Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 02:15:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/05_2023/7cm6_30402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/05_2023/7cm6_30402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/05_2023/7cm6_30402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/05_2023/7cm6_30402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/05_2023/7cm6_30402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/05_2023/7cm6_30402_updated.pdb" } resolution = 3.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 184 5.16 5 C 24384 2.51 5 N 6960 2.21 5 O 7136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 468": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 468": "NH1" <-> "NH2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 468": "NH1" <-> "NH2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E ARG 543": "NH1" <-> "NH2" Residue "E ARG 615": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 201": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ARG 307": "NH1" <-> "NH2" Residue "F ARG 322": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 434": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 468": "NH1" <-> "NH2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 543": "NH1" <-> "NH2" Residue "F ARG 615": "NH1" <-> "NH2" Residue "G ARG 110": "NH1" <-> "NH2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G ARG 465": "NH1" <-> "NH2" Residue "G ARG 468": "NH1" <-> "NH2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "G ARG 543": "NH1" <-> "NH2" Residue "G ARG 615": "NH1" <-> "NH2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "H ARG 157": "NH1" <-> "NH2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H ARG 201": "NH1" <-> "NH2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H ARG 307": "NH1" <-> "NH2" Residue "H ARG 322": "NH1" <-> "NH2" Residue "H ARG 338": "NH1" <-> "NH2" Residue "H ARG 434": "NH1" <-> "NH2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H ARG 468": "NH1" <-> "NH2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "H ARG 543": "NH1" <-> "NH2" Residue "H ARG 615": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 38680 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "B" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "C" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "D" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "E" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "F" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "G" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "H" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.77, per 1000 atoms: 0.51 Number of scatterers: 38680 At special positions: 0 Unit cell: (214.165, 214.165, 82.29, 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 184 16.00 P 16 15.00 O 7136 8.00 N 6960 7.00 C 24384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.21 Conformation dependent library (CDL) restraints added in 6.1 seconds 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 296 helices and 8 sheets defined 59.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 63 through 81 Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 87 through 103 Processing helix chain 'A' and resid 109 through 123 Processing helix chain 'A' and resid 125 through 134 removed outlier: 4.077A pdb=" N GLN A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.941A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 168 through 171 No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.211A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.721A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 294 through 301 Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 358 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 384 through 396 Processing helix chain 'A' and resid 414 through 424 removed outlier: 3.601A pdb=" N ILE A 424 " --> pdb=" O TRP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.937A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A 506 " --> pdb=" O TYR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 532 through 544 Processing helix chain 'A' and resid 574 through 585 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU A 676 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 677 " --> pdb=" O ALA A 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 677' Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'B' and resid 63 through 81 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 87 through 103 Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 125 through 134 removed outlier: 4.077A pdb=" N GLN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 removed outlier: 3.941A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 168 through 171 No H-bonds generated for 'chain 'B' and resid 168 through 171' Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.212A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 235 Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 265 through 279 removed outlier: 3.723A pdb=" N THR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 294 through 301 Proline residue: B 298 - end of helix Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 384 through 396 Processing helix chain 'B' and resid 414 through 424 removed outlier: 3.600A pdb=" N ILE B 424 " --> pdb=" O TRP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 440 through 443 No H-bonds generated for 'chain 'B' and resid 440 through 443' Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 487 through 494 removed outlier: 3.937A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR B 503 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B 506 " --> pdb=" O TYR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 574 through 585 Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU B 676 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 677 " --> pdb=" O ALA B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 677' Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'C' and resid 63 through 81 Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 87 through 103 Processing helix chain 'C' and resid 109 through 123 Processing helix chain 'C' and resid 125 through 134 removed outlier: 4.077A pdb=" N GLN C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.942A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 Processing helix chain 'C' and resid 168 through 171 No H-bonds generated for 'chain 'C' and resid 168 through 171' Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.211A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 204 Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 235 Processing helix chain 'C' and resid 239 through 247 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 265 through 279 removed outlier: 3.722A pdb=" N THR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 294 through 301 Proline residue: C 298 - end of helix Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 358 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 384 through 396 Processing helix chain 'C' and resid 414 through 424 removed outlier: 3.600A pdb=" N ILE C 424 " --> pdb=" O TRP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 440 through 443 No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 460 through 475 Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 removed outlier: 4.407A pdb=" N TYR C 503 " --> pdb=" O GLN C 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL C 506 " --> pdb=" O TYR C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 532 through 544 Processing helix chain 'C' and resid 574 through 585 Processing helix chain 'C' and resid 608 through 613 Processing helix chain 'C' and resid 638 through 649 Processing helix chain 'C' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU C 676 " --> pdb=" O GLN C 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 677 " --> pdb=" O ALA C 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 673 through 677' Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'D' and resid 63 through 81 Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 87 through 103 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 125 through 134 removed outlier: 4.078A pdb=" N GLN D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.941A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 Processing helix chain 'D' and resid 168 through 171 No H-bonds generated for 'chain 'D' and resid 168 through 171' Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.212A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 265 through 279 removed outlier: 3.722A pdb=" N THR D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 294 through 301 Proline residue: D 298 - end of helix Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 358 Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 384 through 396 Processing helix chain 'D' and resid 414 through 424 removed outlier: 3.601A pdb=" N ILE D 424 " --> pdb=" O TRP D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 440 through 443 No H-bonds generated for 'chain 'D' and resid 440 through 443' Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 460 through 475 Processing helix chain 'D' and resid 487 through 494 removed outlier: 3.937A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 506 removed outlier: 4.407A pdb=" N TYR D 503 " --> pdb=" O GLN D 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL D 506 " --> pdb=" O TYR D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 532 through 544 Processing helix chain 'D' and resid 574 through 585 Processing helix chain 'D' and resid 608 through 613 Processing helix chain 'D' and resid 638 through 649 Processing helix chain 'D' and resid 673 through 677 removed outlier: 3.876A pdb=" N LEU D 676 " --> pdb=" O GLN D 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 677 " --> pdb=" O ALA D 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 673 through 677' Processing helix chain 'D' and resid 688 through 697 Processing helix chain 'E' and resid 63 through 81 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 87 through 103 Processing helix chain 'E' and resid 109 through 123 Processing helix chain 'E' and resid 125 through 134 removed outlier: 4.077A pdb=" N GLN E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.942A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 162 Processing helix chain 'E' and resid 168 through 171 No H-bonds generated for 'chain 'E' and resid 168 through 171' Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.212A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'E' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 265 through 279 removed outlier: 3.721A pdb=" N THR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 294 through 301 Proline residue: E 298 - end of helix Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 384 through 396 Processing helix chain 'E' and resid 414 through 424 removed outlier: 3.600A pdb=" N ILE E 424 " --> pdb=" O TRP E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 460 through 475 Processing helix chain 'E' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR E 503 " --> pdb=" O GLN E 500 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL E 506 " --> pdb=" O TYR E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 517 No H-bonds generated for 'chain 'E' and resid 515 through 517' Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 532 through 544 Processing helix chain 'E' and resid 574 through 585 Processing helix chain 'E' and resid 608 through 613 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 673 through 677 removed outlier: 3.876A pdb=" N LEU E 676 " --> pdb=" O GLN E 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR E 677 " --> pdb=" O ALA E 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 673 through 677' Processing helix chain 'E' and resid 688 through 697 Processing helix chain 'F' and resid 63 through 81 Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 125 through 134 removed outlier: 4.078A pdb=" N GLN F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 151 removed outlier: 3.942A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 162 Processing helix chain 'F' and resid 168 through 171 No H-bonds generated for 'chain 'F' and resid 168 through 171' Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.212A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 204 Processing helix chain 'F' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 235 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 255 through 259 Processing helix chain 'F' and resid 265 through 279 removed outlier: 3.722A pdb=" N THR F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 294 through 301 Proline residue: F 298 - end of helix Processing helix chain 'F' and resid 305 through 311 Processing helix chain 'F' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 358 Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 384 through 396 Processing helix chain 'F' and resid 414 through 424 removed outlier: 3.601A pdb=" N ILE F 424 " --> pdb=" O TRP F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 434 Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 448 through 452 Processing helix chain 'F' and resid 460 through 475 Processing helix chain 'F' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR F 503 " --> pdb=" O GLN F 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL F 506 " --> pdb=" O TYR F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 517 No H-bonds generated for 'chain 'F' and resid 515 through 517' Processing helix chain 'F' and resid 520 through 525 Processing helix chain 'F' and resid 532 through 544 Processing helix chain 'F' and resid 574 through 585 Processing helix chain 'F' and resid 608 through 613 Processing helix chain 'F' and resid 638 through 649 Processing helix chain 'F' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU F 676 " --> pdb=" O GLN F 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR F 677 " --> pdb=" O ALA F 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 673 through 677' Processing helix chain 'F' and resid 688 through 697 Processing helix chain 'G' and resid 63 through 81 Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 87 through 103 Processing helix chain 'G' and resid 109 through 123 Processing helix chain 'G' and resid 125 through 134 removed outlier: 4.076A pdb=" N GLN G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.943A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 162 Processing helix chain 'G' and resid 168 through 171 No H-bonds generated for 'chain 'G' and resid 168 through 171' Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.211A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 204 Processing helix chain 'G' and resid 208 through 216 removed outlier: 4.785A pdb=" N ARG G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 235 Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 255 through 259 Processing helix chain 'G' and resid 265 through 279 removed outlier: 3.721A pdb=" N THR G 279 " --> pdb=" O ALA G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 294 through 301 Proline residue: G 298 - end of helix Processing helix chain 'G' and resid 305 through 311 Processing helix chain 'G' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL G 331 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 358 Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 384 through 396 Processing helix chain 'G' and resid 414 through 424 removed outlier: 3.601A pdb=" N ILE G 424 " --> pdb=" O TRP G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 434 Processing helix chain 'G' and resid 440 through 443 No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 448 through 452 Processing helix chain 'G' and resid 460 through 475 Processing helix chain 'G' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR G 503 " --> pdb=" O GLN G 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL G 506 " --> pdb=" O TYR G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 515 through 517 No H-bonds generated for 'chain 'G' and resid 515 through 517' Processing helix chain 'G' and resid 520 through 525 Processing helix chain 'G' and resid 532 through 544 Processing helix chain 'G' and resid 574 through 585 Processing helix chain 'G' and resid 608 through 613 Processing helix chain 'G' and resid 638 through 649 Processing helix chain 'G' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU G 676 " --> pdb=" O GLN G 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR G 677 " --> pdb=" O ALA G 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 673 through 677' Processing helix chain 'G' and resid 688 through 697 Processing helix chain 'H' and resid 63 through 81 Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 87 through 103 Processing helix chain 'H' and resid 109 through 123 Processing helix chain 'H' and resid 125 through 134 removed outlier: 4.078A pdb=" N GLN H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 151 removed outlier: 3.942A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 162 Processing helix chain 'H' and resid 168 through 171 No H-bonds generated for 'chain 'H' and resid 168 through 171' Processing helix chain 'H' and resid 178 through 193 removed outlier: 4.211A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS H 193 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 204 Processing helix chain 'H' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 235 Processing helix chain 'H' and resid 239 through 247 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'H' and resid 265 through 279 removed outlier: 3.722A pdb=" N THR H 279 " --> pdb=" O ALA H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 294 through 301 Proline residue: H 298 - end of helix Processing helix chain 'H' and resid 305 through 311 Processing helix chain 'H' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL H 331 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 358 Processing helix chain 'H' and resid 364 through 368 Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 384 through 396 Processing helix chain 'H' and resid 414 through 424 removed outlier: 3.600A pdb=" N ILE H 424 " --> pdb=" O TRP H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 434 Processing helix chain 'H' and resid 440 through 443 No H-bonds generated for 'chain 'H' and resid 440 through 443' Processing helix chain 'H' and resid 448 through 452 Processing helix chain 'H' and resid 460 through 475 Processing helix chain 'H' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 506 removed outlier: 4.407A pdb=" N TYR H 503 " --> pdb=" O GLN H 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL H 506 " --> pdb=" O TYR H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 517 No H-bonds generated for 'chain 'H' and resid 515 through 517' Processing helix chain 'H' and resid 520 through 525 Processing helix chain 'H' and resid 532 through 544 Processing helix chain 'H' and resid 574 through 585 Processing helix chain 'H' and resid 608 through 613 Processing helix chain 'H' and resid 638 through 649 Processing helix chain 'H' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU H 676 " --> pdb=" O GLN H 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 677 " --> pdb=" O ALA H 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 673 through 677' Processing helix chain 'H' and resid 688 through 697 Processing sheet with id= A, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.496A pdb=" N ASN A 616 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N SER A 567 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 618 " --> pdb=" O SER A 567 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.496A pdb=" N ASN B 616 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N SER B 567 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL B 618 " --> pdb=" O SER B 567 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.496A pdb=" N ASN C 616 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER C 567 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL C 618 " --> pdb=" O SER C 567 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 564 through 567 removed outlier: 6.495A pdb=" N ASN D 616 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N SER D 567 " --> pdb=" O ASN D 616 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 618 " --> pdb=" O SER D 567 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 564 through 567 removed outlier: 6.495A pdb=" N ASN E 616 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER E 567 " --> pdb=" O ASN E 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 618 " --> pdb=" O SER E 567 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 564 through 567 removed outlier: 6.496A pdb=" N ASN F 616 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER F 567 " --> pdb=" O ASN F 616 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL F 618 " --> pdb=" O SER F 567 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 564 through 567 removed outlier: 6.495A pdb=" N ASN G 616 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER G 567 " --> pdb=" O ASN G 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL G 618 " --> pdb=" O SER G 567 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 564 through 567 removed outlier: 6.495A pdb=" N ASN H 616 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER H 567 " --> pdb=" O ASN H 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL H 618 " --> pdb=" O SER H 567 " (cutoff:3.500A) 1608 hydrogen bonds defined for protein. 4752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.30 Time building geometry restraints manager: 16.28 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: 8549 1.33 - 1.45: 7943 1.45 - 1.57: 22572 1.57 - 1.69: 24 1.69 - 1.81: 248 Bond restraints: 39336 Sorted by residual: bond pdb=" C2D NAD A1000 " pdb=" O2D NAD A1000 " ideal model delta sigma weight residual 1.393 1.478 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C2D NAD D1000 " pdb=" O2D NAD D1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD B1000 " pdb=" O2D NAD B1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD H1000 " pdb=" O2D NAD H1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD G1000 " pdb=" O2D NAD G1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 39331 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.18: 857 106.18 - 113.22: 21301 113.22 - 120.25: 16008 120.25 - 127.29: 14644 127.29 - 134.32: 414 Bond angle restraints: 53224 Sorted by residual: angle pdb=" C SER F 336 " pdb=" N ASN F 337 " pdb=" CA ASN F 337 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" N VAL H 108 " pdb=" CA VAL H 108 " pdb=" C VAL H 108 " ideal model delta sigma weight residual 112.12 108.41 3.71 8.40e-01 1.42e+00 1.95e+01 angle pdb=" C SER B 336 " pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N VAL B 108 " pdb=" CA VAL B 108 " pdb=" C VAL B 108 " ideal model delta sigma weight residual 112.12 108.42 3.70 8.40e-01 1.42e+00 1.94e+01 angle pdb=" C SER D 336 " pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 ... (remaining 53219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 23006 15.00 - 30.00: 610 30.00 - 45.01: 136 45.01 - 60.01: 16 60.01 - 75.01: 16 Dihedral angle restraints: 23784 sinusoidal: 9736 harmonic: 14048 Sorted by residual: dihedral pdb=" CA TRP B 412 " pdb=" C TRP B 412 " pdb=" N LYS B 413 " pdb=" CA LYS B 413 " ideal model delta harmonic sigma weight residual 180.00 164.22 15.78 0 5.00e+00 4.00e-02 9.96e+00 dihedral pdb=" CA TRP H 412 " pdb=" C TRP H 412 " pdb=" N LYS H 413 " pdb=" CA LYS H 413 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CA TRP G 412 " pdb=" C TRP G 412 " pdb=" N LYS G 413 " pdb=" CA LYS G 413 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.93e+00 ... (remaining 23781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5433 0.069 - 0.138: 592 0.138 - 0.207: 36 0.207 - 0.276: 19 0.276 - 0.345: 8 Chirality restraints: 6088 Sorted by residual: chirality pdb=" C2D NAD D1000 " pdb=" C1D NAD D1000 " pdb=" C3D NAD D1000 " pdb=" O2D NAD D1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C2D NAD F1000 " pdb=" C1D NAD F1000 " pdb=" C3D NAD F1000 " pdb=" O2D NAD F1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C2D NAD H1000 " pdb=" C1D NAD H1000 " pdb=" C3D NAD H1000 " pdb=" O2D NAD H1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 6085 not shown) Planarity restraints: 6848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 283 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C VAL G 283 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL G 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU G 284 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 283 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C VAL F 283 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL F 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU F 284 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 283 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C VAL B 283 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL B 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU B 284 " 0.013 2.00e-02 2.50e+03 ... (remaining 6845 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 10059 2.80 - 3.33: 33540 3.33 - 3.85: 61659 3.85 - 4.38: 73030 4.38 - 4.90: 124944 Nonbonded interactions: 303232 Sorted by model distance: nonbonded pdb=" OE1 GLN D 436 " pdb=" OG SER E 459 " model vdw 2.281 2.440 nonbonded pdb=" OE1 GLN A 436 " pdb=" OG SER B 459 " model vdw 2.320 2.440 nonbonded pdb=" OH TYR B 568 " pdb=" OD1 ASP B 594 " model vdw 2.359 2.440 nonbonded pdb=" OH TYR F 568 " pdb=" OD1 ASP F 594 " model vdw 2.359 2.440 nonbonded pdb=" OH TYR A 568 " pdb=" OD1 ASP A 594 " model vdw 2.359 2.440 ... (remaining 303227 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' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.390 Check model and map are aligned: 0.560 Set scattering table: 0.300 Process input model: 90.080 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 39336 Z= 0.262 Angle : 0.822 13.125 53224 Z= 0.435 Chirality : 0.047 0.345 6088 Planarity : 0.006 0.053 6848 Dihedral : 8.419 75.011 14664 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: -4.13 (0.09), residues: 4824 helix: -2.88 (0.06), residues: 3184 sheet: -1.48 (0.42), residues: 136 loop : -2.00 (0.14), residues: 1504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1045 time to evaluate : 5.006 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 8 residues processed: 1045 average time/residue: 1.8198 time to fit residues: 2228.3683 Evaluate side-chains 408 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 400 time to evaluate : 4.442 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 6.1697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 2.9990 chunk 369 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 197 optimal weight: 0.6980 chunk 382 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 443 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 134 GLN A 236 HIS A 239 GLN A 280 ASN A 575 GLN A 652 ASN B 170 ASN B 236 HIS B 280 ASN B 585 GLN B 652 ASN C 236 HIS C 652 ASN D 134 GLN D 236 HIS D 585 GLN D 652 ASN E 134 GLN E 236 HIS E 652 ASN F 134 GLN F 236 HIS F 585 GLN F 616 ASN F 652 ASN G 134 GLN G 236 HIS G 280 ASN G 575 GLN G 616 ASN G 652 ASN G 700 GLN H 134 GLN H 236 HIS H 280 ASN H 585 GLN H 652 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 39336 Z= 0.218 Angle : 0.542 7.982 53224 Z= 0.272 Chirality : 0.038 0.134 6088 Planarity : 0.004 0.038 6848 Dihedral : 4.435 41.023 5352 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 3.28 % 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: -1.88 (0.11), residues: 4824 helix: -1.03 (0.08), residues: 3312 sheet: -1.14 (0.44), residues: 136 loop : -1.38 (0.16), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 449 time to evaluate : 4.493 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 49 residues processed: 555 average time/residue: 1.7388 time to fit residues: 1146.7515 Evaluate side-chains 348 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 299 time to evaluate : 4.566 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 38 residues processed: 11 average time/residue: 0.4544 time to fit residues: 14.5844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 368 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 443 optimal weight: 0.9990 chunk 479 optimal weight: 0.9980 chunk 395 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 151 optimal weight: 0.0970 chunk 356 optimal weight: 6.9990 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 97 GLN B 280 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 97 GLN C 280 ASN C 575 GLN C 609 GLN D 62 GLN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 616 ASN F 62 GLN G 280 ASN G 609 GLN H 62 GLN H 97 GLN H 134 GLN H 575 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 39336 Z= 0.279 Angle : 0.561 7.715 53224 Z= 0.280 Chirality : 0.040 0.145 6088 Planarity : 0.004 0.040 6848 Dihedral : 4.391 38.654 5352 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 3.90 % 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: -0.87 (0.12), residues: 4824 helix: -0.26 (0.09), residues: 3304 sheet: -1.39 (0.43), residues: 144 loop : -0.91 (0.16), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 337 time to evaluate : 4.679 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 66 residues processed: 449 average time/residue: 1.6540 time to fit residues: 894.8305 Evaluate side-chains 346 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 280 time to evaluate : 4.389 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 51 residues processed: 15 average time/residue: 0.6356 time to fit residues: 20.3082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 445 optimal weight: 1.9990 chunk 471 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 422 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 383 ASN A 585 GLN A 616 ASN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN E 134 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN F 134 GLN F 170 ASN G 700 GLN H 700 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 39336 Z= 0.424 Angle : 0.651 8.044 53224 Z= 0.326 Chirality : 0.044 0.257 6088 Planarity : 0.005 0.043 6848 Dihedral : 4.685 41.058 5352 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 3.87 % 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: -0.69 (0.12), residues: 4824 helix: -0.13 (0.09), residues: 3280 sheet: -1.55 (0.43), residues: 144 loop : -0.79 (0.16), residues: 1400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 284 time to evaluate : 4.750 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 78 residues processed: 406 average time/residue: 1.5900 time to fit residues: 779.0310 Evaluate side-chains 322 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 244 time to evaluate : 4.213 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 63 residues processed: 15 average time/residue: 0.5565 time to fit residues: 18.4860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 351 optimal weight: 0.9980 chunk 194 optimal weight: 0.0470 chunk 402 optimal weight: 1.9990 chunk 326 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 423 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 700 GLN B 328 GLN C 328 GLN C 609 GLN D 575 GLN D 700 GLN E 62 GLN E 328 GLN E 609 GLN E 616 ASN F 700 GLN G 62 GLN G 328 GLN G 383 ASN G 609 GLN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 39336 Z= 0.188 Angle : 0.500 11.015 53224 Z= 0.248 Chirality : 0.038 0.155 6088 Planarity : 0.003 0.039 6848 Dihedral : 4.142 38.841 5352 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 3.16 % 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: 0.05 (0.12), residues: 4824 helix: 0.41 (0.09), residues: 3256 sheet: -1.26 (0.44), residues: 144 loop : -0.41 (0.16), residues: 1424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 297 time to evaluate : 4.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 80 residues processed: 396 average time/residue: 1.4486 time to fit residues: 698.8468 Evaluate side-chains 329 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 249 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 61 residues processed: 19 average time/residue: 0.3695 time to fit residues: 16.4678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 4.9990 chunk 424 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 472 optimal weight: 1.9990 chunk 391 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 247 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: