Starting phenix.real_space_refine on Sat Mar 23 11:12:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypk_34003/03_2024/7ypk_34003_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypk_34003/03_2024/7ypk_34003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypk_34003/03_2024/7ypk_34003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypk_34003/03_2024/7ypk_34003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypk_34003/03_2024/7ypk_34003_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypk_34003/03_2024/7ypk_34003_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 130 5.16 5 C 23219 2.51 5 N 6457 2.21 5 O 6974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 198": "NH1" <-> "NH2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F GLU 517": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 655": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 655": "OE1" <-> "OE2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "C GLU 517": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "D GLU 773": "OE1" <-> "OE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E GLU 441": "OE1" <-> "OE2" Residue "E GLU 537": "OE1" <-> "OE2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E GLU 635": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36792 Number of models: 1 Model: "" Number of chains: 13 Chain: "S" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6117 Classifications: {'peptide': 779} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "A" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6117 Classifications: {'peptide': 779} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6075 Classifications: {'peptide': 774} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 725} Chain breaks: 1 Chain: "C" Number of atoms: 6035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6035 Classifications: {'peptide': 769} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 720} Chain breaks: 1 Chain: "D" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6074 Classifications: {'peptide': 774} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 725} Chain breaks: 1 Chain: "E" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6117 Classifications: {'peptide': 779} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.34, per 1000 atoms: 0.50 Number of scatterers: 36792 At special positions: 0 Unit cell: (164.455, 198.407, 206.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 130 16.00 P 12 15.00 O 6974 8.00 N 6457 7.00 C 23219 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: 15.25 Conformation dependent library (CDL) restraints added in 7.1 seconds 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 39 sheets defined 42.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.06 Creating SS restraints... Processing helix chain 'F' and resid 31 through 38 removed outlier: 4.153A pdb=" N GLU F 35 " --> pdb=" O ARG F 32 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET F 38 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 118 through 138 removed outlier: 3.589A pdb=" N VAL F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 152 No H-bonds generated for 'chain 'F' and resid 149 through 152' Processing helix chain 'F' and resid 158 through 168 removed outlier: 3.765A pdb=" N ASP F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 180 Processing helix chain 'F' and resid 185 through 238 Processing helix chain 'F' and resid 244 through 256 Processing helix chain 'F' and resid 260 through 275 removed outlier: 5.566A pdb=" N LYS F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 295 removed outlier: 4.155A pdb=" N TYR F 289 " --> pdb=" O VAL F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 318 removed outlier: 3.702A pdb=" N GLN F 313 " --> pdb=" O ASN F 309 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 338 removed outlier: 3.757A pdb=" N LEU F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 336 " --> pdb=" O TYR F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 371 removed outlier: 4.491A pdb=" N ILE F 368 " --> pdb=" O GLY F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 390 No H-bonds generated for 'chain 'F' and resid 387 through 390' Processing helix chain 'F' and resid 404 through 411 removed outlier: 4.267A pdb=" N GLN F 411 " --> pdb=" O HIS F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 442 removed outlier: 4.279A pdb=" N GLU F 441 " --> pdb=" O SER F 437 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 449 No H-bonds generated for 'chain 'F' and resid 447 through 449' Processing helix chain 'F' and resid 479 through 484 removed outlier: 4.026A pdb=" N ARG F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 506 through 513 Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'F' and resid 541 through 560 Processing helix chain 'F' and resid 574 through 578 Processing helix chain 'F' and resid 631 through 646 Processing helix chain 'F' and resid 657 through 660 No H-bonds generated for 'chain 'F' and resid 657 through 660' Processing helix chain 'F' and resid 677 through 692 removed outlier: 5.129A pdb=" N ILE F 681 " --> pdb=" O ALA F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 727 removed outlier: 3.634A pdb=" N ALA F 724 " --> pdb=" O GLU F 720 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA F 725 " --> pdb=" O LYS F 721 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 740 Processing helix chain 'F' and resid 742 through 745 removed outlier: 4.217A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 742 through 745' Processing helix chain 'F' and resid 748 through 753 Processing helix chain 'F' and resid 762 through 769 removed outlier: 3.524A pdb=" N GLU F 767 " --> pdb=" O GLY F 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.982A pdb=" N MET A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 removed outlier: 5.310A pdb=" N ALA A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.659A pdb=" N LYS A 153 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.850A pdb=" N ALA A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 237 Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.657A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 3.591A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 4.122A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.549A pdb=" N GLN A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.680A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.520A pdb=" N SER A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.546A pdb=" N ARG A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 407 No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 435 through 442 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.501A pdb=" N ARG A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 506 through 514 Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.708A pdb=" N ILE A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 631 through 646 removed outlier: 3.529A pdb=" N GLU A 635 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 636 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA A 637 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 660 No H-bonds generated for 'chain 'A' and resid 657 through 660' Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.597A pdb=" N SER A 692 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 727 removed outlier: 3.734A pdb=" N ALA A 725 " --> pdb=" O LYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 4.240A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 743 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 Processing helix chain 'A' and resid 766 through 769 No H-bonds generated for 'chain 'A' and resid 766 through 769' Processing helix chain 'B' and resid 28 through 39 removed outlier: 4.043A pdb=" N ARG B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 138 removed outlier: 3.569A pdb=" N LYS B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.210A pdb=" N ILE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 185 through 255 removed outlier: 3.554A pdb=" N LEU B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.703A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 323 through 338 removed outlier: 3.802A pdb=" N GLU B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ARG B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 removed outlier: 3.565A pdb=" N ARG B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 435 through 442 removed outlier: 4.024A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.778A pdb=" N ARG B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 524 through 534 removed outlier: 3.522A pdb=" N LEU B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG B 529 " --> pdb=" O ALA B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 631 through 645 removed outlier: 3.716A pdb=" N SER B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 651 No H-bonds generated for 'chain 'B' and resid 648 through 651' Processing helix chain 'B' and resid 658 through 660 No H-bonds generated for 'chain 'B' and resid 658 through 660' Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 748 through 753 removed outlier: 3.506A pdb=" N GLU B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 753' Processing helix chain 'B' and resid 762 through 768 removed outlier: 4.853A pdb=" N GLU B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'C' and resid 150 through 153 No H-bonds generated for 'chain 'C' and resid 150 through 153' Processing helix chain 'C' and resid 158 through 168 removed outlier: 4.060A pdb=" N HIS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 185 through 237 removed outlier: 3.713A pdb=" N MET C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 254 removed outlier: 5.459A pdb=" N LYS C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU C 254 " --> pdb=" O ARG C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 271 Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 318 removed outlier: 4.124A pdb=" N GLU C 317 " --> pdb=" O GLN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 339 removed outlier: 4.018A pdb=" N GLU C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 372 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.644A pdb=" N MET C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 443 removed outlier: 4.332A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 495 through 504 removed outlier: 3.570A pdb=" N ALA C 500 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 513 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 541 through 560 removed outlier: 3.749A pdb=" N ARG C 545 " --> pdb=" O ARG C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 578 Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 680 through 691 removed outlier: 3.506A pdb=" N ALA C 684 " --> pdb=" O GLY C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 728 Processing helix chain 'C' and resid 737 through 745 removed outlier: 4.561A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 Processing helix chain 'C' and resid 762 through 768 Processing helix chain 'D' and resid 28 through 37 removed outlier: 3.671A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 135 Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.689A pdb=" N SER D 141 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 173 through 180 removed outlier: 3.584A pdb=" N GLU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 241 removed outlier: 3.517A pdb=" N LYS D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 256 removed outlier: 3.678A pdb=" N GLU D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 275 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.658A pdb=" N LEU D 290 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 4.439A pdb=" N GLU D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 removed outlier: 3.549A pdb=" N GLU D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 387 through 390 No H-bonds generated for 'chain 'D' and resid 387 through 390' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 435 through 443 Processing helix chain 'D' and resid 479 through 482 No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 506 through 512 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 543 through 560 removed outlier: 3.877A pdb=" N LEU D 547 " --> pdb=" O LEU D 543 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 578 Processing helix chain 'D' and resid 631 through 646 Processing helix chain 'D' and resid 658 through 660 No H-bonds generated for 'chain 'D' and resid 658 through 660' Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 719 through 727 Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.899A pdb=" N GLU D 740 " --> pdb=" O LYS D 737 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 Processing helix chain 'D' and resid 765 through 769 Processing helix chain 'E' and resid 31 through 39 removed outlier: 4.243A pdb=" N MET E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLY E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 118 through 135 Processing helix chain 'E' and resid 158 through 167 removed outlier: 3.504A pdb=" N ASP E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 185 through 237 Processing helix chain 'E' and resid 242 through 255 removed outlier: 4.983A pdb=" N ARG E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LYS E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 270 removed outlier: 3.641A pdb=" N LYS E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.662A pdb=" N GLU E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 323 through 338 Processing helix chain 'E' and resid 362 through 371 removed outlier: 4.111A pdb=" N ARG E 366 " --> pdb=" O THR E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.758A pdb=" N MET E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 443 Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 479 through 482 No H-bonds generated for 'chain 'E' and resid 479 through 482' Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 506 through 514 Processing helix chain 'E' and resid 524 through 533 removed outlier: 4.089A pdb=" N LEU E 528 " --> pdb=" O ASP E 524 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG E 529 " --> pdb=" O ALA E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 560 removed outlier: 4.063A pdb=" N ARG E 545 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 546 " --> pdb=" O GLY E 542 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 578 Processing helix chain 'E' and resid 631 through 646 removed outlier: 4.134A pdb=" N GLU E 635 " --> pdb=" O GLU E 631 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER E 636 " --> pdb=" O VAL E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 692 removed outlier: 4.337A pdb=" N ILE E 681 " --> pdb=" O ALA E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 727 removed outlier: 3.777A pdb=" N HIS E 726 " --> pdb=" O LEU E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 742 removed outlier: 4.471A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 removed outlier: 3.775A pdb=" N GLY E 753 " --> pdb=" O GLU E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'F' and resid 20 through 25 removed outlier: 3.775A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN F 83 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET F 75 " --> pdb=" O GLN F 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 43 through 47 Processing sheet with id= C, first strand: chain 'F' and resid 487 through 489 removed outlier: 5.892A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU F 353 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR F 469 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.306A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'F' and resid 600 through 603 Processing sheet with id= F, first strand: chain 'F' and resid 622 through 626 Processing sheet with id= G, first strand: chain 'F' and resid 732 through 736 removed outlier: 6.498A pdb=" N GLU F 755 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU F 735 " --> pdb=" O GLU F 755 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS F 757 " --> pdb=" O LEU F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 94 through 98 removed outlier: 4.216A pdb=" N THR F 95 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ARG F 106 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR F 97 " --> pdb=" O ARG F 104 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG F 104 " --> pdb=" O TYR F 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 7 through 9 removed outlier: 7.093A pdb=" N PHE A 45 " --> pdb=" O ILE A 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.992A pdb=" N THR A 21 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 87 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 70 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 89 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLN A 68 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG A 91 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY A 66 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.623A pdb=" N GLU A 486 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE A 467 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 353 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR A 469 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS A 377 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 420 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 596 through 603 removed outlier: 3.993A pdb=" N ALA A 601 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR A 608 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 603 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR A 611 " --> pdb=" O PRO A 668 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 615 " --> pdb=" O HIS A 664 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS A 664 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 617 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 700 through 702 removed outlier: 7.667A pdb=" N LYS A 732 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS A 757 " --> pdb=" O LEU A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 43 through 46 removed outlier: 3.735A pdb=" N VAL B 67 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= P, first strand: chain 'B' and resid 376 through 379 removed outlier: 7.023A pdb=" N VAL B 418 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE B 379 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 420 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE B 466 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU B 421 " --> pdb=" O PHE B 466 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 468 " --> pdb=" O LEU B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.356A pdb=" N ARG B 567 " --> pdb=" O GLU B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'B' and resid 596 through 598 Processing sheet with id= S, first strand: chain 'B' and resid 601 through 603 Processing sheet with id= T, first strand: chain 'B' and resid 622 through 626 Processing sheet with id= U, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.335A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU B 735 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS B 757 " --> pdb=" O LEU B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'C' and resid 7 through 9 removed outlier: 8.003A pdb=" N ILE C 8 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE C 45 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 485 through 489 removed outlier: 5.619A pdb=" N ILE C 350 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 488 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR C 469 " --> pdb=" O LEU C 353 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 600 through 602 Processing sheet with id= Y, first strand: chain 'C' and resid 732 through 736 removed outlier: 6.037A pdb=" N GLU C 755 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU C 735 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS C 757 " --> pdb=" O LEU C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 20 through 25 removed outlier: 4.132A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU D 87 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 70 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG D 89 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLN D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARG D 91 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY D 66 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 485 through 490 removed outlier: 5.802A pdb=" N ILE D 350 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE D 488 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL D 352 " --> pdb=" O ILE D 488 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE D 490 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 354 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE D 467 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU D 353 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR D 469 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N GLY D 355 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA D 471 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 419 " --> pdb=" O PHE D 466 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.203A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'D' and resid 596 through 602 removed outlier: 3.533A pdb=" N ALA D 597 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.874A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= AF, first strand: chain 'E' and resid 23 through 25 removed outlier: 3.570A pdb=" N VAL E 23 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 25 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN E 83 " --> pdb=" O MET E 75 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN E 73 " --> pdb=" O MET E 85 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 43 through 47 removed outlier: 5.918A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 467 through 471 removed outlier: 6.211A pdb=" N GLU E 486 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL E 354 " --> pdb=" O GLU E 486 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE E 488 " --> pdb=" O VAL E 354 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 376 through 379 removed outlier: 6.900A pdb=" N VAL E 418 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE E 379 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU E 420 " --> pdb=" O ILE E 379 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.144A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'E' and resid 600 through 603 Processing sheet with id= AL, first strand: chain 'E' and resid 613 through 618 Processing sheet with id= AM, first strand: chain 'E' and resid 732 through 736 removed outlier: 6.194A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM 1277 hydrogen bonds defined for protein. 3570 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: 12.58 Time building geometry restraints manager: 16.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6361 1.29 - 1.42: 8381 1.42 - 1.55: 22440 1.55 - 1.68: 18 1.68 - 1.82: 260 Bond restraints: 37460 Sorted by residual: bond pdb=" C LEU D 270 " pdb=" O LEU D 270 " ideal model delta sigma weight residual 1.236 1.156 0.080 1.19e-02 7.06e+03 4.54e+01 bond pdb=" C4 ADP F 801 " pdb=" C5 ADP F 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP E 801 " pdb=" C5 ADP E 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 37455 not shown) Histogram of bond angle deviations from ideal: 98.67 - 106.15: 1288 106.15 - 113.64: 21041 113.64 - 121.12: 18259 121.12 - 128.61: 10004 128.61 - 136.09: 223 Bond angle restraints: 50815 Sorted by residual: angle pdb=" CA GLY B 606 " pdb=" C GLY B 606 " pdb=" O GLY B 606 " ideal model delta sigma weight residual 122.45 118.23 4.22 7.20e-01 1.93e+00 3.43e+01 angle pdb=" CA GLY E 403 " pdb=" C GLY E 403 " pdb=" O GLY E 403 " ideal model delta sigma weight residual 122.29 118.17 4.12 8.10e-01 1.52e+00 2.59e+01 angle pdb=" N LEU A 381 " pdb=" CA LEU A 381 " pdb=" C LEU A 381 " ideal model delta sigma weight residual 113.01 106.93 6.08 1.20e+00 6.94e-01 2.57e+01 angle pdb=" N LYS F 265 " pdb=" CA LYS F 265 " pdb=" CB LYS F 265 " ideal model delta sigma weight residual 110.01 117.34 -7.33 1.45e+00 4.76e-01 2.56e+01 angle pdb=" CA ARG D 287 " pdb=" C ARG D 287 " pdb=" O ARG D 287 " ideal model delta sigma weight residual 120.82 115.55 5.27 1.05e+00 9.07e-01 2.52e+01 ... (remaining 50810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.58: 22381 28.58 - 57.16: 681 57.16 - 85.75: 48 85.75 - 114.33: 6 114.33 - 142.91: 6 Dihedral angle restraints: 23122 sinusoidal: 9631 harmonic: 13491 Sorted by residual: dihedral pdb=" C5' ADP C 801 " pdb=" O5' ADP C 801 " pdb=" PA ADP C 801 " pdb=" O2A ADP C 801 " ideal model delta sinusoidal sigma weight residual 300.00 157.09 142.91 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" O2A ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PA ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 76.00 -136.00 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 176.63 123.37 1 2.00e+01 2.50e-03 3.72e+01 ... (remaining 23119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4355 0.056 - 0.112: 1109 0.112 - 0.169: 280 0.169 - 0.225: 53 0.225 - 0.281: 6 Chirality restraints: 5803 Sorted by residual: chirality pdb=" CB VAL D 213 " pdb=" CA VAL D 213 " pdb=" CG1 VAL D 213 " pdb=" CG2 VAL D 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ARG B 391 " pdb=" N ARG B 391 " pdb=" C ARG B 391 " pdb=" CB ARG B 391 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE F 424 " pdb=" N ILE F 424 " pdb=" C ILE F 424 " pdb=" CB ILE F 424 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5800 not shown) Planarity restraints: 6590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 213 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL D 213 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL D 213 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS D 214 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 258 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C MET F 258 " -0.052 2.00e-02 2.50e+03 pdb=" O MET F 258 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO F 259 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 243 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C LEU A 243 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 243 " 0.018 2.00e-02 2.50e+03 pdb=" N SER A 244 " 0.017 2.00e-02 2.50e+03 ... (remaining 6587 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3371 2.74 - 3.28: 39765 3.28 - 3.82: 63073 3.82 - 4.36: 74783 4.36 - 4.90: 119564 Nonbonded interactions: 300556 Sorted by model distance: nonbonded pdb=" OH TYR F 534 " pdb=" O GLY F 579 " model vdw 2.204 2.440 nonbonded pdb=" NE ARG E 374 " pdb=" O ASN E 416 " model vdw 2.232 2.520 nonbonded pdb=" NH2 ARG F 541 " pdb=" OD1 ASP A 444 " model vdw 2.239 2.520 nonbonded pdb=" O TYR A 63 " pdb=" OH TYR A 97 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR E 603 " pdb=" O GLY E 606 " model vdw 2.248 2.440 ... (remaining 300551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 424 or resid 435 through 780 or resid 801)) selection = (chain 'B' and (resid 2 through 424 or resid 435 through 780 or resid 801)) selection = chain 'C' selection = (chain 'D' and (resid 2 through 424 or resid 435 through 780 or resid 801)) selection = (chain 'E' and (resid 2 through 424 or resid 435 through 780 or resid 801)) selection = (chain 'F' and (resid 2 through 424 or resid 435 through 780 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 9.280 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 97.720 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 0.109 37460 Z= 0.368 Angle : 0.880 12.860 50815 Z= 0.574 Chirality : 0.056 0.281 5803 Planarity : 0.004 0.050 6590 Dihedral : 13.089 142.909 14432 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 0.46 % Allowed : 2.00 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 4636 helix: 0.12 (0.12), residues: 1985 sheet: -0.22 (0.23), residues: 493 loop : -1.33 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 563 HIS 0.004 0.001 HIS C 393 PHE 0.018 0.001 PHE A 466 TYR 0.021 0.001 TYR C 225 ARG 0.008 0.000 ARG F 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 324 time to evaluate : 4.170 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: F 328 ARG cc_start: 0.7173 (tpt170) cc_final: 0.5549 (tpt170) REVERT: A 258 MET cc_start: 0.5783 (mpp) cc_final: 0.4589 (mpp) REVERT: A 427 MET cc_start: 0.5910 (mmm) cc_final: 0.5449 (tmm) REVERT: A 516 MET cc_start: 0.8300 (ppp) cc_final: 0.7659 (ppp) REVERT: A 683 MET cc_start: 0.8565 (mtm) cc_final: 0.8173 (mtm) REVERT: C 309 ASN cc_start: 0.8796 (m-40) cc_final: 0.8569 (m-40) REVERT: C 516 MET cc_start: 0.5546 (ppp) cc_final: 0.5182 (ppp) REVERT: D 260 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8411 (tm-30) REVERT: D 409 MET cc_start: 0.4971 (tpt) cc_final: 0.4477 (tpt) REVERT: D 698 MET cc_start: 0.7482 (mpp) cc_final: 0.6891 (mpp) outliers start: 18 outliers final: 4 residues processed: 340 average time/residue: 0.4416 time to fit residues: 251.4188 Evaluate side-chains 260 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 256 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain E residue 665 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 0.9990 chunk 350 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 236 optimal weight: 20.0000 chunk 187 optimal weight: 0.7980 chunk 362 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 419 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 GLN F 393 HIS ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 278 GLN D 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37460 Z= 0.173 Angle : 0.616 8.545 50815 Z= 0.296 Chirality : 0.043 0.208 5803 Planarity : 0.004 0.050 6590 Dihedral : 6.508 149.882 5208 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.06 % Favored : 95.92 % Rotamer: Outliers : 1.15 % Allowed : 7.55 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4636 helix: 0.36 (0.12), residues: 2013 sheet: -0.45 (0.22), residues: 521 loop : -1.18 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 431 HIS 0.008 0.001 HIS F 664 PHE 0.042 0.001 PHE D 203 TYR 0.017 0.001 TYR B 460 ARG 0.008 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 283 time to evaluate : 4.287 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: F 328 ARG cc_start: 0.7239 (tpt170) cc_final: 0.5573 (tpt170) REVERT: F 401 MET cc_start: 0.7559 (ttp) cc_final: 0.7237 (ttt) REVERT: A 516 MET cc_start: 0.8390 (ppp) cc_final: 0.7767 (ppp) REVERT: A 633 MET cc_start: 0.7486 (mpp) cc_final: 0.7196 (mpp) REVERT: A 683 MET cc_start: 0.8622 (mtm) cc_final: 0.8351 (mtm) REVERT: B 496 MET cc_start: 0.8322 (mpp) cc_final: 0.8056 (mpp) REVERT: B 633 MET cc_start: 0.7847 (mpp) cc_final: 0.7217 (mpp) REVERT: B 635 GLU cc_start: 0.8150 (mp0) cc_final: 0.7945 (pm20) REVERT: C 276 MET cc_start: 0.6061 (mtm) cc_final: 0.5178 (mtt) REVERT: D 260 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8343 (tm-30) REVERT: D 262 VAL cc_start: 0.4839 (OUTLIER) cc_final: 0.4556 (p) REVERT: D 409 MET cc_start: 0.5021 (tpt) cc_final: 0.4535 (tpt) REVERT: D 698 MET cc_start: 0.7575 (mpp) cc_final: 0.7104 (mpp) REVERT: E 217 MET cc_start: 0.1064 (OUTLIER) cc_final: 0.0817 (pmm) REVERT: E 516 MET cc_start: 0.7823 (ppp) cc_final: 0.7523 (ppp) outliers start: 45 outliers final: 22 residues processed: 312 average time/residue: 0.4571 time to fit residues: 238.1894 Evaluate side-chains 269 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 758 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 349 optimal weight: 0.0670 chunk 285 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 420 optimal weight: 10.0000 chunk 454 optimal weight: 0.9980 chunk 374 optimal weight: 0.0060 chunk 416 optimal weight: 10.0000 chunk 143 optimal weight: 0.5980 chunk 337 optimal weight: 0.4980 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN E 454 HIS E 659 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 37460 Z= 0.148 Angle : 0.581 8.853 50815 Z= 0.277 Chirality : 0.041 0.171 5803 Planarity : 0.004 0.053 6590 Dihedral : 6.047 145.939 5208 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 1.08 % Allowed : 9.70 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 4636 helix: 0.47 (0.12), residues: 2009 sheet: -0.35 (0.23), residues: 521 loop : -1.07 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 602 HIS 0.007 0.001 HIS D 454 PHE 0.032 0.001 PHE D 203 TYR 0.014 0.001 TYR D 289 ARG 0.009 0.000 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 278 time to evaluate : 4.443 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: F 328 ARG cc_start: 0.7274 (tpt170) cc_final: 0.6587 (mmt180) REVERT: F 426 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7854 (mtpt) REVERT: F 439 MET cc_start: 0.9165 (mmm) cc_final: 0.8707 (mmm) REVERT: A 258 MET cc_start: 0.5466 (mpp) cc_final: 0.4175 (mpp) REVERT: A 516 MET cc_start: 0.8248 (ppp) cc_final: 0.7892 (ppp) REVERT: A 633 MET cc_start: 0.7328 (mpp) cc_final: 0.6954 (mpp) REVERT: B 260 GLU cc_start: 0.8887 (pm20) cc_final: 0.8434 (mm-30) REVERT: B 702 MET cc_start: 0.3706 (mmt) cc_final: 0.3395 (mmt) REVERT: C 276 MET cc_start: 0.6078 (mtm) cc_final: 0.5251 (mtt) REVERT: D 409 MET cc_start: 0.5014 (tpt) cc_final: 0.4564 (tpt) REVERT: D 633 MET cc_start: 0.9204 (mtt) cc_final: 0.8941 (mtp) REVERT: D 698 MET cc_start: 0.7685 (mpp) cc_final: 0.7241 (mpp) REVERT: E 217 MET cc_start: 0.0695 (OUTLIER) cc_final: 0.0425 (pmm) REVERT: E 516 MET cc_start: 0.7984 (ppp) cc_final: 0.7623 (ppp) outliers start: 42 outliers final: 25 residues processed: 304 average time/residue: 0.4391 time to fit residues: 225.8654 Evaluate side-chains 271 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 758 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 0.9990 chunk 316 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 200 optimal weight: 0.6980 chunk 282 optimal weight: 1.9990 chunk 421 optimal weight: 0.9980 chunk 446 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 399 optimal weight: 50.0000 chunk 120 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN F 664 HIS ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 37460 Z= 0.164 Angle : 0.571 11.534 50815 Z= 0.271 Chirality : 0.041 0.173 5803 Planarity : 0.004 0.060 6590 Dihedral : 5.729 130.863 5208 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 1.77 % Allowed : 11.57 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4636 helix: 0.63 (0.12), residues: 2005 sheet: -0.32 (0.23), residues: 521 loop : -1.08 (0.14), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 602 HIS 0.004 0.001 HIS F 664 PHE 0.024 0.001 PHE D 203 TYR 0.012 0.001 TYR B 167 ARG 0.007 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 263 time to evaluate : 3.917 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: F 75 MET cc_start: 0.2160 (tpt) cc_final: 0.0843 (pmm) REVERT: F 328 ARG cc_start: 0.7315 (tpt170) cc_final: 0.6670 (mmt180) REVERT: F 401 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7231 (ttt) REVERT: F 426 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7905 (mtpt) REVERT: F 439 MET cc_start: 0.9224 (mmm) cc_final: 0.8789 (mmm) REVERT: A 258 MET cc_start: 0.5399 (mpp) cc_final: 0.4116 (mpp) REVERT: A 516 MET cc_start: 0.8300 (ppp) cc_final: 0.8005 (ppp) REVERT: A 663 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7797 (tp) REVERT: B 260 GLU cc_start: 0.8840 (pm20) cc_final: 0.8427 (mm-30) REVERT: B 485 MET cc_start: 0.6821 (pmm) cc_final: 0.6455 (pmm) REVERT: B 702 MET cc_start: 0.3919 (mmt) cc_final: 0.3663 (mmt) REVERT: C 160 MET cc_start: -0.4132 (mpp) cc_final: -0.4593 (mmm) REVERT: C 276 MET cc_start: 0.6030 (mtm) cc_final: 0.5198 (mtt) REVERT: D 409 MET cc_start: 0.5009 (tpt) cc_final: 0.4541 (tpt) REVERT: D 496 MET cc_start: 0.8515 (mmt) cc_final: 0.8049 (mpp) REVERT: D 633 MET cc_start: 0.9206 (mtt) cc_final: 0.8960 (mtp) REVERT: D 683 MET cc_start: 0.8601 (mtm) cc_final: 0.8387 (mtm) REVERT: D 698 MET cc_start: 0.7700 (mpp) cc_final: 0.7317 (mpp) REVERT: E 217 MET cc_start: 0.0694 (OUTLIER) cc_final: 0.0427 (pmm) REVERT: E 516 MET cc_start: 0.8009 (ppp) cc_final: 0.7740 (ppp) outliers start: 69 outliers final: 34 residues processed: 309 average time/residue: 0.4475 time to fit residues: 233.4272 Evaluate side-chains 279 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 242 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 758 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 4.9990 chunk 253 optimal weight: 20.0000 chunk 6 optimal weight: 0.2980 chunk 332 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 228 optimal weight: 0.7980 chunk 400 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS E 659 ASN ** E 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37460 Z= 0.286 Angle : 0.651 12.971 50815 Z= 0.314 Chirality : 0.043 0.379 5803 Planarity : 0.005 0.075 6590 Dihedral : 5.847 125.496 5205 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.84 % Rotamer: Outliers : 2.10 % Allowed : 13.06 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4636 helix: 0.64 (0.12), residues: 1986 sheet: -0.53 (0.22), residues: 542 loop : -1.15 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 431 HIS 0.009 0.001 HIS F 664 PHE 0.035 0.002 PHE D 203 TYR 0.019 0.002 TYR E 332 ARG 0.008 0.000 ARG F 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 244 time to evaluate : 4.113 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: F 75 MET cc_start: 0.1804 (tpt) cc_final: 0.0602 (pmm) REVERT: F 328 ARG cc_start: 0.7276 (tpt170) cc_final: 0.6687 (mmt180) REVERT: F 426 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7871 (mtpt) REVERT: F 501 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8108 (mt) REVERT: F 633 MET cc_start: 0.7956 (mpp) cc_final: 0.7714 (mpp) REVERT: A 217 MET cc_start: 0.3023 (tpp) cc_final: 0.2659 (ttm) REVERT: A 258 MET cc_start: 0.5463 (mpp) cc_final: 0.4054 (mpp) REVERT: A 516 MET cc_start: 0.8320 (ppp) cc_final: 0.8102 (ppp) REVERT: A 663 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8129 (tp) REVERT: B 260 GLU cc_start: 0.8862 (pm20) cc_final: 0.8542 (mm-30) REVERT: B 702 MET cc_start: 0.4270 (mmt) cc_final: 0.3867 (mmt) REVERT: C 276 MET cc_start: 0.5834 (mtm) cc_final: 0.4918 (mtt) REVERT: C 516 MET cc_start: 0.5371 (ppp) cc_final: 0.4915 (ppp) REVERT: D 345 ARG cc_start: 0.6897 (mmt180) cc_final: 0.6497 (mpt180) REVERT: D 409 MET cc_start: 0.5172 (tpt) cc_final: 0.4464 (tpt) REVERT: D 698 MET cc_start: 0.7603 (mpp) cc_final: 0.7345 (mpp) REVERT: E 217 MET cc_start: 0.0724 (OUTLIER) cc_final: 0.0453 (pmm) REVERT: E 427 MET cc_start: 0.6844 (mmt) cc_final: 0.6537 (mmt) REVERT: E 713 MET cc_start: 0.8465 (mmp) cc_final: 0.8223 (mmp) outliers start: 82 outliers final: 55 residues processed: 300 average time/residue: 0.4547 time to fit residues: 232.6064 Evaluate side-chains 290 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 232 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 758 LEU Chi-restraints excluded: chain E residue 779 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 0.8980 chunk 402 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 447 optimal weight: 6.9990 chunk 371 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 147 optimal weight: 0.7980 chunk 234 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37460 Z= 0.190 Angle : 0.594 11.659 50815 Z= 0.281 Chirality : 0.042 0.201 5803 Planarity : 0.004 0.067 6590 Dihedral : 5.634 113.081 5205 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 1.89 % Allowed : 14.36 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 4636 helix: 0.73 (0.12), residues: 1978 sheet: -0.56 (0.22), residues: 537 loop : -1.01 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 431 HIS 0.005 0.001 HIS F 664 PHE 0.017 0.001 PHE B 203 TYR 0.042 0.001 TYR F 224 ARG 0.007 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 247 time to evaluate : 4.170 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: F 75 MET cc_start: 0.1761 (tpt) cc_final: 0.0579 (pmm) REVERT: F 328 ARG cc_start: 0.7198 (tpt170) cc_final: 0.6960 (tpt170) REVERT: A 217 MET cc_start: 0.2991 (tpp) cc_final: 0.2591 (ttm) REVERT: A 258 MET cc_start: 0.5698 (mpp) cc_final: 0.4343 (mpp) REVERT: A 663 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8164 (tp) REVERT: B 260 GLU cc_start: 0.8853 (pm20) cc_final: 0.8540 (mm-30) REVERT: B 505 TYR cc_start: 0.7131 (m-10) cc_final: 0.6858 (m-80) REVERT: B 702 MET cc_start: 0.4430 (mmt) cc_final: 0.4012 (mmt) REVERT: C 276 MET cc_start: 0.6057 (mtm) cc_final: 0.5188 (mtt) REVERT: C 516 MET cc_start: 0.5548 (ppp) cc_final: 0.4979 (ppp) REVERT: D 228 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5898 (tm-30) REVERT: D 235 LYS cc_start: 0.3931 (OUTLIER) cc_final: 0.1569 (tttm) REVERT: D 345 ARG cc_start: 0.6894 (mmt180) cc_final: 0.5961 (ptt-90) REVERT: D 409 MET cc_start: 0.5070 (tpt) cc_final: 0.4420 (tpt) REVERT: D 698 MET cc_start: 0.7515 (mpp) cc_final: 0.7268 (mpp) REVERT: E 217 MET cc_start: 0.0725 (OUTLIER) cc_final: 0.0454 (pmm) outliers start: 74 outliers final: 49 residues processed: 294 average time/residue: 0.4527 time to fit residues: 226.0078 Evaluate side-chains 289 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 236 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 665 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 0.0470 chunk 50 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 326 optimal weight: 20.0000 chunk 252 optimal weight: 50.0000 chunk 376 optimal weight: 0.0570 chunk 249 optimal weight: 30.0000 chunk 445 optimal weight: 0.9980 chunk 278 optimal weight: 10.0000 chunk 271 optimal weight: 0.0570 chunk 205 optimal weight: 2.9990 overall best weight: 0.8316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 37460 Z= 0.155 Angle : 0.593 14.484 50815 Z= 0.278 Chirality : 0.042 0.303 5803 Planarity : 0.004 0.069 6590 Dihedral : 5.448 96.684 5205 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 1.97 % Allowed : 14.82 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 4636 helix: 0.83 (0.12), residues: 1963 sheet: -0.58 (0.23), residues: 520 loop : -0.92 (0.14), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 563 HIS 0.004 0.001 HIS F 454 PHE 0.019 0.001 PHE B 203 TYR 0.041 0.001 TYR F 224 ARG 0.006 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 251 time to evaluate : 4.161 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: F 75 MET cc_start: 0.1702 (tpt) cc_final: 0.0559 (pmm) REVERT: F 328 ARG cc_start: 0.7241 (tpt170) cc_final: 0.6648 (mmt180) REVERT: F 453 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8716 (p0) REVERT: F 635 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: A 217 MET cc_start: 0.3100 (tpp) cc_final: 0.2708 (ttm) REVERT: A 258 MET cc_start: 0.5808 (mpp) cc_final: 0.4498 (mpp) REVERT: A 663 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8218 (tp) REVERT: B 260 GLU cc_start: 0.8846 (pm20) cc_final: 0.8541 (mm-30) REVERT: B 485 MET cc_start: 0.6998 (pmm) cc_final: 0.6665 (pmm) REVERT: B 505 TYR cc_start: 0.7047 (m-10) cc_final: 0.6819 (m-80) REVERT: B 702 MET cc_start: 0.4395 (mmt) cc_final: 0.4060 (mmt) REVERT: C 276 MET cc_start: 0.6054 (mtm) cc_final: 0.5198 (mtt) REVERT: D 228 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5826 (tm-30) REVERT: D 345 ARG cc_start: 0.6862 (mmt180) cc_final: 0.5934 (ptt-90) REVERT: D 409 MET cc_start: 0.5080 (tpt) cc_final: 0.4507 (tpt) REVERT: D 496 MET cc_start: 0.8568 (mmt) cc_final: 0.8198 (mpp) REVERT: D 698 MET cc_start: 0.7518 (mpp) cc_final: 0.7218 (mpp) REVERT: E 217 MET cc_start: 0.0725 (OUTLIER) cc_final: 0.0456 (pmm) outliers start: 77 outliers final: 48 residues processed: 305 average time/residue: 0.4497 time to fit residues: 233.2637 Evaluate side-chains 291 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 238 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 635 GLU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 665 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 265 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 chunk 86 optimal weight: 0.8980 chunk 283 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 350 optimal weight: 20.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37460 Z= 0.231 Angle : 0.629 14.373 50815 Z= 0.297 Chirality : 0.042 0.176 5803 Planarity : 0.004 0.070 6590 Dihedral : 5.533 96.567 5205 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 2.07 % Allowed : 14.90 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4636 helix: 0.76 (0.12), residues: 1990 sheet: -0.51 (0.23), residues: 531 loop : -1.02 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 563 HIS 0.006 0.001 HIS D 664 PHE 0.020 0.002 PHE B 203 TYR 0.040 0.001 TYR F 224 ARG 0.006 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 242 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 75 MET cc_start: 0.1705 (tpt) cc_final: 0.0601 (pmm) REVERT: F 328 ARG cc_start: 0.7186 (tpt170) cc_final: 0.6973 (tpt170) REVERT: F 391 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7122 (ttp-110) REVERT: F 401 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7139 (ttt) REVERT: F 453 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8870 (p0) REVERT: F 501 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8141 (mt) REVERT: F 635 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: A 217 MET cc_start: 0.3119 (tpp) cc_final: 0.2719 (ttm) REVERT: A 258 MET cc_start: 0.5871 (mpp) cc_final: 0.4385 (mpp) REVERT: A 663 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8322 (tp) REVERT: B 260 GLU cc_start: 0.8848 (pm20) cc_final: 0.8562 (mm-30) REVERT: B 372 MET cc_start: 0.8280 (mtt) cc_final: 0.7901 (mpp) REVERT: B 485 MET cc_start: 0.7053 (pmm) cc_final: 0.6704 (pmm) REVERT: B 505 TYR cc_start: 0.7073 (m-10) cc_final: 0.6796 (m-80) REVERT: B 702 MET cc_start: 0.4416 (mmt) cc_final: 0.3964 (mmt) REVERT: C 276 MET cc_start: 0.6079 (mtm) cc_final: 0.5187 (mtt) REVERT: C 516 MET cc_start: 0.5670 (ppp) cc_final: 0.5380 (ppp) REVERT: D 345 ARG cc_start: 0.6926 (mmt180) cc_final: 0.6443 (mpt180) REVERT: D 409 MET cc_start: 0.5084 (tpt) cc_final: 0.4427 (tpt) REVERT: E 217 MET cc_start: 0.0669 (OUTLIER) cc_final: 0.0404 (pmm) outliers start: 81 outliers final: 58 residues processed: 299 average time/residue: 0.4569 time to fit residues: 230.9206 Evaluate side-chains 300 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 235 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 391 ARG Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 635 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 779 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 50.0000 chunk 426 optimal weight: 0.6980 chunk 389 optimal weight: 9.9990 chunk 414 optimal weight: 0.8980 chunk 249 optimal weight: 50.0000 chunk 180 optimal weight: 7.9990 chunk 325 optimal weight: 40.0000 chunk 127 optimal weight: 0.6980 chunk 374 optimal weight: 0.9980 chunk 392 optimal weight: 9.9990 chunk 413 optimal weight: 6.9990 overall best weight: 2.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN E 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37460 Z= 0.205 Angle : 0.628 13.616 50815 Z= 0.294 Chirality : 0.042 0.297 5803 Planarity : 0.004 0.070 6590 Dihedral : 5.504 95.807 5205 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 2.05 % Allowed : 15.44 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4636 helix: 0.74 (0.12), residues: 1997 sheet: -0.48 (0.23), residues: 528 loop : -1.01 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 563 HIS 0.005 0.001 HIS D 664 PHE 0.023 0.001 PHE B 203 TYR 0.041 0.001 TYR F 224 ARG 0.006 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 241 time to evaluate : 4.161 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: F 75 MET cc_start: 0.1650 (tpt) cc_final: 0.0547 (pmm) REVERT: F 328 ARG cc_start: 0.7201 (tpt170) cc_final: 0.6976 (tpt170) REVERT: F 391 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7219 (ttp-110) REVERT: F 501 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8123 (mt) REVERT: F 635 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: A 217 MET cc_start: 0.3138 (tpp) cc_final: 0.2735 (ttm) REVERT: A 258 MET cc_start: 0.6055 (mpp) cc_final: 0.4517 (mpp) REVERT: A 663 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8342 (tp) REVERT: B 260 GLU cc_start: 0.8848 (pm20) cc_final: 0.8593 (mm-30) REVERT: B 372 MET cc_start: 0.8391 (mtt) cc_final: 0.7964 (mpp) REVERT: B 485 MET cc_start: 0.7062 (pmm) cc_final: 0.6732 (pmm) REVERT: B 505 TYR cc_start: 0.6999 (m-10) cc_final: 0.6770 (m-80) REVERT: B 702 MET cc_start: 0.4348 (mmt) cc_final: 0.3925 (mmt) REVERT: C 276 MET cc_start: 0.6050 (mtm) cc_final: 0.5145 (mtt) REVERT: C 516 MET cc_start: 0.5789 (ppp) cc_final: 0.5434 (ppp) REVERT: D 345 ARG cc_start: 0.6939 (mmt180) cc_final: 0.6456 (mpt180) REVERT: D 409 MET cc_start: 0.5105 (tpt) cc_final: 0.4496 (tpt) REVERT: D 496 MET cc_start: 0.8474 (mmt) cc_final: 0.8115 (mpp) REVERT: E 217 MET cc_start: 0.0676 (OUTLIER) cc_final: 0.0408 (pmm) outliers start: 80 outliers final: 63 residues processed: 294 average time/residue: 0.4714 time to fit residues: 234.9887 Evaluate side-chains 305 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 237 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 391 ARG Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 635 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 9.9990 chunk 438 optimal weight: 7.9990 chunk 267 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 460 optimal weight: 2.9990 chunk 423 optimal weight: 0.2980 chunk 366 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 224 optimal weight: 0.1980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37460 Z= 0.174 Angle : 0.625 13.588 50815 Z= 0.291 Chirality : 0.043 0.645 5803 Planarity : 0.004 0.073 6590 Dihedral : 5.439 96.334 5205 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.07 % Favored : 94.91 % Rotamer: Outliers : 1.87 % Allowed : 15.80 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.26 (0.13), residues: 4636 helix: 0.78 (0.12), residues: 1992 sheet: -0.46 (0.23), residues: 534 loop : -0.96 (0.14), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 563 HIS 0.003 0.001 HIS F 454 PHE 0.026 0.001 PHE B 203 TYR 0.043 0.001 TYR F 224 ARG 0.006 0.000 ARG E 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 244 time to evaluate : 4.386 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: F 75 MET cc_start: 0.1648 (tpt) cc_final: 0.0555 (pmm) REVERT: F 328 ARG cc_start: 0.7185 (tpt170) cc_final: 0.6964 (tpt170) REVERT: F 391 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7323 (ttp-110) REVERT: F 501 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8183 (mt) REVERT: F 635 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: A 217 MET cc_start: 0.3132 (tpp) cc_final: 0.2728 (ttm) REVERT: A 258 MET cc_start: 0.6269 (mpp) cc_final: 0.4808 (mpp) REVERT: A 431 TRP cc_start: 0.5757 (OUTLIER) cc_final: 0.5360 (p-90) REVERT: A 663 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8359 (tp) REVERT: B 260 GLU cc_start: 0.8858 (pm20) cc_final: 0.8599 (mm-30) REVERT: B 372 MET cc_start: 0.8293 (mtt) cc_final: 0.7882 (mpp) REVERT: B 485 MET cc_start: 0.7041 (pmm) cc_final: 0.6724 (pmm) REVERT: B 702 MET cc_start: 0.4551 (mmt) cc_final: 0.4072 (mmt) REVERT: C 276 MET cc_start: 0.6055 (mtm) cc_final: 0.5156 (mtt) REVERT: C 516 MET cc_start: 0.6037 (ppp) cc_final: 0.5680 (ppp) REVERT: D 345 ARG cc_start: 0.6928 (mmt180) cc_final: 0.5944 (ptt-90) REVERT: D 409 MET cc_start: 0.5043 (tpt) cc_final: 0.4457 (tpt) REVERT: D 496 MET cc_start: 0.8513 (mmt) cc_final: 0.8158 (mpp) REVERT: D 516 MET cc_start: 0.7938 (mpp) cc_final: 0.7597 (mpp) REVERT: D 683 MET cc_start: 0.8436 (mtm) cc_final: 0.8199 (mtm) REVERT: E 217 MET cc_start: 0.0671 (OUTLIER) cc_final: 0.0403 (pmm) outliers start: 73 outliers final: 60 residues processed: 294 average time/residue: 0.4740 time to fit residues: 236.3570 Evaluate side-chains 306 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 240 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 391 ARG Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 635 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 0.8980 chunk 390 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 367 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 376 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.155372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.103673 restraints weight = 90993.696| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 8.35 r_work: 0.3838 rms_B_bonded: 6.90 restraints_weight: 2.0000 r_work: 0.3923 rms_B_bonded: 5.50 restraints_weight: 4.0000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37460 Z= 0.205 Angle : 0.637 13.263 50815 Z= 0.298 Chirality : 0.043 0.453 5803 Planarity : 0.004 0.074 6590 Dihedral : 5.465 97.313 5205 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.95 % Allowed : 15.72 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.27 (0.13), residues: 4636 helix: 0.80 (0.12), residues: 1986 sheet: -0.50 (0.23), residues: 532 loop : -0.99 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 563 HIS 0.005 0.001 HIS D 664 PHE 0.025 0.001 PHE B 203 TYR 0.044 0.001 TYR F 224 ARG 0.006 0.000 ARG E 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9795.80 seconds wall clock time: 176 minutes 4.25 seconds (10564.25 seconds total)