS ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 HIS ** E 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.224310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.159627 restraints weight = 32320.623| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 7.11 r_work: 0.3266 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 1.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 30840 Z= 0.215 Angle : 0.642 12.835 41868 Z= 0.335 Chirality : 0.049 0.458 4740 Planarity : 0.005 0.112 5448 Dihedral : 4.694 54.074 4138 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.13 % Favored : 91.55 % Rotamer: Outliers : 2.07 % Allowed : 31.47 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3774 helix: 0.92 (0.16), residues: 1154 sheet: 0.29 (0.22), residues: 710 loop : -2.36 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 129 HIS 0.014 0.001 HIS D 366 PHE 0.015 0.002 PHE D 44 TYR 0.025 0.002 TYR A 66 ARG 0.009 0.000 ARG A 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11107.02 seconds wall clock time: 199 minutes 53.61 seconds (11993.61 seconds total)