Starting phenix.real_space_refine on Fri Feb 23 17:41:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm7_30403/02_2024/7cm7_30403_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm7_30403/02_2024/7cm7_30403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm7_30403/02_2024/7cm7_30403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm7_30403/02_2024/7cm7_30403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm7_30403/02_2024/7cm7_30403_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm7_30403/02_2024/7cm7_30403_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 24744 2.51 5 N 7048 2.21 5 O 7224 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39216 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 21, 'TRANS': 598} Chain breaks: 2 Chain: "B" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 21, 'TRANS': 598} Chain breaks: 2 Chain: "C" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 21, 'TRANS': 598} Chain breaks: 2 Chain: "D" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 21, 'TRANS': 598} Chain breaks: 2 Chain: "E" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 21, 'TRANS': 598} Chain breaks: 2 Chain: "F" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 21, 'TRANS': 598} Chain breaks: 2 Chain: "G" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 21, 'TRANS': 598} Chain breaks: 2 Chain: "H" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 21, 'TRANS': 598} Chain breaks: 2 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: 19.51, per 1000 atoms: 0.50 Number of scatterers: 39216 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 7224 8.00 N 7048 7.00 C 24744 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: 13.71 Conformation dependent library (CDL) restraints added in 7.0 seconds 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 304 helices and 8 sheets defined 60.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.33 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: 3.878A pdb=" N GLN A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.922A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.908A pdb=" N ASP A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) 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: 4.255A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 4.155A 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: 4.751A pdb=" N ARG A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 294 through 302 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: 4.016A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.785A 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 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 414 through 424 removed outlier: 3.667A pdb=" N ILE A 424 " --> pdb=" O TRP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.741A pdb=" N CYS A 430 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 433 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 435 " --> pdb=" O SER A 432 " (cutoff:3.500A) 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 492 Processing helix chain 'A' and resid 498 through 506 removed outlier: 3.506A pdb=" N TYR A 501 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 502 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.534A 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 587 removed outlier: 4.232A pdb=" N HIS A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.607A pdb=" N GLY A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.940A pdb=" N LEU A 676 " --> pdb=" O GLN A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 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: 3.879A pdb=" N GLN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.922A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.909A pdb=" N ASP B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) 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: 4.255A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.156A 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: 4.751A pdb=" N ARG B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 236 Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 264 through 279 Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 294 through 302 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: 4.016A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 3.785A 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 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 414 through 424 removed outlier: 3.668A pdb=" N ILE B 424 " --> pdb=" O TRP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 436 removed outlier: 3.741A pdb=" N CYS B 430 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU B 431 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 433 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B 435 " --> pdb=" O SER B 432 " (cutoff:3.500A) 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 492 Processing helix chain 'B' and resid 498 through 506 removed outlier: 3.506A pdb=" N TYR B 501 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 502 " --> pdb=" O ARG B 499 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR B 503 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 3.535A 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 587 removed outlier: 4.233A pdb=" N HIS B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 598 No H-bonds generated for 'chain 'B' and resid 596 through 598' Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.607A pdb=" N GLY B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.940A pdb=" N LEU B 676 " --> pdb=" O GLN B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 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: 3.879A pdb=" N GLN C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.924A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.910A pdb=" N ASP C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) 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: 4.255A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 4.155A 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: 4.750A pdb=" N ARG C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 294 through 302 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: 4.017A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 3.785A 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 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 414 through 424 removed outlier: 3.667A pdb=" N ILE C 424 " --> pdb=" O TRP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 436 removed outlier: 3.741A pdb=" N CYS C 430 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU C 431 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 433 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C 435 " --> pdb=" O SER C 432 " (cutoff:3.500A) 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 492 Processing helix chain 'C' and resid 498 through 506 removed outlier: 3.505A pdb=" N TYR C 501 " --> pdb=" O PHE C 498 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 502 " --> pdb=" O ARG C 499 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR C 503 " --> pdb=" O GLN C 500 " (cutoff:3.500A) removed outlier: 3.535A 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 587 removed outlier: 4.234A pdb=" N HIS C 587 " --> pdb=" O HIS C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.608A pdb=" N GLY C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 649 Processing helix chain 'C' and resid 673 through 677 removed outlier: 3.940A pdb=" N LEU C 676 " --> pdb=" O GLN C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 698 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: 3.880A pdb=" N GLN D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.923A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 3.909A pdb=" N ASP D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) 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: 4.255A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 4.155A 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: 4.751A pdb=" N ARG D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 236 Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 294 through 302 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: 4.016A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) removed outlier: 3.785A 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 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 414 through 424 removed outlier: 3.668A pdb=" N ILE D 424 " --> pdb=" O TRP D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.741A pdb=" N CYS D 430 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU D 431 " --> pdb=" O LYS D 428 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 433 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG D 434 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 435 " --> pdb=" O SER D 432 " (cutoff:3.500A) 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 492 Processing helix chain 'D' and resid 498 through 506 removed outlier: 3.505A pdb=" N TYR D 501 " --> pdb=" O PHE D 498 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 502 " --> pdb=" O ARG D 499 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR D 503 " --> pdb=" O GLN D 500 " (cutoff:3.500A) removed outlier: 3.535A 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 587 removed outlier: 4.232A pdb=" N HIS D 587 " --> pdb=" O HIS D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 598 No H-bonds generated for 'chain 'D' and resid 596 through 598' Processing helix chain 'D' and resid 607 through 613 removed outlier: 3.607A pdb=" N GLY D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 649 Processing helix chain 'D' and resid 673 through 677 removed outlier: 3.940A pdb=" N LEU D 676 " --> pdb=" O GLN D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 698 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: 3.880A pdb=" N GLN E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.923A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.909A pdb=" N ASP E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) 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: 4.255A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.155A 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: 4.750A pdb=" N ARG E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 264 through 279 Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 294 through 302 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: 4.016A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 3.785A 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 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 414 through 424 removed outlier: 3.669A pdb=" N ILE E 424 " --> pdb=" O TRP E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 436 removed outlier: 3.741A pdb=" N CYS E 430 " --> pdb=" O SER E 427 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU E 431 " --> pdb=" O LYS E 428 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE E 433 " --> pdb=" O CYS E 430 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG E 434 " --> pdb=" O GLU E 431 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU E 435 " --> pdb=" O SER E 432 " (cutoff:3.500A) 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 492 Processing helix chain 'E' and resid 498 through 506 removed outlier: 3.506A pdb=" N TYR E 501 " --> pdb=" O PHE E 498 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 502 " --> pdb=" O ARG E 499 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR E 503 " --> pdb=" O GLN E 500 " (cutoff:3.500A) removed outlier: 3.535A 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 587 removed outlier: 4.232A pdb=" N HIS E 587 " --> pdb=" O HIS E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 598 No H-bonds generated for 'chain 'E' and resid 596 through 598' Processing helix chain 'E' and resid 607 through 613 removed outlier: 3.607A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 673 through 677 removed outlier: 3.940A pdb=" N LEU E 676 " --> pdb=" O GLN E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 698 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: 3.878A pdb=" N GLN F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 removed outlier: 3.923A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 162 removed outlier: 3.908A pdb=" N ASP F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) 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: 4.255A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 4.155A 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: 4.750A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 236 Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 264 through 279 Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 294 through 302 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: 4.016A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 3.785A 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 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 414 through 424 removed outlier: 3.668A pdb=" N ILE F 424 " --> pdb=" O TRP F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 436 removed outlier: 3.740A pdb=" N CYS F 430 " --> pdb=" O SER F 427 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU F 431 " --> pdb=" O LYS F 428 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE F 433 " --> pdb=" O CYS F 430 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG F 434 " --> pdb=" O GLU F 431 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU F 435 " --> pdb=" O SER F 432 " (cutoff:3.500A) 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 492 Processing helix chain 'F' and resid 498 through 506 removed outlier: 3.505A pdb=" N TYR F 501 " --> pdb=" O PHE F 498 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR F 502 " --> pdb=" O ARG F 499 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR F 503 " --> pdb=" O GLN F 500 " (cutoff:3.500A) removed outlier: 3.535A 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 587 removed outlier: 4.233A pdb=" N HIS F 587 " --> pdb=" O HIS F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 598 No H-bonds generated for 'chain 'F' and resid 596 through 598' Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.607A pdb=" N GLY F 613 " --> pdb=" O GLN F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 649 Processing helix chain 'F' and resid 673 through 677 removed outlier: 3.941A pdb=" N LEU F 676 " --> pdb=" O GLN F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 698 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: 3.878A pdb=" N GLN G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.923A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 removed outlier: 3.909A pdb=" N ASP G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) 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: 4.255A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 4.155A 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: 4.751A pdb=" N ARG G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 236 Processing helix chain 'G' and resid 239 through 246 Processing helix chain 'G' and resid 264 through 279 Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 294 through 302 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: 4.016A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) removed outlier: 3.785A 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 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 414 through 424 removed outlier: 3.668A pdb=" N ILE G 424 " --> pdb=" O TRP G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 436 removed outlier: 3.741A pdb=" N CYS G 430 " --> pdb=" O SER G 427 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU G 431 " --> pdb=" O LYS G 428 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 433 " --> pdb=" O CYS G 430 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG G 434 " --> pdb=" O GLU G 431 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU G 435 " --> pdb=" O SER G 432 " (cutoff:3.500A) 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 492 Processing helix chain 'G' and resid 498 through 506 removed outlier: 3.505A pdb=" N TYR G 501 " --> pdb=" O PHE G 498 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR G 502 " --> pdb=" O ARG G 499 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR G 503 " --> pdb=" O GLN G 500 " (cutoff:3.500A) removed outlier: 3.535A 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 587 removed outlier: 4.233A pdb=" N HIS G 587 " --> pdb=" O HIS G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 596 through 598 No H-bonds generated for 'chain 'G' and resid 596 through 598' Processing helix chain 'G' and resid 607 through 613 removed outlier: 3.608A pdb=" N GLY G 613 " --> pdb=" O GLN G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 649 Processing helix chain 'G' and resid 673 through 677 removed outlier: 3.940A pdb=" N LEU G 676 " --> pdb=" O GLN G 673 " (cutoff:3.500A) Processing helix chain 'G' and resid 688 through 698 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: 3.879A pdb=" N GLN H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 151 removed outlier: 3.923A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 162 removed outlier: 3.909A pdb=" N ASP H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) 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: 4.255A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.157A 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: 4.751A pdb=" N ARG H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 236 Processing helix chain 'H' and resid 239 through 246 Processing helix chain 'H' and resid 264 through 279 Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 294 through 302 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: 4.016A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) removed outlier: 3.785A 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 409 through 411 No H-bonds generated for 'chain 'H' and resid 409 through 411' Processing helix chain 'H' and resid 414 through 424 removed outlier: 3.668A pdb=" N ILE H 424 " --> pdb=" O TRP H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 436 removed outlier: 3.741A pdb=" N CYS H 430 " --> pdb=" O SER H 427 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU H 431 " --> pdb=" O LYS H 428 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE H 433 " --> pdb=" O CYS H 430 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG H 434 " --> pdb=" O GLU H 431 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU H 435 " --> pdb=" O SER H 432 " (cutoff:3.500A) 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 492 Processing helix chain 'H' and resid 498 through 506 removed outlier: 3.506A pdb=" N TYR H 501 " --> pdb=" O PHE H 498 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 502 " --> pdb=" O ARG H 499 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR H 503 " --> pdb=" O GLN H 500 " (cutoff:3.500A) removed outlier: 3.535A 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 587 removed outlier: 4.233A pdb=" N HIS H 587 " --> pdb=" O HIS H 583 " (cutoff:3.500A) Processing helix chain 'H' and resid 596 through 598 No H-bonds generated for 'chain 'H' and resid 596 through 598' Processing helix chain 'H' and resid 607 through 613 removed outlier: 3.607A pdb=" N GLY H 613 " --> pdb=" O GLN H 609 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 649 Processing helix chain 'H' and resid 673 through 677 removed outlier: 3.940A pdb=" N LEU H 676 " --> pdb=" O GLN H 673 " (cutoff:3.500A) Processing helix chain 'H' and resid 688 through 698 Processing sheet with id= A, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.716A pdb=" N ASN A 616 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER A 567 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 618 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN A 652 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A 619 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 654 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A 621 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 656 " --> pdb=" O LEU A 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.715A pdb=" N ASN B 616 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER B 567 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 618 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN B 652 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU B 619 " --> pdb=" O ASN B 652 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 654 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B 621 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 656 " --> pdb=" O LEU B 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.716A pdb=" N ASN C 616 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER C 567 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 618 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN C 652 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU C 619 " --> pdb=" O ASN C 652 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 654 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU C 621 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 656 " --> pdb=" O LEU C 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'D' and resid 564 through 567 removed outlier: 6.716A pdb=" N ASN D 616 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER D 567 " --> pdb=" O ASN D 616 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL D 618 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASN D 652 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU D 619 " --> pdb=" O ASN D 652 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL D 654 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU D 621 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE D 656 " --> pdb=" O LEU D 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'E' and resid 564 through 567 removed outlier: 6.716A pdb=" N ASN E 616 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N SER E 567 " --> pdb=" O ASN E 616 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL E 618 " --> pdb=" O SER E 567 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN E 652 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU E 619 " --> pdb=" O ASN E 652 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL E 654 " --> pdb=" O LEU E 619 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU E 621 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE E 656 " --> pdb=" O LEU E 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 564 through 567 removed outlier: 6.716A pdb=" N ASN F 616 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER F 567 " --> pdb=" O ASN F 616 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL F 618 " --> pdb=" O SER F 567 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN F 652 " --> pdb=" O PHE F 617 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU F 619 " --> pdb=" O ASN F 652 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL F 654 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU F 621 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE F 656 " --> pdb=" O LEU F 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'G' and resid 564 through 567 removed outlier: 6.716A pdb=" N ASN G 616 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER G 567 " --> pdb=" O ASN G 616 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL G 618 " --> pdb=" O SER G 567 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN G 652 " --> pdb=" O PHE G 617 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU G 619 " --> pdb=" O ASN G 652 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL G 654 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU G 621 " --> pdb=" O VAL G 654 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE G 656 " --> pdb=" O LEU G 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'H' and resid 564 through 567 removed outlier: 6.716A pdb=" N ASN H 616 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER H 567 " --> pdb=" O ASN H 616 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL H 618 " --> pdb=" O SER H 567 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN H 652 " --> pdb=" O PHE H 617 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU H 619 " --> pdb=" O ASN H 652 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL H 654 " --> pdb=" O LEU H 619 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU H 621 " --> pdb=" O VAL H 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE H 656 " --> pdb=" O LEU H 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 1600 hydrogen bonds defined for protein. 4680 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: 12.90 Time building geometry restraints manager: 14.94 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: 8453 1.33 - 1.45: 8245 1.45 - 1.57: 22918 1.57 - 1.69: 24 1.69 - 1.81: 248 Bond restraints: 39888 Sorted by residual: bond pdb=" C2D NAD C1000 " pdb=" O2D NAD C1000 " ideal model delta sigma weight residual 1.393 1.479 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C2D NAD A1000 " pdb=" O2D NAD A1000 " ideal model delta sigma weight residual 1.393 1.479 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C2D NAD F1000 " pdb=" O2D NAD F1000 " ideal model delta sigma weight residual 1.393 1.478 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C2D NAD H1000 " pdb=" O2D NAD H1000 " 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 G1000 " pdb=" O2D NAD G1000 " ideal model delta sigma weight residual 1.393 1.478 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 39883 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.25: 920 106.25 - 113.43: 21968 113.43 - 120.61: 18048 120.61 - 127.79: 12669 127.79 - 134.97: 363 Bond angle restraints: 53968 Sorted by residual: angle pdb=" C SER C 336 " pdb=" N ASN C 337 " pdb=" CA ASN C 337 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C SER H 336 " pdb=" N ASN H 337 " pdb=" CA ASN H 337 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C SER E 336 " pdb=" N ASN E 337 " pdb=" CA ASN E 337 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C SER B 336 " pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C SER D 336 " pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.37e+01 ... (remaining 53963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 23628 15.06 - 30.12: 676 30.12 - 45.18: 152 45.18 - 60.24: 13 60.24 - 75.29: 51 Dihedral angle restraints: 24520 sinusoidal: 10264 harmonic: 14256 Sorted by residual: dihedral pdb=" CA TRP D 412 " pdb=" C TRP D 412 " pdb=" N LYS D 413 " pdb=" CA LYS D 413 " ideal model delta harmonic sigma weight residual 180.00 164.62 15.38 0 5.00e+00 4.00e-02 9.46e+00 dihedral pdb=" CA TRP F 412 " pdb=" C TRP F 412 " pdb=" N LYS F 413 " pdb=" CA LYS F 413 " ideal model delta harmonic sigma weight residual 180.00 164.65 15.35 0 5.00e+00 4.00e-02 9.43e+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 180.00 164.66 15.34 0 5.00e+00 4.00e-02 9.41e+00 ... (remaining 24517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5443 0.069 - 0.139: 660 0.139 - 0.208: 33 0.208 - 0.277: 24 0.277 - 0.347: 8 Chirality restraints: 6168 Sorted by residual: chirality pdb=" C2D NAD G1000 " pdb=" C1D NAD G1000 " pdb=" C3D NAD G1000 " pdb=" O2D NAD G1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C2D NAD B1000 " pdb=" C1D NAD B1000 " pdb=" C3D NAD B1000 " pdb=" O2D NAD B1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C2D NAD C1000 " pdb=" C1D NAD C1000 " pdb=" C3D NAD C1000 " pdb=" O2D NAD C1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 6165 not shown) Planarity restraints: 6944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 283 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C VAL E 283 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL E 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU E 284 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 283 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C VAL F 283 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL F 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU F 284 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 283 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C VAL A 283 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU A 284 " 0.014 2.00e-02 2.50e+03 ... (remaining 6941 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 11970 2.84 - 3.35: 34453 3.35 - 3.87: 62957 3.87 - 4.38: 73271 4.38 - 4.90: 125958 Nonbonded interactions: 308609 Sorted by model distance: nonbonded pdb=" OE1 GLN C 436 " pdb=" OG SER D 459 " model vdw 2.319 2.440 nonbonded pdb=" OE1 GLN A 436 " pdb=" OG SER B 459 " model vdw 2.332 2.440 nonbonded pdb=" OE1 GLN E 436 " pdb=" OG SER F 459 " model vdw 2.352 2.440 nonbonded pdb=" OE1 GLN F 436 " pdb=" OG SER G 459 " model vdw 2.391 2.440 nonbonded pdb=" O THR B 475 " pdb=" NH1 ARG B 499 " model vdw 2.399 2.520 ... (remaining 308604 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: 2.930 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: 0.050 Extract box with map and model: 14.970 Check model and map are aligned: 0.570 Set scattering table: 0.400 Process input model: 96.690 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.270 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: 0.000 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 0.086 39888 Z= 0.267 Angle : 0.837 13.113 53968 Z= 0.449 Chirality : 0.047 0.347 6168 Planarity : 0.006 0.053 6944 Dihedral : 9.039 75.294 15272 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.09), residues: 4912 helix: -2.87 (0.06), residues: 3248 sheet: -0.42 (0.45), residues: 136 loop : -2.20 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 490 HIS 0.008 0.001 HIS F 269 PHE 0.034 0.002 PHE F 192 TYR 0.009 0.001 TYR D 568 ARG 0.008 0.001 ARG F 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 914 time to evaluate : 4.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 LYS cc_start: 0.5779 (mttm) cc_final: 0.5578 (tttp) REVERT: A 672 MET cc_start: 0.3453 (ptm) cc_final: 0.2879 (pp-130) REVERT: B 457 MET cc_start: 0.8407 (ttm) cc_final: 0.7646 (ttm) REVERT: B 643 ILE cc_start: 0.6740 (mt) cc_final: 0.6268 (mt) REVERT: C 118 ASP cc_start: 0.6532 (m-30) cc_final: 0.6280 (m-30) REVERT: C 672 MET cc_start: 0.3261 (ptm) cc_final: 0.2941 (pp-130) REVERT: D 114 GLN cc_start: 0.6258 (mt0) cc_final: 0.5896 (tp-100) REVERT: D 259 PHE cc_start: 0.6182 (t80) cc_final: 0.5964 (t80) REVERT: D 457 MET cc_start: 0.8289 (ttm) cc_final: 0.7513 (ttm) REVERT: D 641 LYS cc_start: 0.5950 (mttm) cc_final: 0.5744 (tttt) REVERT: D 643 ILE cc_start: 0.6712 (mt) cc_final: 0.6291 (mp) REVERT: E 104 LEU cc_start: 0.7710 (mt) cc_final: 0.7496 (mp) REVERT: E 118 ASP cc_start: 0.6556 (m-30) cc_final: 0.6304 (m-30) REVERT: E 672 MET cc_start: 0.3482 (ptm) cc_final: 0.2999 (pp-130) REVERT: F 457 MET cc_start: 0.8336 (ttm) cc_final: 0.7570 (ttm) REVERT: F 641 LYS cc_start: 0.5832 (mttm) cc_final: 0.5572 (tttp) REVERT: F 672 MET cc_start: 0.3429 (ptm) cc_final: 0.3030 (pp-130) REVERT: G 569 ARG cc_start: 0.6425 (tpp-160) cc_final: 0.5810 (mpt180) REVERT: G 672 MET cc_start: 0.3311 (ptm) cc_final: 0.3040 (pp-130) REVERT: H 457 MET cc_start: 0.8451 (ttm) cc_final: 0.7668 (ttm) REVERT: H 641 LYS cc_start: 0.5984 (mttm) cc_final: 0.5698 (tttp) REVERT: H 643 ILE cc_start: 0.6575 (mt) cc_final: 0.6027 (mp) outliers start: 0 outliers final: 0 residues processed: 914 average time/residue: 1.8041 time to fit residues: 1936.1014 Evaluate side-chains 416 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 4.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 418 optimal weight: 2.9990 chunk 375 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 450 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 150 GLN A 269 HIS A 337 ASN A 359 GLN A 452 GLN B 114 GLN B 150 GLN B 269 HIS B 337 ASN B 452 GLN B 521 GLN C 143 GLN C 150 GLN C 269 HIS C 337 ASN C 359 GLN C 521 GLN C 652 ASN D 269 HIS D 337 ASN D 452 GLN D 521 GLN E 143 GLN E 150 GLN E 269 HIS E 337 ASN E 359 GLN E 452 GLN E 652 ASN F 150 GLN F 236 HIS F 269 HIS F 337 ASN F 359 GLN F 452 GLN F 587 HIS G 143 GLN G 150 GLN G 269 HIS G 337 ASN G 359 GLN G 452 GLN H 114 GLN H 150 GLN H 269 HIS H 337 ASN H 452 GLN H 575 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 39888 Z= 0.310 Angle : 0.616 8.150 53968 Z= 0.313 Chirality : 0.042 0.171 6168 Planarity : 0.005 0.042 6944 Dihedral : 6.701 54.817 5832 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.06 % Allowed : 10.00 % Favored : 87.94 % 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: -1.79 (0.11), residues: 4912 helix: -0.93 (0.08), residues: 3432 sheet: -0.90 (0.42), residues: 152 loop : -1.44 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 214 HIS 0.009 0.002 HIS A 269 PHE 0.037 0.003 PHE B 433 TYR 0.021 0.003 TYR E 380 ARG 0.008 0.001 ARG E 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 449 time to evaluate : 4.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7469 (mpt180) cc_final: 0.7251 (mtm110) REVERT: A 385 THR cc_start: 0.8212 (p) cc_final: 0.7957 (m) REVERT: A 630 MET cc_start: 0.3148 (ppp) cc_final: 0.2226 (ptm) REVERT: A 672 MET cc_start: 0.3291 (ptm) cc_final: 0.2819 (pp-130) REVERT: B 247 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: B 259 PHE cc_start: 0.6829 (t80) cc_final: 0.6464 (t80) REVERT: B 307 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6933 (mtp-110) REVERT: B 630 MET cc_start: 0.3162 (OUTLIER) cc_final: 0.2660 (ppp) REVERT: B 672 MET cc_start: 0.3816 (ttp) cc_final: 0.3424 (ttp) REVERT: C 159 ARG cc_start: 0.7716 (tpt170) cc_final: 0.7497 (tpt170) REVERT: C 457 MET cc_start: 0.8989 (ttm) cc_final: 0.8781 (ttm) REVERT: C 630 MET cc_start: 0.4005 (ppp) cc_final: 0.2853 (ptm) REVERT: C 672 MET cc_start: 0.3172 (ptm) cc_final: 0.2851 (pp-130) REVERT: D 114 GLN cc_start: 0.6322 (mt0) cc_final: 0.6105 (tp-100) REVERT: D 259 PHE cc_start: 0.6966 (t80) cc_final: 0.6620 (t80) REVERT: D 363 LYS cc_start: 0.7861 (tppp) cc_final: 0.7438 (tptt) REVERT: D 575 GLN cc_start: 0.7010 (tm-30) cc_final: 0.6741 (tm130) REVERT: D 641 LYS cc_start: 0.5925 (mttm) cc_final: 0.5685 (tttt) REVERT: E 147 LEU cc_start: 0.8377 (tp) cc_final: 0.8111 (tp) REVERT: E 630 MET cc_start: 0.3738 (ppp) cc_final: 0.2690 (ptm) REVERT: E 672 MET cc_start: 0.3264 (ptm) cc_final: 0.2862 (pp-130) REVERT: F 123 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6606 (t0) REVERT: F 247 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7071 (pt0) REVERT: F 672 MET cc_start: 0.3291 (ptm) cc_final: 0.2918 (pp-130) REVERT: G 147 LEU cc_start: 0.8443 (tp) cc_final: 0.8242 (tp) REVERT: G 403 ARG cc_start: 0.7380 (mtp-110) cc_final: 0.7156 (mtm-85) REVERT: G 569 ARG cc_start: 0.6362 (tpp-160) cc_final: 0.6041 (mmp-170) REVERT: G 630 MET cc_start: 0.3533 (ppp) cc_final: 0.2457 (ptm) REVERT: G 672 MET cc_start: 0.3221 (ptm) cc_final: 0.2716 (pp-130) REVERT: H 259 PHE cc_start: 0.6883 (t80) cc_final: 0.6479 (t80) outliers start: 85 outliers final: 24 residues processed: 501 average time/residue: 1.9329 time to fit residues: 1129.0443 Evaluate side-chains 352 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 324 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 374 optimal weight: 6.9990 chunk 306 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 451 optimal weight: 3.9990 chunk 487 optimal weight: 0.0060 chunk 401 optimal weight: 7.9990 chunk 447 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 361 optimal weight: 0.7980 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 337 ASN B 587 HIS C 337 ASN C 547 HIS D 337 ASN D 587 HIS D 652 ASN E 337 ASN E 547 HIS F 587 HIS G 337 ASN G 547 HIS ** G 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 652 ASN H 337 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 39888 Z= 0.297 Angle : 0.591 8.125 53968 Z= 0.298 Chirality : 0.042 0.163 6168 Planarity : 0.005 0.035 6944 Dihedral : 6.795 58.469 5832 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.00 % Allowed : 11.29 % Favored : 85.71 % 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: -0.86 (0.12), residues: 4912 helix: -0.27 (0.09), residues: 3464 sheet: -0.94 (0.40), residues: 152 loop : -0.97 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 214 HIS 0.006 0.001 HIS E 194 PHE 0.020 0.002 PHE E 466 TYR 0.016 0.002 TYR A 380 ARG 0.007 0.001 ARG C 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 363 time to evaluate : 4.569 Fit side-chains REVERT: A 159 ARG cc_start: 0.7719 (tpt170) cc_final: 0.7339 (tpp80) REVERT: A 224 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7112 (mmm-85) REVERT: A 259 PHE cc_start: 0.7988 (t80) cc_final: 0.7692 (t80) REVERT: A 395 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6334 (mtp180) REVERT: A 414 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: A 589 PHE cc_start: 0.7095 (m-10) cc_final: 0.6856 (m-80) REVERT: A 672 MET cc_start: 0.3481 (ptm) cc_final: 0.2936 (pp-130) REVERT: B 217 ARG cc_start: 0.7496 (mmt-90) cc_final: 0.7066 (mmp80) REVERT: B 259 PHE cc_start: 0.7963 (t80) cc_final: 0.7753 (t80) REVERT: B 285 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7272 (mtp-110) REVERT: B 363 LYS cc_start: 0.7794 (tppp) cc_final: 0.7594 (tptt) REVERT: B 672 MET cc_start: 0.4023 (OUTLIER) cc_final: 0.3623 (ttp) REVERT: C 224 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7167 (mtt180) REVERT: C 259 PHE cc_start: 0.8016 (t80) cc_final: 0.7680 (t80) REVERT: C 363 LYS cc_start: 0.7680 (tppp) cc_final: 0.7274 (tptt) REVERT: C 395 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6318 (mtp180) REVERT: C 414 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: C 484 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7611 (ttp-170) REVERT: C 520 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7316 (tp30) REVERT: C 630 MET cc_start: 0.3774 (ppp) cc_final: 0.2943 (ptm) REVERT: C 672 MET cc_start: 0.3440 (ptm) cc_final: 0.2841 (pp-130) REVERT: D 114 GLN cc_start: 0.6328 (mt0) cc_final: 0.6122 (tp-100) REVERT: D 149 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: D 259 PHE cc_start: 0.8045 (t80) cc_final: 0.7807 (t80) REVERT: D 307 ARG cc_start: 0.7372 (mtm110) cc_final: 0.7134 (mtp-110) REVERT: D 363 LYS cc_start: 0.7734 (tppp) cc_final: 0.7420 (tptt) REVERT: D 575 GLN cc_start: 0.7312 (tm-30) cc_final: 0.7041 (tm130) REVERT: D 630 MET cc_start: 0.3702 (OUTLIER) cc_final: 0.3399 (ppp) REVERT: D 672 MET cc_start: 0.4428 (ttp) cc_final: 0.3955 (ttp) REVERT: E 217 ARG cc_start: 0.7183 (mmt-90) cc_final: 0.6873 (mmp80) REVERT: E 224 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7174 (mtt180) REVERT: E 259 PHE cc_start: 0.7982 (t80) cc_final: 0.7715 (t80) REVERT: E 363 LYS cc_start: 0.7786 (tppp) cc_final: 0.7385 (tptt) REVERT: E 395 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6356 (mtp180) REVERT: E 414 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: E 520 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7470 (tp30) REVERT: E 569 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.7123 (mmp-170) REVERT: E 630 MET cc_start: 0.4026 (ppp) cc_final: 0.2806 (ptm) REVERT: E 672 MET cc_start: 0.3356 (ptm) cc_final: 0.2812 (pp-130) REVERT: F 100 GLU cc_start: 0.6396 (mt-10) cc_final: 0.6021 (mt-10) REVERT: F 114 GLN cc_start: 0.6383 (mt0) cc_final: 0.6098 (tp-100) REVERT: F 149 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: F 307 ARG cc_start: 0.7463 (mtm110) cc_final: 0.7215 (mtp-110) REVERT: F 363 LYS cc_start: 0.7791 (tppp) cc_final: 0.7549 (tptt) REVERT: F 385 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8316 (m) REVERT: F 672 MET cc_start: 0.3349 (ptm) cc_final: 0.2775 (pp-130) REVERT: G 159 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7415 (tpt170) REVERT: G 179 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5880 (mp0) REVERT: G 224 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7146 (mtt180) REVERT: G 259 PHE cc_start: 0.8120 (t80) cc_final: 0.7836 (t80) REVERT: G 367 ASP cc_start: 0.6725 (m-30) cc_final: 0.6479 (m-30) REVERT: G 395 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6340 (mtp180) REVERT: G 403 ARG cc_start: 0.7386 (mtp-110) cc_final: 0.7127 (mtm-85) REVERT: G 414 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: G 520 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: G 569 ARG cc_start: 0.6512 (tpp-160) cc_final: 0.6001 (mmt180) REVERT: G 672 MET cc_start: 0.3418 (ptm) cc_final: 0.2801 (pp-130) REVERT: H 259 PHE cc_start: 0.8074 (t80) cc_final: 0.7805 (t80) outliers start: 124 outliers final: 29 residues processed: 456 average time/residue: 1.8215 time to fit residues: 979.0129 Evaluate side-chains 353 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 299 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 484 ARG Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 569 ARG Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 520 GLU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 408 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 445 optimal weight: 0.6980 chunk 339 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 302 optimal weight: 6.9990 chunk 452 optimal weight: 0.7980 chunk 479 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 429 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 575 GLN B 575 GLN B 587 HIS C 575 GLN C 652 ASN C 700 GLN D 337 ASN D 587 HIS E 652 ASN E 700 GLN F 587 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 ASN G 575 GLN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 39888 Z= 0.308 Angle : 0.586 8.430 53968 Z= 0.295 Chirality : 0.042 0.160 6168 Planarity : 0.004 0.035 6944 Dihedral : 6.766 58.775 5832 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.96 % Allowed : 11.41 % Favored : 85.63 % 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: -0.36 (0.12), residues: 4912 helix: 0.09 (0.09), residues: 3464 sheet: -0.86 (0.42), residues: 152 loop : -0.68 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 253 HIS 0.007 0.001 HIS D 587 PHE 0.019 0.002 PHE G 466 TYR 0.014 0.002 TYR E 429 ARG 0.007 0.001 ARG F 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 340 time to evaluate : 4.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6407 (t0) REVERT: A 224 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7147 (mtt180) REVERT: A 259 PHE cc_start: 0.8113 (t80) cc_final: 0.7817 (t80) REVERT: A 363 LYS cc_start: 0.7642 (tppp) cc_final: 0.7333 (tptt) REVERT: A 395 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6297 (mtp180) REVERT: A 414 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: A 520 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7396 (tp30) REVERT: A 589 PHE cc_start: 0.7170 (m-10) cc_final: 0.6957 (m-10) REVERT: A 672 MET cc_start: 0.3588 (ptm) cc_final: 0.2884 (pp-130) REVERT: B 213 TYR cc_start: 0.7821 (t80) cc_final: 0.7600 (t80) REVERT: B 217 ARG cc_start: 0.7516 (mmt-90) cc_final: 0.7088 (mmp80) REVERT: B 285 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7234 (mtp-110) REVERT: B 363 LYS cc_start: 0.7871 (tppp) cc_final: 0.7654 (tptt) REVERT: B 672 MET cc_start: 0.3991 (OUTLIER) cc_final: 0.3546 (ttp) REVERT: C 123 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6326 (t0) REVERT: C 149 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6645 (tm-30) REVERT: C 224 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7151 (mtt180) REVERT: C 363 LYS cc_start: 0.7646 (tppp) cc_final: 0.7365 (tptt) REVERT: C 395 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6383 (mtp180) REVERT: C 414 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: C 484 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7586 (ttp-170) REVERT: C 520 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: C 672 MET cc_start: 0.3392 (ptm) cc_final: 0.2827 (pp-130) REVERT: D 114 GLN cc_start: 0.6221 (mt0) cc_final: 0.5954 (tp-100) REVERT: D 363 LYS cc_start: 0.7773 (tppp) cc_final: 0.7567 (tptt) REVERT: D 672 MET cc_start: 0.4435 (ttp) cc_final: 0.3911 (ttp) REVERT: E 123 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6297 (t0) REVERT: E 217 ARG cc_start: 0.7211 (mmt-90) cc_final: 0.6919 (mmp80) REVERT: E 224 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7155 (mtt180) REVERT: E 259 PHE cc_start: 0.8109 (t80) cc_final: 0.7817 (t80) REVERT: E 363 LYS cc_start: 0.7632 (tppp) cc_final: 0.7348 (tptt) REVERT: E 395 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6332 (mtp180) REVERT: E 414 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: E 520 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: E 569 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7193 (mmp-170) REVERT: E 672 MET cc_start: 0.3596 (ptm) cc_final: 0.2989 (pp-130) REVERT: F 114 GLN cc_start: 0.6285 (mt0) cc_final: 0.5998 (tp-100) REVERT: F 123 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6785 (t0) REVERT: F 149 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: F 363 LYS cc_start: 0.7925 (tppp) cc_final: 0.7686 (tptt) REVERT: F 385 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8334 (m) REVERT: F 672 MET cc_start: 0.3470 (ptm) cc_final: 0.2721 (pp-130) REVERT: G 123 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6370 (t0) REVERT: G 159 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7473 (tpt170) REVERT: G 224 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7185 (mtt180) REVERT: G 259 PHE cc_start: 0.8190 (t80) cc_final: 0.7948 (t80) REVERT: G 367 ASP cc_start: 0.6810 (m-30) cc_final: 0.6577 (m-30) REVERT: G 395 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6335 (mtp180) REVERT: G 403 ARG cc_start: 0.7389 (mtp-110) cc_final: 0.7116 (mtm-85) REVERT: G 414 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: G 520 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7431 (tp30) REVERT: G 589 PHE cc_start: 0.7168 (m-10) cc_final: 0.6940 (m-10) REVERT: G 672 MET cc_start: 0.3506 (ptm) cc_final: 0.2804 (pp-130) REVERT: H 520 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7547 (tt0) outliers start: 122 outliers final: 47 residues processed: 436 average time/residue: 1.8101 time to fit residues: 929.3547 Evaluate side-chains 377 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 301 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 484 ARG Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 569 ARG Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain F residue 694 LYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 520 GLU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 399 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 356 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 409 optimal weight: 0.8980 chunk 331 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 430 optimal weight: 40.0000 chunk 120 optimal weight: 50.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN A 652 ASN A 700 GLN B 337 ASN B 575 GLN C 575 GLN E 97 GLN F 337 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 GLN G 652 ASN G 700 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39888 Z= 0.159 Angle : 0.470 8.394 53968 Z= 0.239 Chirality : 0.037 0.145 6168 Planarity : 0.003 0.032 6944 Dihedral : 6.023 51.939 5832 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.16 % Allowed : 12.38 % Favored : 85.47 % 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: 0.39 (0.12), residues: 4912 helix: 0.68 (0.09), residues: 3368 sheet: -0.33 (0.45), residues: 152 loop : -0.45 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 638 HIS 0.002 0.001 HIS A 269 PHE 0.017 0.001 PHE F 259 TYR 0.009 0.001 TYR A 429 ARG 0.006 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 338 time to evaluate : 4.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.5990 (tp30) cc_final: 0.5761 (tp30) REVERT: A 159 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7419 (tpp80) REVERT: A 224 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7042 (mmm-85) REVERT: A 259 PHE cc_start: 0.8021 (t80) cc_final: 0.7745 (t80) REVERT: A 363 LYS cc_start: 0.7681 (tppp) cc_final: 0.7406 (tptt) REVERT: A 395 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6284 (mtp180) REVERT: A 414 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: A 589 PHE cc_start: 0.7161 (m-10) cc_final: 0.6942 (m-10) REVERT: A 672 MET cc_start: 0.3437 (ptm) cc_final: 0.3001 (pp-130) REVERT: B 167 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7556 (p) REVERT: B 217 ARG cc_start: 0.7516 (mmt-90) cc_final: 0.7039 (mmp80) REVERT: B 285 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7222 (mtp-110) REVERT: B 385 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8318 (m) REVERT: B 672 MET cc_start: 0.4259 (OUTLIER) cc_final: 0.3835 (ttp) REVERT: C 149 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6725 (tm-30) REVERT: C 159 ARG cc_start: 0.7827 (tpt170) cc_final: 0.7600 (tpt170) REVERT: C 217 ARG cc_start: 0.7632 (mmt-90) cc_final: 0.7154 (mmp80) REVERT: C 224 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7041 (mmm-85) REVERT: C 363 LYS cc_start: 0.7692 (tppp) cc_final: 0.7437 (tptt) REVERT: C 395 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6314 (mtp180) REVERT: C 630 MET cc_start: 0.3682 (OUTLIER) cc_final: 0.3155 (ppp) REVERT: C 672 MET cc_start: 0.3327 (ptm) cc_final: 0.2763 (pp-130) REVERT: D 100 GLU cc_start: 0.6172 (tp30) cc_final: 0.5968 (tp30) REVERT: D 114 GLN cc_start: 0.6295 (mt0) cc_final: 0.6044 (tp-100) REVERT: D 167 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7562 (p) REVERT: D 672 MET cc_start: 0.4449 (ttp) cc_final: 0.3978 (ttp) REVERT: E 217 ARG cc_start: 0.7140 (mmt-90) cc_final: 0.6886 (mmp80) REVERT: E 363 LYS cc_start: 0.7675 (tppp) cc_final: 0.7402 (tptt) REVERT: E 395 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6348 (mtp180) REVERT: E 414 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: E 569 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.7020 (mmp-170) REVERT: E 672 MET cc_start: 0.3361 (ptm) cc_final: 0.2816 (pp-130) REVERT: F 100 GLU cc_start: 0.6258 (tp30) cc_final: 0.5972 (tp30) REVERT: F 385 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8350 (m) REVERT: F 672 MET cc_start: 0.3387 (ptm) cc_final: 0.2789 (pp-130) REVERT: G 162 ARG cc_start: 0.6677 (mmp-170) cc_final: 0.6435 (mmt180) REVERT: G 224 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7033 (mmm-85) REVERT: G 259 PHE cc_start: 0.8077 (t80) cc_final: 0.7869 (t80) REVERT: G 285 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7203 (mpt180) REVERT: G 367 ASP cc_start: 0.6776 (m-30) cc_final: 0.6529 (m-30) REVERT: G 395 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6297 (mtp180) REVERT: G 414 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: G 589 PHE cc_start: 0.7205 (m-10) cc_final: 0.6994 (m-10) REVERT: G 630 MET cc_start: 0.3976 (OUTLIER) cc_final: 0.3670 (ppp) REVERT: G 672 MET cc_start: 0.3274 (ptm) cc_final: 0.2798 (pp-130) REVERT: H 167 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7530 (p) REVERT: H 249 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7290 (mmt90) outliers start: 89 outliers final: 35 residues processed: 411 average time/residue: 1.7674 time to fit residues: 860.3569 Evaluate side-chains 366 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 310 time to evaluate : 4.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 569 ARG Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 506 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 161 optimal weight: 3.9990 chunk 431 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 281 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 479 optimal weight: 0.1980 chunk 398 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 158 optimal weight: 0.0980 chunk 251 optimal weight: 5.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 575 GLN B 575 GLN B 587 HIS C 97 GLN C 575 GLN D 587 HIS F 114 GLN F 337 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 39888 Z= 0.126 Angle : 0.446 8.927 53968 Z= 0.225 Chirality : 0.037 0.152 6168 Planarity : 0.003 0.031 6944 Dihedral : 5.524 46.689 5832 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.65 % Allowed : 13.03 % Favored : 85.32 % 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: 0.89 (0.12), residues: 4912 helix: 1.09 (0.09), residues: 3312 sheet: 0.09 (0.46), residues: 152 loop : -0.34 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 638 HIS 0.005 0.001 HIS D 587 PHE 0.021 0.001 PHE F 259 TYR 0.006 0.001 TYR E 429 ARG 0.006 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 338 time to evaluate : 5.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.5944 (tp30) cc_final: 0.5630 (tp30) REVERT: A 104 LEU cc_start: 0.7561 (mt) cc_final: 0.7252 (mp) REVERT: A 159 ARG cc_start: 0.7779 (tpt170) cc_final: 0.7372 (tpp80) REVERT: A 395 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6365 (mtp180) REVERT: A 414 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: A 630 MET cc_start: 0.3467 (ppp) cc_final: 0.2227 (ttp) REVERT: A 672 MET cc_start: 0.3405 (ptm) cc_final: 0.2964 (pp-130) REVERT: B 217 ARG cc_start: 0.7479 (mmt-90) cc_final: 0.6991 (mmp80) REVERT: B 249 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7261 (mmt90) REVERT: B 285 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7229 (mtp-110) REVERT: B 672 MET cc_start: 0.4216 (OUTLIER) cc_final: 0.3817 (ttp) REVERT: C 159 ARG cc_start: 0.7842 (tpt170) cc_final: 0.7587 (tpt170) REVERT: C 217 ARG cc_start: 0.7672 (mmt-90) cc_final: 0.7246 (mmp80) REVERT: C 285 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7240 (mpt180) REVERT: C 395 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6365 (mtp180) REVERT: C 589 PHE cc_start: 0.7136 (m-10) cc_final: 0.6925 (m-10) REVERT: C 655 PRO cc_start: 0.7504 (Cg_exo) cc_final: 0.7256 (Cg_endo) REVERT: C 672 MET cc_start: 0.3593 (ptm) cc_final: 0.2934 (pp-130) REVERT: D 114 GLN cc_start: 0.6376 (mt0) cc_final: 0.6139 (tp-100) REVERT: D 249 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7246 (mmt90) REVERT: D 575 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6837 (tm130) REVERT: D 586 LEU cc_start: 0.7605 (mt) cc_final: 0.7387 (mt) REVERT: D 641 LYS cc_start: 0.6036 (mttm) cc_final: 0.5592 (tttp) REVERT: D 672 MET cc_start: 0.4263 (ttp) cc_final: 0.3811 (ttp) REVERT: E 100 GLU cc_start: 0.5661 (tp30) cc_final: 0.5430 (tp30) REVERT: E 395 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6373 (mtp180) REVERT: E 414 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: E 630 MET cc_start: 0.2896 (ppp) cc_final: 0.1848 (ptm) REVERT: E 672 MET cc_start: 0.3534 (ptm) cc_final: 0.2925 (pp-130) REVERT: F 100 GLU cc_start: 0.6248 (tp30) cc_final: 0.6029 (tp30) REVERT: F 249 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7253 (mmt90) REVERT: F 672 MET cc_start: 0.3331 (ptm) cc_final: 0.2781 (pp-130) REVERT: G 100 GLU cc_start: 0.5641 (tp30) cc_final: 0.5422 (tp30) REVERT: G 159 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7634 (tpt170) REVERT: G 217 ARG cc_start: 0.7671 (mmt-90) cc_final: 0.7132 (mmp80) REVERT: G 285 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7239 (mpt180) REVERT: G 367 ASP cc_start: 0.6763 (m-30) cc_final: 0.6538 (m-30) REVERT: G 395 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6352 (mtp180) REVERT: G 414 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: G 672 MET cc_start: 0.3339 (ptm) cc_final: 0.2897 (pp-130) REVERT: H 100 GLU cc_start: 0.5980 (tp30) cc_final: 0.5744 (tp30) REVERT: H 249 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7310 (mmt90) outliers start: 68 outliers final: 22 residues processed: 391 average time/residue: 1.7284 time to fit residues: 805.2993 Evaluate side-chains 334 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 301 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 408 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 462 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 273 optimal weight: 0.9980 chunk 350 optimal weight: 0.0770 chunk 271 optimal weight: 5.9990 chunk 403 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 478 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 291 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN B 134 GLN C 575 GLN F 114 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 575 GLN H 652 ASN H 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39888 Z= 0.160 Angle : 0.471 10.065 53968 Z= 0.237 Chirality : 0.037 0.148 6168 Planarity : 0.003 0.031 6944 Dihedral : 5.567 47.193 5832 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.99 % Allowed : 13.28 % Favored : 84.74 % 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: 1.02 (0.13), residues: 4912 helix: 1.17 (0.09), residues: 3312 sheet: 0.23 (0.47), residues: 152 loop : -0.26 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 253 HIS 0.002 0.001 HIS D 225 PHE 0.030 0.001 PHE F 259 TYR 0.008 0.001 TYR F 380 ARG 0.006 0.000 ARG D 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 332 time to evaluate : 4.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6027 (tp30) cc_final: 0.5815 (tp30) REVERT: A 159 ARG cc_start: 0.7778 (tpt170) cc_final: 0.7375 (tpp80) REVERT: A 395 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6320 (mtp180) REVERT: A 403 ARG cc_start: 0.7187 (ptt180) cc_final: 0.6981 (ptt180) REVERT: A 414 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: A 672 MET cc_start: 0.3304 (ptm) cc_final: 0.2918 (pp-130) REVERT: B 217 ARG cc_start: 0.7481 (mmt-90) cc_final: 0.7000 (mmp80) REVERT: B 249 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.7261 (mmt90) REVERT: B 285 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7218 (mtp-110) REVERT: B 363 LYS cc_start: 0.7855 (tptt) cc_final: 0.7640 (tptm) REVERT: B 385 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8273 (m) REVERT: B 672 MET cc_start: 0.4369 (OUTLIER) cc_final: 0.3910 (ttp) REVERT: C 100 GLU cc_start: 0.6185 (tp30) cc_final: 0.5973 (tp30) REVERT: C 217 ARG cc_start: 0.7609 (mmt-90) cc_final: 0.7192 (mmp80) REVERT: C 285 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7227 (mpt180) REVERT: C 395 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6339 (mtp180) REVERT: C 589 PHE cc_start: 0.7161 (m-10) cc_final: 0.6943 (m-10) REVERT: C 672 MET cc_start: 0.3385 (ptm) cc_final: 0.2864 (pp-130) REVERT: D 100 GLU cc_start: 0.6118 (tp30) cc_final: 0.5889 (tp30) REVERT: D 114 GLN cc_start: 0.6393 (mt0) cc_final: 0.6114 (tp-100) REVERT: D 249 ARG cc_start: 0.7633 (mmm-85) cc_final: 0.7357 (mmt90) REVERT: D 363 LYS cc_start: 0.7822 (tptt) cc_final: 0.7558 (tptm) REVERT: D 575 GLN cc_start: 0.7201 (tm-30) cc_final: 0.6806 (tm130) REVERT: D 630 MET cc_start: 0.3873 (OUTLIER) cc_final: 0.3617 (ppp) REVERT: D 641 LYS cc_start: 0.5942 (mttm) cc_final: 0.5478 (tttp) REVERT: D 672 MET cc_start: 0.4321 (ttp) cc_final: 0.3893 (ttp) REVERT: E 224 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7120 (mtt180) REVERT: E 395 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6325 (mtp180) REVERT: E 414 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: E 630 MET cc_start: 0.3056 (ppp) cc_final: 0.1974 (ptm) REVERT: E 672 MET cc_start: 0.3464 (ptm) cc_final: 0.2875 (pp-130) REVERT: F 100 GLU cc_start: 0.6194 (tp30) cc_final: 0.5992 (tp30) REVERT: F 249 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7271 (mmt90) REVERT: F 395 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6587 (mtp180) REVERT: F 672 MET cc_start: 0.3357 (ptm) cc_final: 0.2797 (pp-130) REVERT: G 217 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7139 (mmp80) REVERT: G 285 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7206 (mpt180) REVERT: G 367 ASP cc_start: 0.6763 (m-30) cc_final: 0.6540 (m-30) REVERT: G 395 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6335 (mtp180) REVERT: G 414 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: G 672 MET cc_start: 0.3328 (ptm) cc_final: 0.2912 (pp-130) REVERT: H 217 ARG cc_start: 0.7454 (mmp80) cc_final: 0.6830 (mmp80) REVERT: H 249 ARG cc_start: 0.7659 (mmm-85) cc_final: 0.7361 (mmt90) REVERT: H 385 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8122 (m) outliers start: 82 outliers final: 38 residues processed: 400 average time/residue: 1.6958 time to fit residues: 808.0808 Evaluate side-chains 369 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 315 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 295 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 303 optimal weight: 0.7980 chunk 325 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 375 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN C 575 GLN E 575 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 39888 Z= 0.153 Angle : 0.467 10.810 53968 Z= 0.235 Chirality : 0.037 0.149 6168 Planarity : 0.003 0.032 6944 Dihedral : 5.454 45.852 5832 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.89 % Allowed : 13.54 % Favored : 84.57 % 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: 1.12 (0.13), residues: 4912 helix: 1.22 (0.09), residues: 3328 sheet: 0.33 (0.48), residues: 152 loop : -0.15 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 253 HIS 0.002 0.001 HIS F 516 PHE 0.032 0.001 PHE F 259 TYR 0.007 0.001 TYR G 429 ARG 0.008 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 339 time to evaluate : 4.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6168 (tp30) cc_final: 0.5937 (tp30) REVERT: A 159 ARG cc_start: 0.7784 (tpt170) cc_final: 0.7383 (tpp80) REVERT: A 217 ARG cc_start: 0.7687 (mmt-90) cc_final: 0.6940 (mmp80) REVERT: A 363 LYS cc_start: 0.7693 (tppt) cc_final: 0.7468 (tptt) REVERT: A 395 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6358 (mtp180) REVERT: A 414 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: A 672 MET cc_start: 0.3299 (ptm) cc_final: 0.2924 (pp-130) REVERT: B 217 ARG cc_start: 0.7478 (mmt-90) cc_final: 0.7000 (mmp80) REVERT: B 249 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7430 (mmt90) REVERT: B 285 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7253 (mtp-110) REVERT: B 385 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8200 (m) REVERT: B 672 MET cc_start: 0.4381 (OUTLIER) cc_final: 0.3775 (ttt) REVERT: C 159 ARG cc_start: 0.7799 (tpt170) cc_final: 0.7521 (tpt170) REVERT: C 217 ARG cc_start: 0.7603 (mmt-90) cc_final: 0.7188 (mmp80) REVERT: C 285 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7149 (mpt180) REVERT: C 395 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6431 (mtp180) REVERT: C 589 PHE cc_start: 0.7166 (m-10) cc_final: 0.6949 (m-10) REVERT: C 672 MET cc_start: 0.3474 (ptm) cc_final: 0.2875 (pp-130) REVERT: D 114 GLN cc_start: 0.6396 (mt0) cc_final: 0.6120 (tp-100) REVERT: D 249 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.7426 (mmt90) REVERT: D 363 LYS cc_start: 0.7760 (tptt) cc_final: 0.7548 (tptm) REVERT: D 395 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6688 (mtp180) REVERT: D 575 GLN cc_start: 0.7195 (tm-30) cc_final: 0.6928 (tm130) REVERT: D 630 MET cc_start: 0.3833 (OUTLIER) cc_final: 0.3606 (ppp) REVERT: D 641 LYS cc_start: 0.5935 (mttm) cc_final: 0.5475 (tttp) REVERT: D 672 MET cc_start: 0.4111 (ttp) cc_final: 0.3654 (ttp) REVERT: E 224 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7079 (mtt180) REVERT: E 395 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6338 (mtp180) REVERT: E 414 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: E 520 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: E 630 MET cc_start: 0.3041 (ppp) cc_final: 0.1962 (ptm) REVERT: E 672 MET cc_start: 0.3498 (ptm) cc_final: 0.2914 (pp-130) REVERT: F 167 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7596 (p) REVERT: F 249 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.7445 (mmt90) REVERT: F 395 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6588 (mtp180) REVERT: F 672 MET cc_start: 0.3329 (ptm) cc_final: 0.2788 (pp-130) REVERT: G 217 ARG cc_start: 0.7670 (mmt-90) cc_final: 0.7152 (mmp80) REVERT: G 224 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7065 (mtt180) REVERT: G 285 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7201 (mpt180) REVERT: G 367 ASP cc_start: 0.6746 (m-30) cc_final: 0.6509 (m-30) REVERT: G 395 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6322 (mtp180) REVERT: G 414 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: G 672 MET cc_start: 0.3326 (ptm) cc_final: 0.2901 (pp-130) REVERT: H 249 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.7345 (mmt90) REVERT: H 363 LYS cc_start: 0.7854 (tptt) cc_final: 0.7632 (tptm) REVERT: H 385 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8116 (m) REVERT: H 395 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6618 (mtp180) REVERT: H 672 MET cc_start: 0.3098 (ptm) cc_final: 0.2866 (pmm) outliers start: 78 outliers final: 37 residues processed: 404 average time/residue: 1.7506 time to fit residues: 840.6921 Evaluate side-chains 381 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 323 time to evaluate : 5.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 506 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 434 optimal weight: 20.0000 chunk 457 optimal weight: 1.9990 chunk 417 optimal weight: 0.9980 chunk 445 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 349 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 402 optimal weight: 6.9990 chunk 421 optimal weight: 0.6980 chunk 443 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN C 575 GLN E 575 GLN F 114 GLN F 587 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 575 GLN H 134 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39888 Z= 0.174 Angle : 0.494 10.827 53968 Z= 0.248 Chirality : 0.038 0.168 6168 Planarity : 0.003 0.031 6944 Dihedral : 5.551 47.052 5832 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 13.91 % Favored : 84.30 % 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: 1.10 (0.13), residues: 4912 helix: 1.17 (0.09), residues: 3336 sheet: 0.34 (0.48), residues: 152 loop : -0.10 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 253 HIS 0.006 0.001 HIS F 587 PHE 0.031 0.001 PHE F 259 TYR 0.009 0.001 TYR D 429 ARG 0.006 0.000 ARG F 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 328 time to evaluate : 4.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6188 (tp30) cc_final: 0.5971 (tp30) REVERT: A 159 ARG cc_start: 0.7799 (tpt170) cc_final: 0.7395 (tpp80) REVERT: A 363 LYS cc_start: 0.7691 (tppt) cc_final: 0.7470 (tptt) REVERT: A 395 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6145 (mtp180) REVERT: A 414 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: A 672 MET cc_start: 0.3297 (ptm) cc_final: 0.2931 (pp-130) REVERT: B 217 ARG cc_start: 0.7482 (mmt-90) cc_final: 0.7009 (mmp80) REVERT: B 249 ARG cc_start: 0.7669 (mmm-85) cc_final: 0.7402 (mmt90) REVERT: B 285 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7254 (mtp-110) REVERT: B 363 LYS cc_start: 0.7883 (tptt) cc_final: 0.7586 (tptm) REVERT: B 385 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8105 (m) REVERT: B 395 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6653 (mtp180) REVERT: B 672 MET cc_start: 0.4380 (OUTLIER) cc_final: 0.3747 (ttt) REVERT: C 217 ARG cc_start: 0.7607 (mmt-90) cc_final: 0.7193 (mmp80) REVERT: C 285 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7136 (mpt180) REVERT: C 395 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6320 (mtp180) REVERT: C 589 PHE cc_start: 0.7186 (m-10) cc_final: 0.6967 (m-10) REVERT: C 630 MET cc_start: 0.3713 (OUTLIER) cc_final: 0.3157 (ppp) REVERT: C 672 MET cc_start: 0.3425 (ptm) cc_final: 0.2826 (pp-130) REVERT: D 114 GLN cc_start: 0.6468 (mt0) cc_final: 0.6108 (tp-100) REVERT: D 249 ARG cc_start: 0.7678 (mmm-85) cc_final: 0.7420 (mmt90) REVERT: D 395 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6741 (mtp180) REVERT: D 575 GLN cc_start: 0.7238 (tm-30) cc_final: 0.6945 (tm130) REVERT: D 630 MET cc_start: 0.3826 (OUTLIER) cc_final: 0.3602 (ppp) REVERT: D 641 LYS cc_start: 0.5931 (mttm) cc_final: 0.5487 (tttp) REVERT: D 672 MET cc_start: 0.4338 (ttp) cc_final: 0.3877 (ttp) REVERT: E 224 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7086 (mtt180) REVERT: E 395 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6318 (mtp180) REVERT: E 414 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: E 520 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: E 672 MET cc_start: 0.3443 (ptm) cc_final: 0.2871 (pp-130) REVERT: F 100 GLU cc_start: 0.6209 (tp30) cc_final: 0.5975 (tp30) REVERT: F 167 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7578 (p) REVERT: F 249 ARG cc_start: 0.7669 (mmm-85) cc_final: 0.7412 (mmt90) REVERT: F 363 LYS cc_start: 0.8030 (tptt) cc_final: 0.7817 (tppp) REVERT: F 395 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6663 (mtp180) REVERT: F 672 MET cc_start: 0.3310 (ptm) cc_final: 0.2794 (pp-130) REVERT: G 217 ARG cc_start: 0.7668 (mmt-90) cc_final: 0.7136 (mmp80) REVERT: G 224 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7086 (mtt180) REVERT: G 285 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7200 (mpt180) REVERT: G 367 ASP cc_start: 0.6795 (m-30) cc_final: 0.6571 (m-30) REVERT: G 395 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6271 (mtp180) REVERT: G 414 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: G 672 MET cc_start: 0.3503 (ptm) cc_final: 0.3024 (pp-130) REVERT: H 249 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7366 (mmt90) REVERT: H 385 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.7940 (m) REVERT: H 395 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6609 (mtp180) outliers start: 74 outliers final: 34 residues processed: 390 average time/residue: 1.7401 time to fit residues: 805.2975 Evaluate side-chains 371 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 314 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 292 optimal weight: 4.9990 chunk 471 optimal weight: 4.9990 chunk 287 optimal weight: 0.7980 chunk 223 optimal weight: 0.6980 chunk 327 optimal weight: 0.7980 chunk 494 optimal weight: 8.9990 chunk 454 optimal weight: 0.9990 chunk 393 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN C 575 GLN D 337 ASN D 652 ASN D 700 GLN E 575 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39888 Z= 0.148 Angle : 0.479 11.508 53968 Z= 0.239 Chirality : 0.037 0.143 6168 Planarity : 0.003 0.033 6944 Dihedral : 5.361 44.629 5832 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.45 % Allowed : 14.29 % Favored : 84.25 % 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: 1.17 (0.13), residues: 4912 helix: 1.23 (0.09), residues: 3336 sheet: 0.45 (0.48), residues: 152 loop : -0.08 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 253 HIS 0.002 0.001 HIS F 516 PHE 0.032 0.001 PHE F 259 TYR 0.007 0.001 TYR D 429 ARG 0.009 0.000 ARG E 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 328 time to evaluate : 4.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6192 (tp30) cc_final: 0.5940 (tp30) REVERT: A 159 ARG cc_start: 0.7786 (tpt170) cc_final: 0.7392 (tpp80) REVERT: A 217 ARG cc_start: 0.7685 (mmt-90) cc_final: 0.7226 (mmp80) REVERT: A 363 LYS cc_start: 0.7715 (tppt) cc_final: 0.7473 (tptt) REVERT: A 395 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6365 (mtp180) REVERT: A 414 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: B 217 ARG cc_start: 0.7469 (mmt-90) cc_final: 0.6996 (mmp80) REVERT: B 249 ARG cc_start: 0.7659 (mmm-85) cc_final: 0.7435 (mmt90) REVERT: B 285 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7217 (mtp-110) REVERT: B 363 LYS cc_start: 0.7799 (tptt) cc_final: 0.7565 (tptm) REVERT: B 395 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6576 (mtp180) REVERT: B 672 MET cc_start: 0.4403 (OUTLIER) cc_final: 0.3772 (ttt) REVERT: C 217 ARG cc_start: 0.7600 (mmt-90) cc_final: 0.7172 (mmp80) REVERT: C 285 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7152 (mpt180) REVERT: C 363 LYS cc_start: 0.7731 (tppt) cc_final: 0.7498 (tptt) REVERT: C 395 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6371 (mtp180) REVERT: C 589 PHE cc_start: 0.7180 (m-10) cc_final: 0.6953 (m-10) REVERT: C 655 PRO cc_start: 0.7552 (Cg_exo) cc_final: 0.7288 (Cg_endo) REVERT: C 672 MET cc_start: 0.3467 (ptm) cc_final: 0.2871 (pp-130) REVERT: D 114 GLN cc_start: 0.6480 (mt0) cc_final: 0.6157 (tp-100) REVERT: D 249 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7430 (mmt90) REVERT: D 575 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6881 (tm130) REVERT: D 641 LYS cc_start: 0.6055 (mttm) cc_final: 0.5632 (tttp) REVERT: D 672 MET cc_start: 0.4517 (ttp) cc_final: 0.4023 (ttp) REVERT: E 224 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7080 (mtt180) REVERT: E 395 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6333 (mtp180) REVERT: E 414 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: E 520 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: E 672 MET cc_start: 0.3494 (ptm) cc_final: 0.2911 (pp-130) REVERT: F 100 GLU cc_start: 0.6099 (tp30) cc_final: 0.5847 (tp30) REVERT: F 167 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7550 (p) REVERT: F 249 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7470 (mmt90) REVERT: F 395 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6586 (mtp180) REVERT: F 672 MET cc_start: 0.3267 (ptm) cc_final: 0.2807 (pp-130) REVERT: G 159 ARG cc_start: 0.7828 (tpt170) cc_final: 0.7581 (tpt170) REVERT: G 217 ARG cc_start: 0.7656 (mmt-90) cc_final: 0.7127 (mmp80) REVERT: G 285 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7120 (mpt180) REVERT: G 367 ASP cc_start: 0.6727 (m-30) cc_final: 0.6501 (m-30) REVERT: G 395 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6374 (mtp180) REVERT: G 414 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: G 672 MET cc_start: 0.3493 (ptm) cc_final: 0.3036 (pp-130) REVERT: H 249 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7346 (mmt90) REVERT: H 385 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8039 (m) REVERT: H 395 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6532 (mtp180) REVERT: H 520 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7475 (tp30) outliers start: 60 outliers final: 33 residues processed: 378 average time/residue: 1.7456 time to fit residues: 787.2313 Evaluate side-chains 369 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 317 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 312 optimal weight: 0.1980 chunk 419 optimal weight: 3.9990 chunk 120 optimal weight: 50.0000 chunk 362 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 chunk 394 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 404 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN C 575 GLN D 652 ASN D 700 GLN E 575 GLN F 114 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 575 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.188985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119989 restraints weight = 42192.906| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.85 r_work: 0.3098 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39888 Z= 0.199 Angle : 0.524 11.950 53968 Z= 0.261 Chirality : 0.039 0.189 6168 Planarity : 0.003 0.032 6944 Dihedral : 5.660 48.205 5832 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.67 % Allowed : 14.44 % Favored : 83.89 % 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: 1.08 (0.13), residues: 4912 helix: 1.14 (0.09), residues: 3336 sheet: 0.40 (0.48), residues: 152 loop : -0.07 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 253 HIS 0.003 0.001 HIS D 225 PHE 0.028 0.001 PHE F 259 TYR 0.010 0.001 TYR H 380 ARG 0.006 0.000 ARG H 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15351.52 seconds wall clock time: 273 minutes 53.12 seconds (16433.12 seconds total)