Starting phenix.real_space_refine (version: dev) on Tue Feb 28 00:33:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqo_9876/02_2023/6jqo_9876_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqo_9876/02_2023/6jqo_9876.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqo_9876/02_2023/6jqo_9876_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqo_9876/02_2023/6jqo_9876_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqo_9876/02_2023/6jqo_9876_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqo_9876/02_2023/6jqo_9876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqo_9876/02_2023/6jqo_9876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqo_9876/02_2023/6jqo_9876_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqo_9876/02_2023/6jqo_9876_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.014 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 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 "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 656": "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 "D TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 656": "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 "E PHE 656": "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" Residue "F PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31254 Number of models: 1 Model: "" Number of chains: 12 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} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.82, per 1000 atoms: 0.57 Number of scatterers: 31254 At special positions: 0 Unit cell: (183.04, 179.92, 111.28, 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 156 16.00 P 36 15.00 O 5934 8.00 N 5508 7.00 C 19620 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: 12.45 Conformation dependent library (CDL) restraints added in 5.2 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... running ksdssp... Secondary structure from input PDB file: 141 helices and 48 sheets defined 32.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.612A pdb=" N GLU A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Proline residue: A 54 - end of helix Processing helix chain 'A' and resid 61 through 77 removed outlier: 3.759A pdb=" N LEU A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.899A pdb=" N TYR A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 84 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 116 removed outlier: 3.705A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.700A pdb=" N ALA A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.603A pdb=" N GLN A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 275 through 292 removed outlier: 3.567A pdb=" N ILE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.658A pdb=" N VAL A 308 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 312 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP A 313 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 315 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 316 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 removed outlier: 3.605A pdb=" N GLN A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.655A pdb=" N ASP A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.037A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 509 " --> pdb=" O MET A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 531 through 533 No H-bonds generated for 'chain 'A' and resid 531 through 533' Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.731A pdb=" N VAL A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 567 No H-bonds generated for 'chain 'A' and resid 564 through 567' Processing helix chain 'A' and resid 584 through 595 removed outlier: 3.803A pdb=" N LEU A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.761A pdb=" N ARG B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 61 through 77 removed outlier: 3.548A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 89 removed outlier: 3.582A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 117 removed outlier: 3.967A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 removed outlier: 4.330A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.960A 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 184 through 200 removed outlier: 3.784A pdb=" N ALA B 187 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLN B 188 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 189 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN B 191 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 195 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP B 199 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.881A pdb=" N MET B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 274 through 292 removed outlier: 3.655A pdb=" N LEU B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALA B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLY B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.729A pdb=" N VAL B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 310 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL B 316 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN B 320 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS B 321 " --> pdb=" O ARG B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 354 removed outlier: 3.606A pdb=" N GLN B 347 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 387 No H-bonds generated for 'chain 'B' and resid 385 through 387' Processing helix chain 'B' and resid 411 through 419 removed outlier: 3.600A pdb=" N ALA B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 removed outlier: 3.584A pdb=" N ASP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 503 through 510 removed outlier: 4.102A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 531 through 533 No H-bonds generated for 'chain 'B' and resid 531 through 533' Processing helix chain 'B' and resid 549 through 559 removed outlier: 3.610A pdb=" N VAL B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 567 No H-bonds generated for 'chain 'B' and resid 564 through 567' Processing helix chain 'B' and resid 570 through 573 No H-bonds generated for 'chain 'B' and resid 570 through 573' Processing helix chain 'B' and resid 584 through 595 removed outlier: 3.505A pdb=" N ALA B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 594 " --> pdb=" O ALA B 590 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 removed outlier: 4.033A pdb=" N ALA C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Proline residue: C 54 - end of helix Processing helix chain 'C' and resid 61 through 77 removed outlier: 3.654A pdb=" N LEU C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.841A pdb=" N TYR C 83 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA C 84 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 116 removed outlier: 4.005A pdb=" N VAL C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 165 No H-bonds generated for 'chain 'C' and resid 162 through 165' Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 187 through 200 removed outlier: 3.629A pdb=" N ALA C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 240 No H-bonds generated for 'chain 'C' and resid 237 through 240' Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 275 through 292 removed outlier: 3.616A pdb=" N ILE C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.669A pdb=" N VAL C 308 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASN C 309 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA C 310 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER C 312 " --> pdb=" O ASN C 309 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP C 313 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU C 315 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL C 316 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 317 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 355 removed outlier: 3.516A pdb=" N GLN C 347 " --> pdb=" O ARG C 343 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 387 No H-bonds generated for 'chain 'C' and resid 385 through 387' Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 434 through 442 removed outlier: 3.682A pdb=" N ASP C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 490 through 493 removed outlier: 3.622A pdb=" N TYR C 493 " --> pdb=" O VAL C 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 490 through 493' Processing helix chain 'C' and resid 503 through 509 removed outlier: 4.130A pdb=" N ALA C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 509 " --> pdb=" O MET C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.541A pdb=" N VAL C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 567 No H-bonds generated for 'chain 'C' and resid 564 through 567' Processing helix chain 'C' and resid 570 through 573 No H-bonds generated for 'chain 'C' and resid 570 through 573' Processing helix chain 'C' and resid 584 through 595 removed outlier: 3.534A pdb=" N ALA C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 594 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 51 removed outlier: 3.710A pdb=" N ARG D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 61 through 77 removed outlier: 3.545A pdb=" N LEU D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 removed outlier: 3.905A pdb=" N ALA D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 117 removed outlier: 3.795A pdb=" N VAL D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 165 No H-bonds generated for 'chain 'D' and resid 162 through 165' Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 184 through 200 removed outlier: 3.827A pdb=" N ALA D 187 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN D 188 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 189 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN D 191 " --> pdb=" O GLN D 188 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER D 200 " --> pdb=" O ILE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 240 removed outlier: 3.758A pdb=" N MET D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 249 No H-bonds generated for 'chain 'D' and resid 246 through 249' Processing helix chain 'D' and resid 274 through 292 removed outlier: 3.669A pdb=" N LEU D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA D 291 " --> pdb=" O MET D 287 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 321 removed outlier: 3.756A pdb=" N VAL D 308 " --> pdb=" O GLN D 305 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN D 309 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA D 310 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU D 315 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL D 316 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN D 320 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS D 321 " --> pdb=" O ARG D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 354 removed outlier: 3.582A pdb=" N GLN D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 387 No H-bonds generated for 'chain 'D' and resid 385 through 387' Processing helix chain 'D' and resid 412 through 419 removed outlier: 3.666A pdb=" N CYS D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 442 removed outlier: 3.630A pdb=" N ASP D 441 " --> pdb=" O GLN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 503 through 509 removed outlier: 4.174A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 528 No H-bonds generated for 'chain 'D' and resid 526 through 528' Processing helix chain 'D' and resid 531 through 533 No H-bonds generated for 'chain 'D' and resid 531 through 533' Processing helix chain 'D' and resid 549 through 559 removed outlier: 3.546A pdb=" N VAL D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 567 No H-bonds generated for 'chain 'D' and resid 564 through 567' Processing helix chain 'D' and resid 584 through 595 removed outlier: 3.519A pdb=" N ALA D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 594 " --> pdb=" O ALA D 590 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 56 removed outlier: 4.160A pdb=" N ALA E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 61 through 77 removed outlier: 3.608A pdb=" N LEU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 removed outlier: 3.950A pdb=" N TYR E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA E 84 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 116 removed outlier: 3.645A pdb=" N VAL E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP E 99 " --> pdb=" O ASP E 95 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 187 through 200 removed outlier: 3.653A pdb=" N ALA E 192 " --> pdb=" O GLN E 188 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 240 No H-bonds generated for 'chain 'E' and resid 237 through 240' Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 274 through 292 removed outlier: 3.689A pdb=" N LEU E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA E 291 " --> pdb=" O MET E 287 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 319 removed outlier: 3.760A pdb=" N VAL E 308 " --> pdb=" O GLN E 305 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASN E 309 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 310 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E 312 " --> pdb=" O ASN E 309 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP E 313 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU E 315 " --> pdb=" O SER E 312 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL E 316 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA E 317 " --> pdb=" O ALA E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 354 removed outlier: 3.580A pdb=" N GLN E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 387 No H-bonds generated for 'chain 'E' and resid 385 through 387' Processing helix chain 'E' and resid 412 through 419 removed outlier: 3.663A pdb=" N CYS E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 442 removed outlier: 3.825A pdb=" N ARG E 436 " --> pdb=" O PRO E 432 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 458 No H-bonds generated for 'chain 'E' and resid 456 through 458' Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 490 through 493 removed outlier: 3.573A pdb=" N TYR E 493 " --> pdb=" O VAL E 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 490 through 493' Processing helix chain 'E' and resid 503 through 510 removed outlier: 3.937A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 528 No H-bonds generated for 'chain 'E' and resid 526 through 528' Processing helix chain 'E' and resid 531 through 533 No H-bonds generated for 'chain 'E' and resid 531 through 533' Processing helix chain 'E' and resid 549 through 559 removed outlier: 3.635A pdb=" N VAL E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 567 No H-bonds generated for 'chain 'E' and resid 564 through 567' Processing helix chain 'E' and resid 572 through 574 No H-bonds generated for 'chain 'E' and resid 572 through 574' Processing helix chain 'E' and resid 584 through 595 removed outlier: 3.598A pdb=" N ALA E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.614A pdb=" N ARG F 45 " --> pdb=" O MET F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 56 No H-bonds generated for 'chain 'F' and resid 53 through 56' Processing helix chain 'F' and resid 61 through 77 removed outlier: 3.518A pdb=" N LEU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 89 removed outlier: 3.589A pdb=" N ALA F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 117 removed outlier: 3.897A pdb=" N VAL F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP F 99 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 107 " --> pdb=" O GLY F 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY F 114 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.002A pdb=" N LYS F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Proline residue: F 170 - end of helix Processing helix chain 'F' and resid 188 through 200 removed outlier: 3.684A pdb=" N ALA F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.765A pdb=" N MET F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 249 No H-bonds generated for 'chain 'F' and resid 246 through 249' Processing helix chain 'F' and resid 274 through 292 removed outlier: 3.642A pdb=" N LEU F 278 " --> pdb=" O PRO F 274 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA F 291 " --> pdb=" O MET F 287 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLY F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 321 removed outlier: 3.805A pdb=" N VAL F 308 " --> pdb=" O GLN F 305 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASN F 309 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA F 310 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU F 315 " --> pdb=" O SER F 312 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN F 320 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS F 321 " --> pdb=" O ARG F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 354 removed outlier: 3.741A pdb=" N GLN F 347 " --> pdb=" O ARG F 343 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU F 348 " --> pdb=" O ALA F 344 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 415 No H-bonds generated for 'chain 'F' and resid 412 through 415' Processing helix chain 'F' and resid 432 through 442 removed outlier: 3.543A pdb=" N ASP F 441 " --> pdb=" O GLN F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 458 No H-bonds generated for 'chain 'F' and resid 456 through 458' Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 490 through 493 removed outlier: 3.562A pdb=" N TYR F 493 " --> pdb=" O VAL F 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 490 through 493' Processing helix chain 'F' and resid 503 through 510 removed outlier: 4.010A pdb=" N ALA F 508 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 528 No H-bonds generated for 'chain 'F' and resid 526 through 528' Processing helix chain 'F' and resid 531 through 533 No H-bonds generated for 'chain 'F' and resid 531 through 533' Processing helix chain 'F' and resid 549 through 559 removed outlier: 3.690A pdb=" N VAL F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 595 removed outlier: 3.531A pdb=" N ALA F 592 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 593 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 594 " --> pdb=" O ALA F 590 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 595 " --> pdb=" O ALA F 591 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 139 through 146 Processing sheet with id= C, first strand: chain 'A' and resid 252 through 254 removed outlier: 7.911A pdb=" N HIS A 153 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 179 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 402 through 406 removed outlier: 6.450A pdb=" N ASN A 261 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 301 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS A 263 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 303 " --> pdb=" O CYS A 263 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 425 through 428 Processing sheet with id= F, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.617A pdb=" N GLU A 650 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 545 through 547 removed outlier: 3.893A pdb=" N ASP A 622 " --> pdb=" O MET A 547 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.573A pdb=" N TRP A 32 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 6 through 8 Processing sheet with id= J, first strand: chain 'B' and resid 139 through 146 Processing sheet with id= K, first strand: chain 'B' and resid 252 through 256 removed outlier: 7.719A pdb=" N HIS B 153 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 179 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 180 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 402 through 406 removed outlier: 6.522A pdb=" N ASN B 261 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE B 301 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS B 263 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL B 303 " --> pdb=" O CYS B 263 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 425 through 428 Processing sheet with id= N, first strand: chain 'B' and resid 539 through 541 removed outlier: 6.589A pdb=" N GLU B 650 " --> pdb=" O LYS B 631 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 545 through 547 removed outlier: 3.960A pdb=" N ASP B 622 " --> pdb=" O MET B 547 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.682A pdb=" N TRP B 32 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 6 through 8 Processing sheet with id= R, first strand: chain 'C' and resid 139 through 146 Processing sheet with id= S, first strand: chain 'C' and resid 252 through 256 removed outlier: 7.806A pdb=" N HIS C 153 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 179 " --> pdb=" O HIS C 153 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 402 through 406 removed outlier: 6.654A pdb=" N ASN C 261 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILE C 301 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS C 263 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL C 303 " --> pdb=" O CYS C 263 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 425 through 428 Processing sheet with id= V, first strand: chain 'C' and resid 539 through 541 removed outlier: 6.638A pdb=" N GLU C 650 " --> pdb=" O LYS C 631 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 545 through 547 removed outlier: 3.704A pdb=" N ASP C 622 " --> pdb=" O MET C 547 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.560A pdb=" N TRP C 32 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 6 through 8 Processing sheet with id= Z, first strand: chain 'D' and resid 139 through 146 Processing sheet with id= AA, first strand: chain 'D' and resid 252 through 254 removed outlier: 7.841A pdb=" N HIS D 153 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE D 179 " --> pdb=" O HIS D 153 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 180 " --> pdb=" O SER D 209 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 402 through 406 removed outlier: 6.423A pdb=" N ASN D 261 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE D 301 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS D 263 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL D 303 " --> pdb=" O CYS D 263 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 425 through 428 Processing sheet with id= AD, first strand: chain 'D' and resid 539 through 541 removed outlier: 6.618A pdb=" N GLU D 650 " --> pdb=" O LYS D 631 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 545 through 547 removed outlier: 3.900A pdb=" N ASP D 622 " --> pdb=" O MET D 547 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 20 through 23 removed outlier: 3.655A pdb=" N TRP D 32 " --> pdb=" O ILE D 22 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 6 through 8 Processing sheet with id= AH, first strand: chain 'E' and resid 139 through 146 Processing sheet with id= AI, first strand: chain 'E' and resid 252 through 254 removed outlier: 7.805A pdb=" N HIS E 153 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 179 " --> pdb=" O HIS E 153 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 402 through 406 removed outlier: 6.432A pdb=" N ASN E 261 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE E 301 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS E 263 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL E 303 " --> pdb=" O CYS E 263 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 425 through 428 Processing sheet with id= AL, first strand: chain 'E' and resid 539 through 541 removed outlier: 6.575A pdb=" N GLU E 650 " --> pdb=" O LYS E 631 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 545 through 547 removed outlier: 3.780A pdb=" N ASP E 622 " --> pdb=" O MET E 547 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.595A pdb=" N TRP E 32 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 6 through 8 Processing sheet with id= AP, first strand: chain 'F' and resid 139 through 146 Processing sheet with id= AQ, first strand: chain 'F' and resid 252 through 256 removed outlier: 7.757A pdb=" N HIS F 153 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 179 " --> pdb=" O HIS F 153 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 402 through 406 removed outlier: 6.563A pdb=" N ASN F 261 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE F 301 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS F 263 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL F 303 " --> pdb=" O CYS F 263 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'F' and resid 425 through 428 Processing sheet with id= AT, first strand: chain 'F' and resid 539 through 541 removed outlier: 6.580A pdb=" N GLU F 650 " --> pdb=" O LYS F 631 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'F' and resid 545 through 547 removed outlier: 3.766A pdb=" N ASP F 622 " --> pdb=" O MET F 547 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'F' and resid 20 through 23 867 hydrogen bonds defined for protein. 2265 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.73 Time building geometry restraints manager: 13.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9169 1.33 - 1.45: 4703 1.45 - 1.57: 17724 1.57 - 1.69: 66 1.69 - 1.81: 246 Bond restraints: 31908 Sorted by residual: bond pdb=" C2X COO D 802 " pdb=" O2X COO D 802 " ideal model delta sigma weight residual 0.000 1.430 -1.430 2.00e-02 2.50e+03 5.11e+03 bond pdb=" C2X COO F 802 " pdb=" O2X COO F 802 " ideal model delta sigma weight residual 0.000 1.430 -1.430 2.00e-02 2.50e+03 5.11e+03 bond pdb=" C2X COO B 802 " pdb=" O2X COO B 802 " ideal model delta sigma weight residual 0.000 1.430 -1.430 2.00e-02 2.50e+03 5.11e+03 bond pdb=" C2X COO E 802 " pdb=" O2X COO E 802 " ideal model delta sigma weight residual 0.000 1.429 -1.429 2.00e-02 2.50e+03 5.11e+03 bond pdb=" C2X COO C 802 " pdb=" O2X COO C 802 " ideal model delta sigma weight residual 0.000 1.429 -1.429 2.00e-02 2.50e+03 5.11e+03 ... (remaining 31903 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.74: 889 105.74 - 113.39: 17684 113.39 - 121.04: 15148 121.04 - 128.70: 9441 128.70 - 136.35: 242 Bond angle restraints: 43404 Sorted by residual: angle pdb=" O1N NAP A 801 " pdb=" PN NAP A 801 " pdb=" O2N NAP A 801 " ideal model delta sigma weight residual 122.51 110.18 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O1N NAP C 801 " pdb=" PN NAP C 801 " pdb=" O2N NAP C 801 " ideal model delta sigma weight residual 122.51 110.24 12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" O1N NAP E 801 " pdb=" PN NAP E 801 " pdb=" O2N NAP E 801 " ideal model delta sigma weight residual 122.51 110.33 12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" O1N NAP B 801 " pdb=" PN NAP B 801 " pdb=" O2N NAP B 801 " ideal model delta sigma weight residual 122.51 110.34 12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C1X COO E 802 " pdb=" N9A COO E 802 " pdb=" C4A COO E 802 " ideal model delta sigma weight residual 115.82 127.99 -12.17 3.00e+00 1.11e-01 1.64e+01 ... (remaining 43399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 18022 16.84 - 33.69: 708 33.69 - 50.53: 191 50.53 - 67.37: 39 67.37 - 84.22: 24 Dihedral angle restraints: 18984 sinusoidal: 7464 harmonic: 11520 Sorted by residual: dihedral pdb=" CA GLU D 521 " pdb=" C GLU D 521 " pdb=" N ASP D 522 " pdb=" CA ASP D 522 " ideal model delta harmonic sigma weight residual -180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP E 522 " pdb=" C ASP E 522 " pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA GLU B 521 " pdb=" C GLU B 521 " pdb=" N ASP B 522 " pdb=" CA ASP B 522 " ideal model delta harmonic sigma weight residual 180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 18981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.026: 4896 1.026 - 2.052: 0 2.052 - 3.077: 0 3.077 - 4.103: 0 4.103 - 5.129: 12 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1X COO D 802 " pdb=" C2X COO D 802 " pdb=" N9A COO D 802 " pdb=" O4X COO D 802 " both_signs ideal model delta sigma weight residual False -2.65 2.48 -5.13 2.00e-01 2.50e+01 6.58e+02 chirality pdb=" C1X COO C 802 " pdb=" C2X COO C 802 " pdb=" N9A COO C 802 " pdb=" O4X COO C 802 " both_signs ideal model delta sigma weight residual False -2.65 2.47 -5.12 2.00e-01 2.50e+01 6.56e+02 chirality pdb=" C1X COO B 802 " pdb=" C2X COO B 802 " pdb=" N9A COO B 802 " pdb=" O4X COO B 802 " both_signs ideal model delta sigma weight residual False -2.65 2.47 -5.12 2.00e-01 2.50e+01 6.56e+02 ... (remaining 4905 not shown) Planarity restraints: 5616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 COO C 802 " -0.010 2.00e-02 2.50e+03 4.90e-02 3.00e+01 pdb=" C13 COO C 802 " 0.044 2.00e-02 2.50e+03 pdb=" C2 COO C 802 " 0.060 2.00e-02 2.50e+03 pdb=" N1 COO C 802 " -0.079 2.00e-02 2.50e+03 pdb=" O2 COO C 802 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 COO D 802 " -0.045 2.00e-02 2.50e+03 4.89e-02 2.99e+01 pdb=" C4 COO D 802 " 0.016 2.00e-02 2.50e+03 pdb=" C5 COO D 802 " -0.060 2.00e-02 2.50e+03 pdb=" N2 COO D 802 " 0.077 2.00e-02 2.50e+03 pdb=" O3 COO D 802 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 COO F 802 " 0.042 2.00e-02 2.50e+03 4.51e-02 2.55e+01 pdb=" C4 COO F 802 " -0.015 2.00e-02 2.50e+03 pdb=" C5 COO F 802 " 0.055 2.00e-02 2.50e+03 pdb=" N2 COO F 802 " -0.071 2.00e-02 2.50e+03 pdb=" O3 COO F 802 " -0.011 2.00e-02 2.50e+03 ... (remaining 5613 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 10019 2.85 - 3.36: 26114 3.36 - 3.87: 50096 3.87 - 4.39: 58093 4.39 - 4.90: 102763 Nonbonded interactions: 247085 Sorted by model distance: nonbonded pdb=" OG1 THR E 270 " pdb=" OD1 ASP E 272 " model vdw 2.337 2.440 nonbonded pdb=" OG1 THR A 270 " pdb=" OD1 ASP A 272 " model vdw 2.346 2.440 nonbonded pdb=" OG1 THR D 426 " pdb=" ND1 HIS D 463 " model vdw 2.348 2.520 nonbonded pdb=" OG1 THR C 270 " pdb=" OD1 ASP C 272 " model vdw 2.349 2.440 nonbonded pdb=" OD2 ASP D 127 " pdb=" ND1 HIS D 142 " model vdw 2.358 2.520 ... (remaining 247080 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 156 5.16 5 C 19620 2.51 5 N 5508 2.21 5 O 5934 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.000 Check model and map are aligned: 0.530 Process input model: 79.580 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.290 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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 : 0.025 1.430 31908 Z= 1.720 Angle : 1.009 12.327 43404 Z= 0.492 Chirality : 0.257 5.129 4908 Planarity : 0.008 0.067 5616 Dihedral : 11.109 84.217 11580 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.13 % 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: -3.99 (0.10), residues: 4056 helix: -3.23 (0.10), residues: 1200 sheet: -1.34 (0.19), residues: 702 loop : -2.80 (0.10), residues: 2154 *********************** 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 624 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 620 time to evaluate : 3.868 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 624 average time/residue: 0.5865 time to fit residues: 531.0300 Evaluate side-chains 300 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 3.878 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2726 time to fit residues: 5.6486 ------------------------------------------------------------------------------- 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: 3.9990 chunk 304 optimal weight: 6.9990 chunk 169 optimal weight: 0.0170 chunk 104 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 365 optimal weight: 3.9990 overall best weight: 1.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 450 GLN A 525 HIS B 46 GLN B 158 ASN B 347 GLN B 392 HIS B 433 GLN B 450 GLN B 463 HIS ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 339 ASN C 392 HIS C 433 GLN C 525 HIS D 3 GLN D 433 GLN D 450 GLN D 554 ASN D 566 HIS ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 347 GLN E 450 GLN ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 HIS F 392 HIS F 433 GLN F 450 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.213 31908 Z= 0.438 Angle : 0.933 18.833 43404 Z= 0.420 Chirality : 0.060 1.268 4908 Planarity : 0.007 0.062 5616 Dihedral : 8.950 83.440 4530 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.11), residues: 4056 helix: -2.75 (0.11), residues: 1212 sheet: -1.17 (0.19), residues: 702 loop : -2.74 (0.10), residues: 2142 *********************** 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 337 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 307 time to evaluate : 4.061 Fit side-chains outliers start: 30 outliers final: 21 residues processed: 329 average time/residue: 0.5483 time to fit residues: 270.3496 Evaluate side-chains 303 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 282 time to evaluate : 3.876 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3508 time to fit residues: 18.0788 ------------------------------------------------------------------------------- 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: 7.9990 chunk 113 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 365 optimal weight: 0.0050 chunk 395 optimal weight: 4.9990 chunk 325 optimal weight: 5.9990 chunk 362 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.307 31908 Z= 0.400 Angle : 0.893 17.723 43404 Z= 0.406 Chirality : 0.066 1.331 4908 Planarity : 0.007 0.056 5616 Dihedral : 8.931 83.997 4530 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.32 % 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: -3.59 (0.11), residues: 4056 helix: -2.65 (0.11), residues: 1212 sheet: -1.13 (0.19), residues: 702 loop : -2.70 (0.10), residues: 2142 *********************** REFINEMENT MACRO_CYCLE 3 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 292 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 282 time to evaluate : 3.978 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 290 average time/residue: 0.5487 time to fit residues: 240.5192 Evaluate side-chains 282 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 276 time to evaluate : 3.880 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2879 time to fit residues: 8.5479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 6.9990 chunk 274 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 245 optimal weight: 5.9990 chunk 367 optimal weight: 0.6980 chunk 388 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 347 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.307 31908 Z= 0.400 Angle : 0.893 17.723 43404 Z= 0.406 Chirality : 0.066 1.331 4908 Planarity : 0.007 0.056 5616 Dihedral : 8.931 83.997 4530 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.00 % 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: -3.59 (0.11), residues: 4056 helix: -2.65 (0.11), residues: 1212 sheet: -1.13 (0.19), residues: 702 loop : -2.70 (0.10), residues: 2142 *********************** REFINEMENT MACRO_CYCLE 4 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 277 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.704 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.5561 time to fit residues: 231.7438 Evaluate side-chains 276 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 331 optimal weight: 0.9990 chunk 268 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 348 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.307 31908 Z= 0.400 Angle : 0.893 17.723 43404 Z= 0.406 Chirality : 0.066 1.330 4908 Planarity : 0.007 0.056 5616 Dihedral : 8.931 83.998 4530 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.00 % 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: -3.59 (0.11), residues: 4056 helix: -2.65 (0.11), residues: 1212 sheet: -1.13 (0.19), residues: 702 loop : -2.70 (0.10), residues: 2142 *********************** REFINEMENT MACRO_CYCLE 5 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 276 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.758 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.5720 time to fit residues: 237.8397 Evaluate side-chains 276 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.754 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 3.9990 chunk 349 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 228 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 322 optimal weight: 0.0870 chunk 180 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 chunk 128 optimal weight: 3.9990 chunk 204 optimal weight: 0.3980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.223 31908 Z= 0.330 Angle : 0.879 17.725 43404 Z= 0.401 Chirality : 0.060 1.124 4908 Planarity : 0.007 0.054 5616 Dihedral : 8.918 84.193 4530 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.28 % 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: -3.58 (0.11), residues: 4056 helix: -2.62 (0.11), residues: 1212 sheet: -1.12 (0.19), residues: 702 loop : -2.70 (0.10), residues: 2142 *********************** REFINEMENT MACRO_CYCLE 6 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 284 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 275 time to evaluate : 3.846 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 280 average time/residue: 0.5634 time to fit residues: 238.5470 Evaluate side-chains 283 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 274 time to evaluate : 4.052 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2927 time to fit residues: 9.9543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 284 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 327 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 387 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 236 optimal weight: 0.0670 chunk 178 optimal weight: 4.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.190 31908 Z= 0.308 Angle : 0.865 17.348 43404 Z= 0.394 Chirality : 0.057 1.078 4908 Planarity : 0.007 0.053 5616 Dihedral : 8.913 84.245 4530 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.00 % 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: -3.56 (0.11), residues: 4056 helix: -2.60 (0.11), residues: 1212 sheet: -1.12 (0.19), residues: 702 loop : -2.69 (0.10), residues: 2142 *********************** REFINEMENT MACRO_CYCLE 7 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 275 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 3.886 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.5755 time to fit residues: 238.1403 Evaluate side-chains 275 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 4.171 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 304 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.190 31908 Z= 0.308 Angle : 0.865 17.348 43404 Z= 0.394 Chirality : 0.057 1.078 4908 Planarity : 0.007 0.053 5616 Dihedral : 8.913 84.245 4530 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.00 % 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: -3.56 (0.11), residues: 4056 helix: -2.60 (0.11), residues: 1212 sheet: -1.12 (0.19), residues: 702 loop : -2.69 (0.10), residues: 2142 *********************** REFINEMENT MACRO_CYCLE 8 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 275 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 3.572 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.5747 time to fit residues: 237.6530 Evaluate side-chains 274 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 4.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 0.0970 chunk 371 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 chunk 217 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 326 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 359 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.170 31908 Z= 0.296 Angle : 0.857 17.102 43404 Z= 0.392 Chirality : 0.056 1.046 4908 Planarity : 0.007 0.053 5616 Dihedral : 8.907 84.311 4530 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.06 % 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: -3.54 (0.11), residues: 4056 helix: -2.58 (0.12), residues: 1212 sheet: -1.10 (0.19), residues: 702 loop : -2.69 (0.10), residues: 2142 *********************** REFINEMENT MACRO_CYCLE 9 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 276 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 3.620 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 275 average time/residue: 0.5498 time to fit residues: 227.6994 Evaluate side-chains 275 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 3.726 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2703 time to fit residues: 5.4191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 3.9990 chunk 381 optimal weight: 0.0170 chunk 233 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 265 optimal weight: 7.9990 chunk 400 optimal weight: 1.9990 chunk 368 optimal weight: 5.9990 chunk 318 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.169 31908 Z= 0.295 Angle : 0.856 17.092 43404 Z= 0.391 Chirality : 0.056 1.040 4908 Planarity : 0.007 0.053 5616 Dihedral : 8.907 84.312 4530 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.00 % 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: -3.54 (0.11), residues: 4056 helix: -2.58 (0.12), residues: 1212 sheet: -1.10 (0.19), residues: 702 loop : -2.69 (0.10), residues: 2142 ********************** REFINEMENT MACRO_CYCLE 10 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 274 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 3.688 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.5706 time to fit residues: 234.4689 Evaluate side-chains 275 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 4.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 0.6980 chunk 339 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 327 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.110709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.084360 restraints weight = 54548.241| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.09 r_work: 0.2691 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.159 31908 Z= 0.296 Angle : 0.843 16.795 43404 Z= 0.386 Chirality : 0.055 0.989 4908 Planarity : 0.007 0.053 5616 Dihedral : 8.897 84.356 4530 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.03 % 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: -3.53 (0.11), residues: 4056 helix: -2.56 (0.12), residues: 1212 sheet: -1.10 (0.19), residues: 702 loop : -2.68 (0.10), residues: 2142 =============================================================================== Job complete usr+sys time: 6546.75 seconds wall clock time: 120 minutes 11.56 seconds (7211.56 seconds total)