Starting phenix.real_space_refine on Fri Dec 15 07:36:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jql_9873/12_2023/6jql_9873.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jql_9873/12_2023/6jql_9873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jql_9873/12_2023/6jql_9873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jql_9873/12_2023/6jql_9873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jql_9873/12_2023/6jql_9873.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jql_9873/12_2023/6jql_9873.pdb" } resolution = 2.9 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 19344 2.51 5 N 5424 2.21 5 O 5730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 544": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 544": "NH1" <-> "NH2" Residue "E ARG 545": "NH1" <-> "NH2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "E PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 545": "NH1" <-> "NH2" Residue "F ARG 580": "NH1" <-> "NH2" Residue "F PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30648 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "C" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "D" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "E" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "F" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Time building chain proxies: 15.76, per 1000 atoms: 0.51 Number of scatterers: 30648 At special positions: 0 Unit cell: (178.08, 174.9, 109.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 5730 8.00 N 5424 7.00 C 19344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.72 Conformation dependent library (CDL) restraints added in 6.0 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7404 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 44 sheets defined 39.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.683A pdb=" N MET A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.742A pdb=" N GLU A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 92 through 117 removed outlier: 3.796A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.123A pdb=" N LYS A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 186 through 199 removed outlier: 4.048A pdb=" N THR A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.714A pdb=" N LEU A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 273 through 289 removed outlier: 4.306A pdb=" N ALA A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 307 through 320 removed outlier: 4.294A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.683A pdb=" N GLN A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.691A pdb=" N ASP A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 485 through 492 removed outlier: 3.851A pdb=" N ALA A 489 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 490 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.953A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.643A pdb=" N ALA A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 Processing helix chain 'B' and resid 40 through 58 removed outlier: 4.067A pdb=" N ALA B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.719A pdb=" N GLU B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 92 through 117 removed outlier: 3.722A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 174 removed outlier: 4.236A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 186 through 199 removed outlier: 4.134A pdb=" N THR B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 4.002A pdb=" N LEU B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.591A pdb=" N VAL B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.299A pdb=" N ALA B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 307 through 320 removed outlier: 4.129A pdb=" N VAL B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.662A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.663A pdb=" N GLN B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.641A pdb=" N ASP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 485 through 489 removed outlier: 3.699A pdb=" N ALA B 489 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 4.052A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 529 Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 568 through 574 removed outlier: 3.524A pdb=" N ALA B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'C' and resid 40 through 52 Processing helix chain 'C' and resid 52 through 59 removed outlier: 3.633A pdb=" N MET C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.782A pdb=" N GLU C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 92 through 117 removed outlier: 3.686A pdb=" N VAL C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 174 removed outlier: 4.103A pdb=" N LYS C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 186 through 199 removed outlier: 4.054A pdb=" N THR C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.665A pdb=" N LEU C 222 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.652A pdb=" N MET C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 Processing helix chain 'C' and resid 273 through 289 removed outlier: 4.254A pdb=" N ALA C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 307 through 320 removed outlier: 4.219A pdb=" N VAL C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 354 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.817A pdb=" N GLN C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.662A pdb=" N ASP C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 443 " --> pdb=" O ILE C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 485 through 492 removed outlier: 3.753A pdb=" N ALA C 489 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 490 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 510 removed outlier: 3.855A pdb=" N ALA C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 548 through 560 Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 568 through 574 removed outlier: 3.500A pdb=" N ALA C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 596 Processing helix chain 'D' and resid 40 through 58 removed outlier: 4.050A pdb=" N ALA D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Proline residue: D 54 - end of helix Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.720A pdb=" N GLU D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 92 through 117 removed outlier: 4.155A pdb=" N GLY D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 4.233A pdb=" N LYS D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 186 through 199 removed outlier: 4.068A pdb=" N THR D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.917A pdb=" N LEU D 222 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.558A pdb=" N GLY D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 273 through 289 removed outlier: 4.400A pdb=" N ALA D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.941A pdb=" N VAL D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 355 removed outlier: 3.704A pdb=" N LYS D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.555A pdb=" N GLU D 387 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 410 through 418 removed outlier: 3.658A pdb=" N GLN D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.672A pdb=" N ASP D 441 " --> pdb=" O GLN D 437 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 443 " --> pdb=" O ILE D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 502 through 511 removed outlier: 4.029A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 529 Processing helix chain 'D' and resid 530 through 534 Processing helix chain 'D' and resid 548 through 560 Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 569 through 574 Processing helix chain 'D' and resid 583 through 596 Processing helix chain 'E' and resid 40 through 52 Processing helix chain 'E' and resid 52 through 59 removed outlier: 3.709A pdb=" N MET E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.739A pdb=" N GLU E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 92 through 117 removed outlier: 3.928A pdb=" N VAL E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 99 " --> pdb=" O ASP E 95 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 174 removed outlier: 4.062A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 186 through 199 removed outlier: 4.094A pdb=" N THR E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.695A pdb=" N LEU E 222 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.599A pdb=" N MET E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 273 through 289 removed outlier: 4.282A pdb=" N ALA E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 293 Processing helix chain 'E' and resid 307 through 320 removed outlier: 4.221A pdb=" N VAL E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 354 Processing helix chain 'E' and resid 410 through 418 removed outlier: 3.855A pdb=" N GLN E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 removed outlier: 3.673A pdb=" N ASP E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 443 " --> pdb=" O ILE E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 485 through 492 removed outlier: 3.791A pdb=" N ALA E 489 " --> pdb=" O GLY E 486 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL E 490 " --> pdb=" O LEU E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 511 removed outlier: 3.920A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 560 Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 568 through 574 removed outlier: 3.501A pdb=" N ALA E 572 " --> pdb=" O ASP E 568 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 596 removed outlier: 3.519A pdb=" N VAL E 596 " --> pdb=" O ALA E 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 58 removed outlier: 3.969A pdb=" N ALA F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Proline residue: F 54 - end of helix Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.732A pdb=" N GLU F 78 " --> pdb=" O HIS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 92 through 117 removed outlier: 4.109A pdb=" N GLY F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 166 Processing helix chain 'F' and resid 168 through 175 Processing helix chain 'F' and resid 186 through 199 removed outlier: 4.085A pdb=" N THR F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 222 removed outlier: 4.043A pdb=" N LEU F 222 " --> pdb=" O LEU F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 242 removed outlier: 3.514A pdb=" N GLY F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 273 through 289 removed outlier: 4.407A pdb=" N ALA F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 293 Processing helix chain 'F' and resid 307 through 320 removed outlier: 4.033A pdb=" N VAL F 316 " --> pdb=" O SER F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 355 removed outlier: 3.673A pdb=" N LYS F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 388 removed outlier: 3.545A pdb=" N GLU F 387 " --> pdb=" O GLN F 384 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR F 388 " --> pdb=" O PRO F 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 384 through 388' Processing helix chain 'F' and resid 410 through 418 removed outlier: 3.600A pdb=" N GLN F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 443 removed outlier: 3.702A pdb=" N ASP F 441 " --> pdb=" O GLN F 437 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 502 through 511 removed outlier: 4.094A pdb=" N ALA F 508 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 534 Processing helix chain 'F' and resid 548 through 560 Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 569 through 574 Processing helix chain 'F' and resid 583 through 596 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.661A pdb=" N GLY B 425 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU B 452 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 427 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN B 261 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.127A pdb=" N ALA A 151 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 181 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N HIS A 153 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.924A pdb=" N TYR A 381 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR A 378 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU A 403 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 380 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ARG A 299 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN A 261 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A 425 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 452 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 427 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 449 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.924A pdb=" N TYR A 381 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR A 378 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU A 403 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 380 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ARG A 299 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN A 261 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A 425 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 452 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 427 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 449 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 539 through 541 Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.415A pdb=" N GLU A 650 " --> pdb=" O LYS A 631 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 671 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 608 through 609 Processing sheet with id=AB1, first strand: chain 'A' and resid 612 through 613 Processing sheet with id=AB2, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AB3, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.595A pdb=" N TRP B 32 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 208 through 210 removed outlier: 6.003A pdb=" N ALA B 151 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS B 181 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS B 153 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 152 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 539 through 541 Processing sheet with id=AB6, first strand: chain 'B' and resid 539 through 541 removed outlier: 5.212A pdb=" N VAL B 626 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE B 656 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 628 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLU B 654 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N CYS B 630 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA B 652 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 655 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 664 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 671 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB8, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=AB9, first strand: chain 'C' and resid 130 through 131 removed outlier: 6.580A pdb=" N GLY D 425 " --> pdb=" O GLN D 450 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU D 452 " --> pdb=" O GLY D 425 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU D 427 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN D 261 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG D 299 " --> pdb=" O THR D 402 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N MET D 404 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE D 301 " --> pdb=" O MET D 404 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA D 406 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL D 303 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR D 378 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU D 403 " --> pdb=" O THR D 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 208 through 210 removed outlier: 6.192A pdb=" N ALA C 151 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS C 181 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS C 153 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.843A pdb=" N TYR C 381 " --> pdb=" O CYS C 358 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG C 299 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN C 261 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 425 " --> pdb=" O GLN C 450 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU C 452 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 427 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C 449 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.843A pdb=" N TYR C 381 " --> pdb=" O CYS C 358 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG C 299 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN C 261 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 425 " --> pdb=" O GLN C 450 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU C 452 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 427 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C 449 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 520 through 521 removed outlier: 6.268A pdb=" N GLU C 520 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU C 541 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C 538 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 520 through 521 removed outlier: 6.268A pdb=" N GLU C 520 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU C 541 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C 538 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL C 626 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 656 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU C 628 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU C 654 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N CYS C 630 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA C 652 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 671 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AC7, first strand: chain 'C' and resid 612 through 613 removed outlier: 6.202A pdb=" N VAL D 603 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA D 673 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 669 " --> pdb=" O TYR D 607 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU D 609 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER D 667 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU D 650 " --> pdb=" O LYS D 631 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 629 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 612 through 613 removed outlier: 6.202A pdb=" N VAL D 603 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA D 673 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 669 " --> pdb=" O TYR D 607 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU D 609 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER D 667 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU D 650 " --> pdb=" O LYS D 631 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 629 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AD1, first strand: chain 'D' and resid 20 through 23 removed outlier: 3.610A pdb=" N TRP D 32 " --> pdb=" O ILE D 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 208 through 210 removed outlier: 6.107A pdb=" N ALA D 151 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS D 181 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N HIS D 153 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AD4, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.509A pdb=" N TRP E 32 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 removed outlier: 6.613A pdb=" N GLY F 425 " --> pdb=" O GLN F 450 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU F 452 " --> pdb=" O GLY F 425 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU F 427 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN F 261 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG F 299 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N MET F 404 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE F 301 " --> pdb=" O MET F 404 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA F 406 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 303 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR F 378 " --> pdb=" O ALA F 401 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU F 403 " --> pdb=" O THR F 378 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 208 through 210 removed outlier: 6.689A pdb=" N ALA E 178 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA E 151 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS E 181 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS E 153 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 358 through 359 removed outlier: 3.997A pdb=" N TYR E 381 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG E 299 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN E 261 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY E 425 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU E 452 " --> pdb=" O GLY E 425 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU E 427 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE E 449 " --> pdb=" O GLN F 500 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 358 through 359 removed outlier: 3.997A pdb=" N TYR E 381 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG E 299 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN E 261 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY E 425 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU E 452 " --> pdb=" O GLY E 425 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU E 427 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE E 449 " --> pdb=" O GLN F 500 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 539 through 541 Processing sheet with id=AE1, first strand: chain 'E' and resid 539 through 541 removed outlier: 5.069A pdb=" N VAL E 626 " --> pdb=" O PHE E 656 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE E 656 " --> pdb=" O VAL E 626 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU E 628 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU E 654 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS E 630 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA E 652 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU E 671 " --> pdb=" O ILE E 604 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 608 through 609 Processing sheet with id=AE3, first strand: chain 'E' and resid 612 through 613 Processing sheet with id=AE4, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=AE5, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.544A pdb=" N TRP F 32 " --> pdb=" O ILE F 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 208 through 210 removed outlier: 5.959A pdb=" N ALA F 151 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS F 181 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N HIS F 153 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL F 152 " --> pdb=" O THR F 229 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 539 through 541 Processing sheet with id=AE8, first strand: chain 'F' and resid 539 through 541 removed outlier: 3.664A pdb=" N THR F 629 " --> pdb=" O ALA F 652 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU F 650 " --> pdb=" O LYS F 631 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU F 671 " --> pdb=" O ILE F 604 " (cutoff:3.500A) 1366 hydrogen bonds defined for protein. 3777 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: 13.67 Time building geometry restraints manager: 12.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9933 1.34 - 1.46: 4689 1.46 - 1.58: 16404 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 31266 Sorted by residual: bond pdb=" C TRP D 124 " pdb=" O TRP D 124 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.17e+00 bond pdb=" N THR A 634 " pdb=" CA THR A 634 " ideal model delta sigma weight residual 1.461 1.481 -0.020 1.38e-02 5.25e+03 2.08e+00 bond pdb=" C ALA C 53 " pdb=" N PRO C 54 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.03e+00 bond pdb=" C ALA B 53 " pdb=" N PRO B 54 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 1.99e+00 bond pdb=" N THR D 634 " pdb=" CA THR D 634 " ideal model delta sigma weight residual 1.461 1.480 -0.019 1.38e-02 5.25e+03 1.98e+00 ... (remaining 31261 not shown) Histogram of bond angle deviations from ideal: 97.55 - 104.89: 681 104.89 - 112.22: 15359 112.22 - 119.55: 10856 119.55 - 126.88: 15118 126.88 - 134.21: 424 Bond angle restraints: 42438 Sorted by residual: angle pdb=" C VAL B 514 " pdb=" N ARG B 515 " pdb=" CA ARG B 515 " ideal model delta sigma weight residual 120.38 126.44 -6.06 1.37e+00 5.33e-01 1.96e+01 angle pdb=" N GLY E 608 " pdb=" CA GLY E 608 " pdb=" C GLY E 608 " ideal model delta sigma weight residual 110.87 116.93 -6.06 1.54e+00 4.22e-01 1.55e+01 angle pdb=" C ASN B 606 " pdb=" N TYR B 607 " pdb=" CA TYR B 607 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C ASN C 606 " pdb=" N TYR C 607 " pdb=" CA TYR C 607 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C ASN E 606 " pdb=" N TYR E 607 " pdb=" CA TYR E 607 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 ... (remaining 42433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 17826 15.45 - 30.90: 678 30.90 - 46.35: 258 46.35 - 61.81: 6 61.81 - 77.26: 18 Dihedral angle restraints: 18786 sinusoidal: 7266 harmonic: 11520 Sorted by residual: dihedral pdb=" CA GLU C 521 " pdb=" C GLU C 521 " pdb=" N ASP C 522 " pdb=" CA ASP C 522 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASP D 522 " pdb=" C ASP D 522 " pdb=" N ARG D 523 " pdb=" CA ARG D 523 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ASP F 522 " pdb=" C ASP F 522 " pdb=" N ARG F 523 " pdb=" CA ARG F 523 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 18783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2980 0.040 - 0.079: 1257 0.079 - 0.119: 491 0.119 - 0.158: 95 0.158 - 0.198: 13 Chirality restraints: 4836 Sorted by residual: chirality pdb=" CA TYR F 607 " pdb=" N TYR F 607 " pdb=" C TYR F 607 " pdb=" CB TYR F 607 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CA TYR E 607 " pdb=" N TYR E 607 " pdb=" C TYR E 607 " pdb=" CB TYR E 607 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CB VAL F 514 " pdb=" CA VAL F 514 " pdb=" CG1 VAL F 514 " pdb=" CG2 VAL F 514 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.46e-01 ... (remaining 4833 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 398 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO A 399 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 124 " -0.013 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP C 124 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 124 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 124 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 124 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 124 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 124 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 124 " -0.012 2.00e-02 2.50e+03 1.45e-02 5.23e+00 pdb=" CG TRP E 124 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E 124 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP E 124 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 124 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 124 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 124 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 124 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 124 " -0.002 2.00e-02 2.50e+03 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 9171 2.82 - 3.34: 27230 3.34 - 3.86: 53926 3.86 - 4.38: 61769 4.38 - 4.90: 108583 Nonbonded interactions: 260679 Sorted by model distance: nonbonded pdb=" OG SER F 19 " pdb=" OE1 GLU F 33 " model vdw 2.305 2.440 nonbonded pdb=" OG SER E 36 " pdb=" O SER E 214 " model vdw 2.310 2.440 nonbonded pdb=" OG SER A 36 " pdb=" O SER A 214 " model vdw 2.318 2.440 nonbonded pdb=" OD2 ASP C 127 " pdb=" ND1 HIS C 142 " model vdw 2.326 2.520 nonbonded pdb=" OD2 ASP B 127 " pdb=" ND1 HIS B 142 " model vdw 2.327 2.520 ... (remaining 260674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 16.800 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 83.210 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.180 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31266 Z= 0.272 Angle : 0.811 9.596 42438 Z= 0.435 Chirality : 0.050 0.198 4836 Planarity : 0.007 0.058 5568 Dihedral : 10.099 77.256 11382 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.16 % Allowed : 3.09 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.10), residues: 4056 helix: -2.80 (0.10), residues: 1338 sheet: -2.65 (0.16), residues: 720 loop : -2.49 (0.11), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 124 HIS 0.010 0.002 HIS E 463 PHE 0.023 0.003 PHE A 595 TYR 0.014 0.002 TYR A 607 ARG 0.016 0.001 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 796 time to evaluate : 3.375 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 outliers start: 5 outliers final: 3 residues processed: 801 average time/residue: 1.6680 time to fit residues: 1526.7024 Evaluate side-chains 340 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 337 time to evaluate : 2.706 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 3.4501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 4.9990 chunk 304 optimal weight: 0.0040 chunk 169 optimal weight: 0.9990 chunk 104 optimal weight: 0.0270 chunk 205 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 365 optimal weight: 4.9990 overall best weight: 1.0056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 329 GLN A 392 HIS A 500 GLN A 660 GLN B 24 HIS B 153 HIS B 261 ASN B 309 ASN B 411 HIS B 450 GLN B 500 GLN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 HIS C 500 GLN ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN D 24 HIS D 46 GLN D 153 HIS D 158 ASN D 191 GLN D 305 GLN D 347 GLN D 500 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 320 GLN E 329 GLN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 ASN E 660 GLN F 24 HIS ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 GLN F 500 GLN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 31266 Z= 0.234 Angle : 0.595 11.591 42438 Z= 0.306 Chirality : 0.043 0.147 4836 Planarity : 0.005 0.046 5568 Dihedral : 4.729 20.425 4332 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.16 % Allowed : 12.04 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.12), residues: 4056 helix: -0.81 (0.13), residues: 1392 sheet: -2.06 (0.17), residues: 738 loop : -1.90 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 124 HIS 0.016 0.001 HIS C 463 PHE 0.035 0.002 PHE F 595 TYR 0.015 0.002 TYR F 607 ARG 0.008 0.001 ARG C 632 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 380 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 31 residues processed: 478 average time/residue: 1.2598 time to fit residues: 700.8278 Evaluate side-chains 326 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 295 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 25 residues processed: 6 average time/residue: 0.2222 time to fit residues: 5.1483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 303 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 365 optimal weight: 0.5980 chunk 395 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 362 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: