Starting phenix.real_space_refine on Thu Mar 21 19:15:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/03_2024/6jqm_9874_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/03_2024/6jqm_9874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/03_2024/6jqm_9874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/03_2024/6jqm_9874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/03_2024/6jqm_9874_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/03_2024/6jqm_9874_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 150 5.16 5 C 19470 2.51 5 N 5466 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 544": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 544": "NH1" <-> "NH2" Residue "E ARG 545": "NH1" <-> "NH2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "E PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 545": "NH1" <-> "NH2" Residue "F ARG 580": "NH1" <-> "NH2" Residue "F PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30936 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "C" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "D" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "E" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "F" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.50, per 1000 atoms: 0.50 Number of scatterers: 30936 At special positions: 0 Unit cell: (179.14, 174.9, 108.12, 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 150 16.00 P 18 15.00 O 5832 8.00 N 5466 7.00 C 19470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 5.5 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7404 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 51 sheets defined 31.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.63 Creating SS restraints... Processing helix chain 'A' and resid 41 through 57 removed outlier: 3.506A pdb=" N ARG A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Proline residue: A 54 - end of helix Processing helix chain 'A' and resid 61 through 77 removed outlier: 3.503A pdb=" N LEU A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.899A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 114 removed outlier: 3.677A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 removed outlier: 4.153A pdb=" N LYS A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 187 through 200 removed outlier: 4.397A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.529A pdb=" N MET A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 removed outlier: 3.505A pdb=" N LEU A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ALA A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.748A pdb=" N VAL A 308 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASN A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 316 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 354 removed outlier: 3.586A pdb=" N LYS A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 removed outlier: 4.416A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.677A pdb=" N GLN A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.061A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.551A pdb=" N VAL A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 567 No H-bonds generated for 'chain 'A' and resid 564 through 567' Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'A' and resid 584 through 595 removed outlier: 3.632A pdb=" N ALA A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 61 through 77 removed outlier: 3.565A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 89 removed outlier: 4.014A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 116 removed outlier: 3.975A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 173 removed outlier: 4.149A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 187 through 200 removed outlier: 4.418A pdb=" N SER B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.580A pdb=" N MET B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 274 through 292 removed outlier: 5.979A pdb=" N LYS B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.781A pdb=" N VAL B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 310 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 319 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN B 320 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 321 " --> pdb=" O ARG B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 355 removed outlier: 3.636A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 419 removed outlier: 4.359A pdb=" N GLY B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 removed outlier: 3.618A pdb=" N ASP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 503 through 509 removed outlier: 4.128A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 584 through 595 removed outlier: 3.643A pdb=" N ALA B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 removed outlier: 3.836A pdb=" N ALA C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Proline residue: C 54 - end of helix Processing helix chain 'C' and resid 61 through 77 removed outlier: 3.596A pdb=" N LEU C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.807A pdb=" N ALA C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 116 removed outlier: 3.808A pdb=" N VAL C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 173 removed outlier: 4.206A pdb=" N LYS C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 187 through 200 removed outlier: 4.399A pdb=" N SER C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.665A pdb=" N MET C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 274 through 292 removed outlier: 6.132A pdb=" N LYS C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.750A pdb=" N VAL C 308 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASN C 309 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER C 312 " --> pdb=" O ASN C 309 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 315 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 354 removed outlier: 3.519A pdb=" N LYS C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 352 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'C' and resid 432 through 442 removed outlier: 3.641A pdb=" N ARG C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 437 " --> pdb=" O GLN C 433 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 503 through 509 removed outlier: 4.015A pdb=" N ALA C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.608A pdb=" N VAL C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 584 through 595 removed outlier: 3.621A pdb=" N ALA C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 80 through 89 removed outlier: 4.036A pdb=" N ALA D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 117 removed outlier: 3.847A pdb=" N VAL D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 165 No H-bonds generated for 'chain 'D' and resid 162 through 165' Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 187 through 200 removed outlier: 4.466A pdb=" N SER D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 234 through 240 removed outlier: 3.689A pdb=" N MET D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 274 through 292 removed outlier: 5.993A pdb=" N LYS D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA D 291 " --> pdb=" O MET D 287 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 321 removed outlier: 3.766A pdb=" N VAL D 308 " --> pdb=" O GLN D 305 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASN D 309 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 310 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D 318 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 319 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN D 320 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 321 " --> pdb=" O ARG D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 354 removed outlier: 3.662A pdb=" N ILE D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 432 through 442 removed outlier: 3.644A pdb=" N ARG D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP D 441 " --> pdb=" O GLN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 503 through 509 removed outlier: 4.041A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 528 No H-bonds generated for 'chain 'D' and resid 526 through 528' Processing helix chain 'D' and resid 549 through 559 Processing helix chain 'D' and resid 564 through 567 No H-bonds generated for 'chain 'D' and resid 564 through 567' Processing helix chain 'D' and resid 569 through 573 removed outlier: 3.510A pdb=" N ALA D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 569 through 573' Processing helix chain 'D' and resid 584 through 595 removed outlier: 3.555A pdb=" N ALA D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 51 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 61 through 77 removed outlier: 3.551A pdb=" N LEU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 89 removed outlier: 3.848A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR E 89 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 117 removed outlier: 3.686A pdb=" N VAL E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 173 removed outlier: 4.287A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 187 through 200 removed outlier: 4.382A pdb=" N SER E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.728A pdb=" N MET E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 292 removed outlier: 6.081A pdb=" N LYS E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ALA E 291 " --> pdb=" O MET E 287 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 319 removed outlier: 3.809A pdb=" N VAL E 308 " --> pdb=" O GLN E 305 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN E 309 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E 312 " --> pdb=" O ASN E 309 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E 313 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 354 removed outlier: 3.544A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 419 removed outlier: 4.397A pdb=" N GLY E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 442 removed outlier: 3.794A pdb=" N ASP E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 490 through 492 No H-bonds generated for 'chain 'E' and resid 490 through 492' Processing helix chain 'E' and resid 503 through 509 removed outlier: 3.914A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 528 No H-bonds generated for 'chain 'E' and resid 526 through 528' Processing helix chain 'E' and resid 549 through 559 Processing helix chain 'E' and resid 564 through 567 No H-bonds generated for 'chain 'E' and resid 564 through 567' Processing helix chain 'E' and resid 569 through 574 removed outlier: 3.551A pdb=" N ALA E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 595 removed outlier: 3.714A pdb=" N ALA E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 50 Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 61 through 77 removed outlier: 3.576A pdb=" N LEU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 89 removed outlier: 3.900A pdb=" N ALA F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 117 removed outlier: 3.868A pdb=" N VAL F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP F 99 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 165 removed outlier: 3.754A pdb=" N MET F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 187 through 200 removed outlier: 4.457A pdb=" N SER F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.830A pdb=" N MET F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 292 removed outlier: 6.066A pdb=" N LYS F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA F 291 " --> pdb=" O MET F 287 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 321 removed outlier: 3.733A pdb=" N VAL F 308 " --> pdb=" O GLN F 305 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN F 309 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA F 310 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU F 315 " --> pdb=" O SER F 312 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN F 320 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F 321 " --> pdb=" O ARG F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 354 removed outlier: 3.590A pdb=" N ILE F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 419 removed outlier: 4.314A pdb=" N GLY F 419 " --> pdb=" O LEU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 442 removed outlier: 3.763A pdb=" N ARG F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing helix chain 'F' and resid 503 through 509 removed outlier: 4.071A pdb=" N ALA F 508 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 559 Processing helix chain 'F' and resid 571 through 573 No H-bonds generated for 'chain 'F' and resid 571 through 573' Processing helix chain 'F' and resid 584 through 595 Processing sheet with id= A, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 139 through 146 Processing sheet with id= C, first strand: chain 'A' and resid 252 through 256 removed outlier: 7.472A pdb=" N HIS A 153 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 179 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 402 through 406 removed outlier: 5.970A pdb=" N ASN A 261 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE A 301 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS A 263 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL A 303 " --> pdb=" O CYS A 263 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 425 through 428 Processing sheet with id= F, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.502A pdb=" N GLU A 650 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 545 through 547 removed outlier: 3.541A pdb=" N ASP A 622 " --> pdb=" O MET A 547 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.663A pdb=" N TRP A 32 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 6 through 8 Processing sheet with id= J, first strand: chain 'B' and resid 139 through 146 Processing sheet with id= K, first strand: chain 'B' and resid 252 through 256 removed outlier: 7.602A pdb=" N HIS B 153 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE B 179 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 402 through 406 removed outlier: 5.961A pdb=" N ASN B 261 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE B 301 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 263 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL B 303 " --> pdb=" O CYS B 263 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 425 through 428 Processing sheet with id= N, first strand: chain 'B' and resid 545 through 547 Processing sheet with id= O, first strand: chain 'B' and resid 665 through 673 removed outlier: 5.368A pdb=" N ALA B 652 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N CYS B 630 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU B 654 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU B 628 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE B 656 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL B 626 " --> pdb=" O PHE B 656 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.710A pdb=" N TRP B 32 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 6 through 8 Processing sheet with id= R, first strand: chain 'C' and resid 139 through 146 Processing sheet with id= S, first strand: chain 'C' and resid 252 through 256 removed outlier: 7.609A pdb=" N HIS C 153 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE C 179 " --> pdb=" O HIS C 153 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 402 through 406 removed outlier: 5.997A pdb=" N ASN C 261 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE C 301 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS C 263 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL C 303 " --> pdb=" O CYS C 263 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 425 through 428 Processing sheet with id= V, first strand: chain 'C' and resid 539 through 541 Processing sheet with id= W, first strand: chain 'C' and resid 545 through 547 removed outlier: 3.569A pdb=" N ASP C 622 " --> pdb=" O MET C 547 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 646 through 651 Processing sheet with id= Y, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.772A pdb=" N TRP C 32 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 6 through 8 Processing sheet with id= AA, first strand: chain 'D' and resid 139 through 146 Processing sheet with id= AB, first strand: chain 'D' and resid 252 through 256 removed outlier: 7.441A pdb=" N HIS D 153 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE D 179 " --> pdb=" O HIS D 153 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 402 through 406 removed outlier: 5.982A pdb=" N ASN D 261 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE D 301 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS D 263 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL D 303 " --> pdb=" O CYS D 263 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 425 through 428 removed outlier: 3.511A pdb=" N LEU D 427 " --> pdb=" O GLN D 450 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 545 through 547 Processing sheet with id= AF, first strand: chain 'D' and resid 625 through 627 Processing sheet with id= AG, first strand: chain 'D' and resid 646 through 651 Processing sheet with id= AH, first strand: chain 'D' and resid 20 through 23 removed outlier: 3.623A pdb=" N TRP D 32 " --> pdb=" O ILE D 22 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 6 through 8 Processing sheet with id= AJ, first strand: chain 'E' and resid 139 through 146 Processing sheet with id= AK, first strand: chain 'E' and resid 252 through 256 removed outlier: 7.497A pdb=" N HIS E 153 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE E 179 " --> pdb=" O HIS E 153 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 402 through 406 removed outlier: 6.039A pdb=" N ASN E 261 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE E 301 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS E 263 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL E 303 " --> pdb=" O CYS E 263 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 425 through 428 Processing sheet with id= AN, first strand: chain 'E' and resid 539 through 541 Processing sheet with id= AO, first strand: chain 'E' and resid 545 through 547 Processing sheet with id= AP, first strand: chain 'E' and resid 646 through 651 Processing sheet with id= AQ, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.723A pdb=" N TRP E 32 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 6 through 8 Processing sheet with id= AS, first strand: chain 'F' and resid 139 through 146 Processing sheet with id= AT, first strand: chain 'F' and resid 252 through 256 removed outlier: 7.509A pdb=" N HIS F 153 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE F 179 " --> pdb=" O HIS F 153 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'F' and resid 402 through 406 removed outlier: 5.976A pdb=" N ASN F 261 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE F 301 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS F 263 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL F 303 " --> pdb=" O CYS F 263 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'F' and resid 425 through 428 Processing sheet with id= AW, first strand: chain 'F' and resid 545 through 547 Processing sheet with id= AX, first strand: chain 'F' and resid 665 through 673 removed outlier: 5.443A pdb=" N ALA F 652 " --> pdb=" O CYS F 630 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS F 630 " --> pdb=" O ALA F 652 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU F 654 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU F 628 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE F 656 " --> pdb=" O VAL F 626 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL F 626 " --> pdb=" O PHE F 656 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.618A pdb=" N TRP F 32 " --> pdb=" O ILE F 22 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2526 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: 11.28 Time building geometry restraints manager: 12.98 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: 9294 1.33 - 1.46: 6728 1.46 - 1.58: 15286 1.58 - 1.71: 18 1.71 - 1.83: 252 Bond restraints: 31578 Sorted by residual: bond pdb=" CA VAL B 648 " pdb=" CB VAL B 648 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.05e-02 9.07e+03 3.14e+00 bond pdb=" N THR D 634 " pdb=" CA THR D 634 " ideal model delta sigma weight residual 1.461 1.481 -0.020 1.38e-02 5.25e+03 2.18e+00 bond pdb=" CB ASN F 158 " pdb=" CG ASN F 158 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.18e+00 bond pdb=" N THR C 634 " pdb=" CA THR C 634 " ideal model delta sigma weight residual 1.461 1.480 -0.019 1.38e-02 5.25e+03 1.94e+00 bond pdb=" CA VAL C 648 " pdb=" CB VAL C 648 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.75e+00 ... (remaining 31573 not shown) Histogram of bond angle deviations from ideal: 96.36 - 103.91: 601 103.91 - 111.46: 13503 111.46 - 119.00: 12189 119.00 - 126.55: 16122 126.55 - 134.10: 503 Bond angle restraints: 42918 Sorted by residual: angle pdb=" C ASN B 606 " pdb=" N TYR B 607 " pdb=" CA TYR B 607 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.38e+01 angle pdb=" C ASN E 606 " pdb=" N TYR E 607 " pdb=" CA TYR E 607 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" C ASN D 606 " pdb=" N TYR D 607 " pdb=" CA TYR D 607 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C ASN F 606 " pdb=" N TYR F 607 " pdb=" CA TYR F 607 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ASN C 606 " pdb=" N TYR C 607 " pdb=" CA TYR C 607 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 ... (remaining 42913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 18654 33.68 - 67.35: 172 67.35 - 101.03: 14 101.03 - 134.70: 1 134.70 - 168.38: 5 Dihedral angle restraints: 18846 sinusoidal: 7326 harmonic: 11520 Sorted by residual: dihedral pdb=" CA ASP E 522 " pdb=" C ASP E 522 " pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASP C 522 " pdb=" C ASP C 522 " pdb=" N ARG C 523 " pdb=" CA ARG C 523 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP A 522 " pdb=" C ASP A 522 " pdb=" N ARG A 523 " pdb=" CA ARG A 523 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 18843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3041 0.042 - 0.083: 1294 0.083 - 0.125: 471 0.125 - 0.167: 69 0.167 - 0.209: 9 Chirality restraints: 4884 Sorted by residual: chirality pdb=" CA TYR C 607 " pdb=" N TYR C 607 " pdb=" C TYR C 607 " pdb=" CB TYR C 607 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA TYR D 607 " pdb=" N TYR D 607 " pdb=" C TYR D 607 " pdb=" CB TYR D 607 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA TYR F 607 " pdb=" N TYR F 607 " pdb=" C TYR F 607 " pdb=" CB TYR F 607 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4881 not shown) Planarity restraints: 5598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 124 " 0.019 2.00e-02 2.50e+03 1.75e-02 7.64e+00 pdb=" CG TRP B 124 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 124 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 124 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 124 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 124 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 124 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 124 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 124 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 124 " 0.019 2.00e-02 2.50e+03 1.60e-02 6.38e+00 pdb=" CG TRP F 124 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP F 124 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 124 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 124 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 124 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 124 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.32e+00 pdb=" CG TRP D 124 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 124 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 124 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 124 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 124 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 124 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 124 " 0.003 2.00e-02 2.50e+03 ... (remaining 5595 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9268 2.82 - 3.34: 27468 3.34 - 3.86: 53265 3.86 - 4.38: 61831 4.38 - 4.90: 108509 Nonbonded interactions: 260341 Sorted by model distance: nonbonded pdb=" OG1 THR D 270 " pdb=" OD1 ASP D 272 " model vdw 2.304 2.440 nonbonded pdb=" OG1 THR F 270 " pdb=" OD1 ASP F 272 " model vdw 2.304 2.440 nonbonded pdb=" OG1 THR B 270 " pdb=" OD1 ASP B 272 " model vdw 2.312 2.440 nonbonded pdb=" OG1 THR A 270 " pdb=" OD1 ASP A 272 " model vdw 2.314 2.440 nonbonded pdb=" OG SER E 36 " pdb=" O SER E 214 " model vdw 2.318 2.440 ... (remaining 260336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 16.680 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 78.900 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.005 0.049 31578 Z= 0.348 Angle : 0.831 10.110 42918 Z= 0.443 Chirality : 0.051 0.209 4884 Planarity : 0.007 0.062 5598 Dihedral : 10.759 168.380 11442 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % 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: -4.47 (0.10), residues: 4056 helix: -3.10 (0.09), residues: 1368 sheet: -3.36 (0.16), residues: 654 loop : -2.67 (0.11), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 124 HIS 0.015 0.002 HIS B 463 PHE 0.023 0.003 PHE E 595 TYR 0.025 0.003 TYR C 607 ARG 0.018 0.001 ARG F 361 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 695 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 59 MET cc_start: 0.8504 (mtt) cc_final: 0.8277 (mtp) REVERT: B 217 ASP cc_start: 0.7800 (t0) cc_final: 0.7597 (t0) REVERT: B 333 LYS cc_start: 0.7837 (mttt) cc_final: 0.7353 (mttm) REVERT: B 532 GLU cc_start: 0.8148 (mp0) cc_final: 0.7890 (mp0) REVERT: B 611 SER cc_start: 0.7599 (t) cc_final: 0.7342 (p) REVERT: B 644 LYS cc_start: 0.8607 (mptm) cc_final: 0.8292 (mtpp) REVERT: C 242 VAL cc_start: 0.8801 (m) cc_final: 0.8547 (p) REVERT: C 417 CYS cc_start: 0.7979 (m) cc_final: 0.7638 (m) REVERT: C 532 GLU cc_start: 0.8135 (mp0) cc_final: 0.7735 (mp0) REVERT: D 164 MET cc_start: 0.9252 (tmt) cc_final: 0.8457 (tmt) REVERT: D 217 ASP cc_start: 0.7120 (t0) cc_final: 0.6859 (t0) REVERT: D 333 LYS cc_start: 0.7575 (mttt) cc_final: 0.7207 (mttm) REVERT: D 394 THR cc_start: 0.8672 (m) cc_final: 0.8246 (p) REVERT: D 505 MET cc_start: 0.8363 (tpp) cc_final: 0.8023 (mmt) REVERT: E 413 LEU cc_start: 0.8326 (mm) cc_final: 0.7717 (mp) REVERT: E 417 CYS cc_start: 0.8195 (m) cc_final: 0.7944 (m) REVERT: E 505 MET cc_start: 0.8072 (tpp) cc_final: 0.7773 (mmt) REVERT: F 7 PHE cc_start: 0.8785 (t80) cc_final: 0.8563 (t80) REVERT: F 333 LYS cc_start: 0.7705 (mttt) cc_final: 0.7243 (mttm) REVERT: F 532 GLU cc_start: 0.8259 (mp0) cc_final: 0.8049 (mp0) REVERT: F 611 SER cc_start: 0.7740 (t) cc_final: 0.7418 (p) outliers start: 2 outliers final: 0 residues processed: 696 average time/residue: 0.5037 time to fit residues: 523.3776 Evaluate side-chains 324 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 4.9990 chunk 304 optimal weight: 8.9990 chunk 169 optimal weight: 0.2980 chunk 104 optimal weight: 0.4980 chunk 205 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 365 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 GLN A 500 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 500 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN D 463 HIS D 500 GLN ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 HIS E 500 GLN ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31578 Z= 0.314 Angle : 0.592 9.196 42918 Z= 0.305 Chirality : 0.044 0.158 4884 Planarity : 0.006 0.049 5598 Dihedral : 7.846 170.435 4392 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.83 % Allowed : 8.00 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.12), residues: 4056 helix: -1.73 (0.13), residues: 1380 sheet: -3.12 (0.16), residues: 678 loop : -2.14 (0.12), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 124 HIS 0.005 0.001 HIS C 463 PHE 0.028 0.002 PHE E 595 TYR 0.025 0.002 TYR C 607 ARG 0.009 0.001 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 339 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7550 (tm-30) REVERT: A 532 GLU cc_start: 0.8055 (mp0) cc_final: 0.7846 (mp0) REVERT: A 538 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: B 59 MET cc_start: 0.8606 (mtt) cc_final: 0.8354 (mtp) REVERT: B 110 TYR cc_start: 0.8928 (m-80) cc_final: 0.8668 (m-80) REVERT: B 217 ASP cc_start: 0.7753 (t0) cc_final: 0.7490 (t0) REVERT: B 268 ASP cc_start: 0.7752 (p0) cc_final: 0.7350 (p0) REVERT: B 333 LYS cc_start: 0.7783 (mttt) cc_final: 0.7370 (mttm) REVERT: B 429 THR cc_start: 0.9378 (p) cc_final: 0.9168 (t) REVERT: B 611 SER cc_start: 0.7740 (t) cc_final: 0.7409 (p) REVERT: C 242 VAL cc_start: 0.8934 (m) cc_final: 0.8720 (p) REVERT: C 339 ASN cc_start: 0.8891 (m110) cc_final: 0.8564 (m-40) REVERT: C 505 MET cc_start: 0.8446 (tpp) cc_final: 0.8007 (mmt) REVERT: C 532 GLU cc_start: 0.8075 (mp0) cc_final: 0.7744 (mp0) REVERT: D 217 ASP cc_start: 0.7149 (t0) cc_final: 0.6868 (t0) REVERT: D 330 GLU cc_start: 0.7646 (tp30) cc_final: 0.7372 (tp30) REVERT: D 333 LYS cc_start: 0.7651 (mttt) cc_final: 0.7272 (mttm) REVERT: D 394 THR cc_start: 0.8713 (m) cc_final: 0.8282 (p) REVERT: D 505 MET cc_start: 0.8344 (tpp) cc_final: 0.8011 (mmt) REVERT: E 164 MET cc_start: 0.8680 (ttp) cc_final: 0.8461 (ttt) REVERT: E 413 LEU cc_start: 0.8306 (mm) cc_final: 0.7800 (mp) REVERT: E 417 CYS cc_start: 0.8171 (m) cc_final: 0.7902 (m) REVERT: E 463 HIS cc_start: 0.8766 (t70) cc_final: 0.8409 (t-90) REVERT: E 505 MET cc_start: 0.7975 (tpp) cc_final: 0.7548 (mmt) REVERT: F 7 PHE cc_start: 0.8746 (t80) cc_final: 0.8535 (t80) REVERT: F 333 LYS cc_start: 0.7654 (mttt) cc_final: 0.7196 (mttm) REVERT: F 643 GLU cc_start: 0.6924 (pt0) cc_final: 0.6613 (pt0) outliers start: 58 outliers final: 30 residues processed: 380 average time/residue: 0.4509 time to fit residues: 267.2961 Evaluate side-chains 310 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 279 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 616 GLU Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 634 THR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 616 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 303 optimal weight: 0.0670 chunk 248 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 365 optimal weight: 0.0040 chunk 395 optimal weight: 0.9990 chunk 325 optimal weight: 2.9990 chunk 362 optimal weight: 0.7980 chunk 124 optimal weight: 0.3980 chunk 293 optimal weight: 0.7980 overall best weight: 0.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN A 384 GLN A 433 GLN A 606 ASN B 409 GLN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 153 HIS ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN C 450 GLN ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 191 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 158 ASN E 384 GLN E 450 GLN F 158 ASN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 31578 Z= 0.151 Angle : 0.511 7.976 42918 Z= 0.258 Chirality : 0.041 0.139 4884 Planarity : 0.004 0.039 5598 Dihedral : 7.402 166.559 4392 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.92 % Allowed : 9.33 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.12), residues: 4056 helix: -1.11 (0.13), residues: 1428 sheet: -2.87 (0.17), residues: 714 loop : -1.72 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 162 HIS 0.007 0.000 HIS C 463 PHE 0.024 0.001 PHE E 595 TYR 0.018 0.001 TYR C 607 ARG 0.011 0.000 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 327 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 HIS cc_start: 0.8642 (t-170) cc_final: 0.8420 (t-170) REVERT: A 532 GLU cc_start: 0.8001 (mp0) cc_final: 0.7750 (mp0) REVERT: B 7 PHE cc_start: 0.8458 (t80) cc_final: 0.8148 (t80) REVERT: B 217 ASP cc_start: 0.7731 (t0) cc_final: 0.7455 (t0) REVERT: B 268 ASP cc_start: 0.7716 (p0) cc_final: 0.7336 (p0) REVERT: B 333 LYS cc_start: 0.7778 (mttt) cc_final: 0.7372 (mttm) REVERT: B 610 GLU cc_start: 0.7202 (tp30) cc_final: 0.6981 (mm-30) REVERT: C 339 ASN cc_start: 0.8817 (m110) cc_final: 0.8540 (m-40) REVERT: C 463 HIS cc_start: 0.8494 (t-170) cc_final: 0.8290 (t-170) REVERT: C 505 MET cc_start: 0.8356 (tpp) cc_final: 0.7925 (mmt) REVERT: C 532 GLU cc_start: 0.8092 (mp0) cc_final: 0.7748 (mp0) REVERT: D 41 MET cc_start: 0.8831 (mmt) cc_final: 0.8307 (mmt) REVERT: D 50 GLU cc_start: 0.8093 (pt0) cc_final: 0.7873 (pt0) REVERT: D 164 MET cc_start: 0.9256 (tmt) cc_final: 0.8600 (tmt) REVERT: D 217 ASP cc_start: 0.7237 (t0) cc_final: 0.6967 (t0) REVERT: D 330 GLU cc_start: 0.7499 (tp30) cc_final: 0.7250 (tp30) REVERT: D 333 LYS cc_start: 0.7633 (mttt) cc_final: 0.7253 (mttm) REVERT: D 334 MET cc_start: 0.8327 (ttm) cc_final: 0.8055 (ttm) REVERT: D 505 MET cc_start: 0.8338 (tpp) cc_final: 0.7990 (mmt) REVERT: D 567 MET cc_start: 0.8312 (mmp) cc_final: 0.8090 (tpt) REVERT: E 158 ASN cc_start: 0.8418 (m110) cc_final: 0.8105 (m110) REVERT: E 413 LEU cc_start: 0.8153 (mm) cc_final: 0.7621 (mp) REVERT: E 417 CYS cc_start: 0.8138 (m) cc_final: 0.7844 (m) REVERT: E 610 GLU cc_start: 0.7114 (tp30) cc_final: 0.6795 (mm-30) REVERT: F 7 PHE cc_start: 0.8553 (t80) cc_final: 0.8319 (t80) REVERT: F 41 MET cc_start: 0.8860 (mmt) cc_final: 0.8464 (mmt) REVERT: F 121 ASP cc_start: 0.8082 (t0) cc_final: 0.7818 (t0) REVERT: F 333 LYS cc_start: 0.7539 (mttt) cc_final: 0.7050 (mttm) REVERT: F 351 ASN cc_start: 0.8711 (m-40) cc_final: 0.8327 (m-40) REVERT: F 643 GLU cc_start: 0.6979 (pt0) cc_final: 0.6650 (pt0) outliers start: 61 outliers final: 26 residues processed: 368 average time/residue: 0.4394 time to fit residues: 260.5107 Evaluate side-chains 296 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 270 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 417 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 367 optimal weight: 4.9990 chunk 388 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN E 659 HIS F 554 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 31578 Z= 0.457 Angle : 0.624 7.829 42918 Z= 0.315 Chirality : 0.046 0.174 4884 Planarity : 0.005 0.042 5598 Dihedral : 7.599 171.838 4392 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.33 % Allowed : 10.08 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.13), residues: 4056 helix: -0.89 (0.14), residues: 1392 sheet: -2.93 (0.16), residues: 756 loop : -1.58 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 124 HIS 0.010 0.001 HIS E 463 PHE 0.025 0.002 PHE F 595 TYR 0.026 0.002 TYR C 607 ARG 0.006 0.001 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 269 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.8882 (m-80) cc_final: 0.8562 (m-80) REVERT: A 532 GLU cc_start: 0.8117 (mp0) cc_final: 0.7831 (mp0) REVERT: B 7 PHE cc_start: 0.8600 (t80) cc_final: 0.8277 (t80) REVERT: B 217 ASP cc_start: 0.7814 (t0) cc_final: 0.7540 (t0) REVERT: B 261 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8781 (m-40) REVERT: B 333 LYS cc_start: 0.7774 (mttt) cc_final: 0.7379 (mttm) REVERT: B 611 SER cc_start: 0.7753 (t) cc_final: 0.7424 (p) REVERT: C 339 ASN cc_start: 0.8878 (m110) cc_final: 0.8607 (m-40) REVERT: C 532 GLU cc_start: 0.8065 (mp0) cc_final: 0.7712 (mp0) REVERT: C 629 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8793 (p) REVERT: D 41 MET cc_start: 0.8816 (mmt) cc_final: 0.8441 (mmt) REVERT: D 217 ASP cc_start: 0.7316 (t0) cc_final: 0.7018 (t0) REVERT: D 330 GLU cc_start: 0.7573 (tp30) cc_final: 0.7285 (tp30) REVERT: D 333 LYS cc_start: 0.7647 (mttt) cc_final: 0.7231 (mttm) REVERT: E 413 LEU cc_start: 0.8271 (mm) cc_final: 0.7752 (mp) REVERT: E 417 CYS cc_start: 0.8101 (m) cc_final: 0.7805 (m) REVERT: F 7 PHE cc_start: 0.8631 (t80) cc_final: 0.8387 (t80) REVERT: F 121 ASP cc_start: 0.8090 (t0) cc_final: 0.7855 (t0) REVERT: F 351 ASN cc_start: 0.8790 (m-40) cc_final: 0.8274 (m110) REVERT: F 643 GLU cc_start: 0.6939 (pt0) cc_final: 0.6564 (pt0) outliers start: 74 outliers final: 48 residues processed: 327 average time/residue: 0.4610 time to fit residues: 236.7151 Evaluate side-chains 287 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 237 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain F residue 616 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 331 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 198 optimal weight: 0.0770 chunk 348 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31578 Z= 0.266 Angle : 0.544 7.278 42918 Z= 0.274 Chirality : 0.042 0.195 4884 Planarity : 0.004 0.043 5598 Dihedral : 7.460 171.365 4392 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.08 % Allowed : 11.66 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.13), residues: 4056 helix: -0.57 (0.14), residues: 1392 sheet: -2.70 (0.17), residues: 714 loop : -1.47 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 124 HIS 0.009 0.001 HIS E 463 PHE 0.022 0.002 PHE E 595 TYR 0.020 0.002 TYR C 607 ARG 0.013 0.000 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 274 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8315 (mtt) cc_final: 0.7898 (mtp) REVERT: A 532 GLU cc_start: 0.8115 (mp0) cc_final: 0.7810 (mp0) REVERT: B 7 PHE cc_start: 0.8498 (t80) cc_final: 0.8155 (t80) REVERT: B 193 MET cc_start: 0.8754 (mtp) cc_final: 0.8413 (mtp) REVERT: B 217 ASP cc_start: 0.7751 (t0) cc_final: 0.7487 (t0) REVERT: B 333 LYS cc_start: 0.7782 (mttt) cc_final: 0.7383 (mttm) REVERT: B 611 SER cc_start: 0.7818 (t) cc_final: 0.7493 (p) REVERT: C 339 ASN cc_start: 0.8810 (m110) cc_final: 0.8559 (m-40) REVERT: C 532 GLU cc_start: 0.8064 (mp0) cc_final: 0.7748 (mp0) REVERT: D 164 MET cc_start: 0.9356 (tmt) cc_final: 0.8952 (tmt) REVERT: D 193 MET cc_start: 0.8525 (mtp) cc_final: 0.8237 (mtt) REVERT: D 217 ASP cc_start: 0.7246 (t0) cc_final: 0.6955 (t0) REVERT: D 330 GLU cc_start: 0.7482 (tp30) cc_final: 0.7258 (tp30) REVERT: D 333 LYS cc_start: 0.7638 (mttt) cc_final: 0.7230 (mttm) REVERT: E 32 TRP cc_start: 0.8135 (m100) cc_final: 0.7681 (m100) REVERT: E 158 ASN cc_start: 0.8372 (m110) cc_final: 0.8135 (m110) REVERT: E 193 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8043 (ttt) REVERT: E 413 LEU cc_start: 0.8275 (mm) cc_final: 0.7745 (mp) REVERT: E 417 CYS cc_start: 0.8120 (m) cc_final: 0.7822 (m) REVERT: E 505 MET cc_start: 0.8059 (mmt) cc_final: 0.7424 (mmt) REVERT: E 532 GLU cc_start: 0.8153 (mp0) cc_final: 0.7920 (mp0) REVERT: F 7 PHE cc_start: 0.8593 (t80) cc_final: 0.8356 (t80) REVERT: F 121 ASP cc_start: 0.8073 (t0) cc_final: 0.7822 (t0) REVERT: F 333 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7350 (mttm) REVERT: F 351 ASN cc_start: 0.8807 (m-40) cc_final: 0.8427 (m-40) REVERT: F 410 ARG cc_start: 0.8015 (tpp-160) cc_final: 0.7795 (tpp-160) REVERT: F 643 GLU cc_start: 0.6878 (pt0) cc_final: 0.6486 (pt0) outliers start: 66 outliers final: 40 residues processed: 324 average time/residue: 0.4951 time to fit residues: 254.2325 Evaluate side-chains 293 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 252 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 616 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 0.6980 chunk 349 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 228 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 322 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN B 659 HIS ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN D 450 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 31578 Z= 0.368 Angle : 0.586 7.057 42918 Z= 0.296 Chirality : 0.044 0.194 4884 Planarity : 0.004 0.041 5598 Dihedral : 7.583 175.283 4392 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.39 % Allowed : 12.29 % 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: -2.06 (0.13), residues: 4056 helix: -0.48 (0.14), residues: 1398 sheet: -2.61 (0.17), residues: 750 loop : -1.40 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 124 HIS 0.008 0.001 HIS E 463 PHE 0.022 0.002 PHE E 595 TYR 0.024 0.002 TYR C 607 ARG 0.007 0.000 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 257 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 GLU cc_start: 0.8139 (mp0) cc_final: 0.7843 (mp0) REVERT: B 7 PHE cc_start: 0.8517 (t80) cc_final: 0.8193 (t80) REVERT: B 217 ASP cc_start: 0.7852 (t0) cc_final: 0.7622 (t0) REVERT: B 333 LYS cc_start: 0.7775 (mttt) cc_final: 0.7387 (mttm) REVERT: B 409 GLN cc_start: 0.8111 (tp40) cc_final: 0.7810 (tp40) REVERT: B 611 SER cc_start: 0.7891 (t) cc_final: 0.7569 (p) REVERT: C 167 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8516 (mtpp) REVERT: C 532 GLU cc_start: 0.8116 (mp0) cc_final: 0.7755 (mp0) REVERT: D 164 MET cc_start: 0.9324 (tmt) cc_final: 0.9094 (tmt) REVERT: D 217 ASP cc_start: 0.7293 (t0) cc_final: 0.6989 (t0) REVERT: D 333 LYS cc_start: 0.7640 (mttt) cc_final: 0.7242 (mttm) REVERT: D 426 THR cc_start: 0.8055 (m) cc_final: 0.7812 (m) REVERT: D 505 MET cc_start: 0.8446 (tpp) cc_final: 0.8046 (mmt) REVERT: E 32 TRP cc_start: 0.8189 (m100) cc_final: 0.7701 (m100) REVERT: E 413 LEU cc_start: 0.8240 (mm) cc_final: 0.7744 (mp) REVERT: E 417 CYS cc_start: 0.8097 (m) cc_final: 0.7838 (m) REVERT: F 7 PHE cc_start: 0.8640 (t80) cc_final: 0.8392 (t80) REVERT: F 121 ASP cc_start: 0.8001 (t0) cc_final: 0.7742 (t0) REVERT: F 333 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7285 (mttm) REVERT: F 410 ARG cc_start: 0.8031 (tpp-160) cc_final: 0.7825 (tpp-160) REVERT: F 643 GLU cc_start: 0.6896 (pt0) cc_final: 0.6574 (pt0) outliers start: 76 outliers final: 51 residues processed: 318 average time/residue: 0.4583 time to fit residues: 227.6455 Evaluate side-chains 291 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 239 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 610 GLU Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 284 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 327 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 387 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN B 309 ASN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 342 GLN C 414 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31578 Z= 0.213 Angle : 0.522 9.725 42918 Z= 0.262 Chirality : 0.041 0.210 4884 Planarity : 0.004 0.051 5598 Dihedral : 7.361 173.566 4392 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.64 % Allowed : 13.30 % Favored : 85.07 % 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: -1.76 (0.13), residues: 4056 helix: -0.16 (0.14), residues: 1386 sheet: -2.38 (0.18), residues: 750 loop : -1.31 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 651 HIS 0.008 0.001 HIS E 463 PHE 0.023 0.001 PHE E 595 TYR 0.019 0.002 TYR E 607 ARG 0.013 0.000 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 275 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.8839 (m-80) cc_final: 0.8574 (m-80) REVERT: A 532 GLU cc_start: 0.8140 (mp0) cc_final: 0.7821 (mp0) REVERT: B 7 PHE cc_start: 0.8429 (t80) cc_final: 0.8138 (t80) REVERT: B 33 GLU cc_start: 0.7371 (pt0) cc_final: 0.7085 (tt0) REVERT: B 121 ASP cc_start: 0.8221 (t0) cc_final: 0.7999 (t0) REVERT: B 193 MET cc_start: 0.8750 (mtp) cc_final: 0.8473 (mtp) REVERT: B 217 ASP cc_start: 0.7690 (t0) cc_final: 0.7411 (t0) REVERT: B 333 LYS cc_start: 0.7858 (mttt) cc_final: 0.7412 (mttm) REVERT: B 409 GLN cc_start: 0.8057 (tp40) cc_final: 0.7822 (tp40) REVERT: B 611 SER cc_start: 0.7786 (t) cc_final: 0.7473 (p) REVERT: C 167 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8428 (mtpp) REVERT: C 532 GLU cc_start: 0.8112 (mp0) cc_final: 0.7743 (mp0) REVERT: D 33 GLU cc_start: 0.7331 (pt0) cc_final: 0.7111 (tt0) REVERT: D 217 ASP cc_start: 0.7272 (t0) cc_final: 0.6982 (t0) REVERT: D 330 GLU cc_start: 0.7595 (tp30) cc_final: 0.7233 (tp30) REVERT: D 333 LYS cc_start: 0.7589 (mttt) cc_final: 0.7217 (mttm) REVERT: D 426 THR cc_start: 0.8020 (m) cc_final: 0.7782 (m) REVERT: D 505 MET cc_start: 0.8478 (tpp) cc_final: 0.8070 (mmt) REVERT: E 32 TRP cc_start: 0.8125 (m100) cc_final: 0.7691 (m100) REVERT: E 158 ASN cc_start: 0.8316 (m110) cc_final: 0.8088 (m110) REVERT: E 351 ASN cc_start: 0.8643 (m-40) cc_final: 0.8393 (m-40) REVERT: E 413 LEU cc_start: 0.8258 (mm) cc_final: 0.7767 (mp) REVERT: E 417 CYS cc_start: 0.8117 (m) cc_final: 0.7846 (m) REVERT: E 505 MET cc_start: 0.8118 (mmt) cc_final: 0.7852 (mmt) REVERT: F 7 PHE cc_start: 0.8579 (t80) cc_final: 0.8330 (t80) REVERT: F 41 MET cc_start: 0.8839 (mmt) cc_final: 0.8425 (mmt) REVERT: F 121 ASP cc_start: 0.7924 (t0) cc_final: 0.7674 (t0) REVERT: F 410 ARG cc_start: 0.8036 (tpp-160) cc_final: 0.7833 (tpp-160) REVERT: F 505 MET cc_start: 0.8469 (tpp) cc_final: 0.7764 (mmt) REVERT: F 643 GLU cc_start: 0.6848 (pt0) cc_final: 0.6491 (pt0) outliers start: 52 outliers final: 42 residues processed: 319 average time/residue: 0.4630 time to fit residues: 229.9264 Evaluate side-chains 295 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 0.0030 chunk 154 optimal weight: 3.9990 chunk 231 optimal weight: 0.0370 chunk 116 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 36 optimal weight: 0.0670 chunk 304 optimal weight: 9.9990 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 HIS C 606 ASN D 409 GLN D 450 GLN E 606 ASN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31578 Z= 0.150 Angle : 0.496 9.531 42918 Z= 0.248 Chirality : 0.040 0.214 4884 Planarity : 0.004 0.052 5598 Dihedral : 7.091 169.890 4392 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.61 % Allowed : 13.71 % Favored : 84.69 % 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: -1.43 (0.13), residues: 4056 helix: 0.14 (0.14), residues: 1398 sheet: -2.13 (0.18), residues: 744 loop : -1.18 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 651 HIS 0.007 0.000 HIS E 463 PHE 0.022 0.001 PHE D 595 TYR 0.019 0.001 TYR A 607 ARG 0.006 0.000 ARG F 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 285 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.8817 (m-80) cc_final: 0.8582 (m-80) REVERT: A 532 GLU cc_start: 0.8147 (mp0) cc_final: 0.7789 (mp0) REVERT: B 7 PHE cc_start: 0.8411 (t80) cc_final: 0.8018 (t80) REVERT: B 217 ASP cc_start: 0.7541 (t0) cc_final: 0.7239 (t0) REVERT: B 333 LYS cc_start: 0.7932 (mttt) cc_final: 0.7473 (mttm) REVERT: B 505 MET cc_start: 0.8370 (tpp) cc_final: 0.7944 (mmp) REVERT: B 518 LYS cc_start: 0.8793 (ptmm) cc_final: 0.8593 (ptmm) REVERT: C 167 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8388 (mtpp) REVERT: C 334 MET cc_start: 0.8794 (ttm) cc_final: 0.8563 (ttm) REVERT: C 505 MET cc_start: 0.8403 (tpp) cc_final: 0.8072 (mmt) REVERT: C 532 GLU cc_start: 0.8120 (mp0) cc_final: 0.7712 (mp0) REVERT: D 333 LYS cc_start: 0.7597 (mttt) cc_final: 0.7226 (mttm) REVERT: D 426 THR cc_start: 0.8031 (m) cc_final: 0.7798 (m) REVERT: D 505 MET cc_start: 0.8465 (tpp) cc_final: 0.8071 (mmt) REVERT: D 679 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.5358 (m-10) REVERT: E 32 TRP cc_start: 0.7957 (m100) cc_final: 0.7601 (m100) REVERT: E 158 ASN cc_start: 0.8251 (m110) cc_final: 0.7981 (m110) REVERT: E 351 ASN cc_start: 0.8605 (m-40) cc_final: 0.8384 (m-40) REVERT: E 413 LEU cc_start: 0.8192 (mm) cc_final: 0.7745 (mp) REVERT: E 417 CYS cc_start: 0.8077 (m) cc_final: 0.7792 (m) REVERT: E 505 MET cc_start: 0.8038 (mmt) cc_final: 0.7724 (mmt) REVERT: F 41 MET cc_start: 0.8849 (mmt) cc_final: 0.8498 (mmt) REVERT: F 121 ASP cc_start: 0.7976 (t0) cc_final: 0.7679 (t0) REVERT: F 333 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7165 (mttm) REVERT: F 410 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7761 (tpp-160) REVERT: F 643 GLU cc_start: 0.6828 (pt0) cc_final: 0.6458 (pt0) outliers start: 51 outliers final: 32 residues processed: 324 average time/residue: 0.4496 time to fit residues: 230.0477 Evaluate side-chains 289 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 255 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 490 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 0.9990 chunk 371 optimal weight: 1.9990 chunk 338 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 283 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 326 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 31578 Z= 0.300 Angle : 0.557 10.792 42918 Z= 0.279 Chirality : 0.043 0.214 4884 Planarity : 0.004 0.060 5598 Dihedral : 7.211 171.673 4392 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.67 % Allowed : 14.02 % Favored : 84.31 % 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: -1.46 (0.13), residues: 4056 helix: 0.11 (0.14), residues: 1398 sheet: -2.21 (0.18), residues: 744 loop : -1.16 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 124 HIS 0.006 0.001 HIS E 463 PHE 0.021 0.002 PHE E 595 TYR 0.024 0.002 TYR A 607 ARG 0.015 0.000 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 247 time to evaluate : 3.465 Fit side-chains revert: symmetry clash REVERT: A 110 TYR cc_start: 0.8822 (m-80) cc_final: 0.8567 (m-80) REVERT: A 193 MET cc_start: 0.8232 (mtm) cc_final: 0.7976 (mtm) REVERT: A 532 GLU cc_start: 0.8177 (mp0) cc_final: 0.7791 (mp0) REVERT: B 7 PHE cc_start: 0.8474 (t80) cc_final: 0.8148 (t80) REVERT: B 193 MET cc_start: 0.8758 (mtp) cc_final: 0.8492 (mtp) REVERT: B 217 ASP cc_start: 0.7621 (t0) cc_final: 0.7343 (t0) REVERT: B 333 LYS cc_start: 0.7929 (mttt) cc_final: 0.7478 (mttm) REVERT: C 167 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8513 (mtpp) REVERT: D 333 LYS cc_start: 0.7377 (mttt) cc_final: 0.7082 (mttm) REVERT: D 426 THR cc_start: 0.8052 (m) cc_final: 0.7797 (m) REVERT: D 505 MET cc_start: 0.8519 (tpp) cc_final: 0.8080 (mmt) REVERT: E 32 TRP cc_start: 0.8161 (m100) cc_final: 0.7736 (m100) REVERT: E 158 ASN cc_start: 0.8389 (m110) cc_final: 0.8160 (m110) REVERT: E 413 LEU cc_start: 0.8233 (mm) cc_final: 0.7786 (mp) REVERT: E 417 CYS cc_start: 0.8098 (m) cc_final: 0.7834 (m) REVERT: E 505 MET cc_start: 0.8108 (mmt) cc_final: 0.7767 (mmt) REVERT: F 41 MET cc_start: 0.8793 (mmt) cc_final: 0.8464 (mmt) REVERT: F 121 ASP cc_start: 0.7953 (t0) cc_final: 0.7706 (t0) REVERT: F 410 ARG cc_start: 0.8056 (tpp-160) cc_final: 0.7814 (tpp-160) REVERT: F 643 GLU cc_start: 0.6823 (pt0) cc_final: 0.6471 (pt0) outliers start: 53 outliers final: 42 residues processed: 292 average time/residue: 0.4708 time to fit residues: 214.5020 Evaluate side-chains 284 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 241 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 0.0370 chunk 381 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 400 optimal weight: 1.9990 chunk 368 optimal weight: 0.0370 chunk 318 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 195 optimal weight: 0.0970 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31578 Z= 0.152 Angle : 0.508 11.106 42918 Z= 0.253 Chirality : 0.041 0.230 4884 Planarity : 0.004 0.044 5598 Dihedral : 6.981 167.110 4392 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.04 % Allowed : 14.62 % Favored : 84.34 % 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: -1.24 (0.13), residues: 4056 helix: 0.35 (0.14), residues: 1398 sheet: -2.07 (0.18), residues: 744 loop : -1.08 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 651 HIS 0.007 0.000 HIS E 463 PHE 0.023 0.001 PHE E 595 TYR 0.019 0.001 TYR A 607 ARG 0.007 0.000 ARG B 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.8806 (m-80) cc_final: 0.8589 (m-80) REVERT: A 193 MET cc_start: 0.8229 (mtm) cc_final: 0.7963 (mtt) REVERT: A 532 GLU cc_start: 0.8180 (mp0) cc_final: 0.7782 (mp0) REVERT: B 7 PHE cc_start: 0.8415 (t80) cc_final: 0.8065 (t80) REVERT: B 193 MET cc_start: 0.8704 (mtp) cc_final: 0.8445 (mtp) REVERT: B 217 ASP cc_start: 0.7535 (t0) cc_final: 0.7256 (t0) REVERT: B 333 LYS cc_start: 0.7910 (mttt) cc_final: 0.7449 (mttm) REVERT: B 505 MET cc_start: 0.8365 (tpp) cc_final: 0.7911 (mmp) REVERT: B 518 LYS cc_start: 0.8785 (ptmm) cc_final: 0.8574 (ptmm) REVERT: B 538 ASP cc_start: 0.8023 (m-30) cc_final: 0.7787 (m-30) REVERT: C 167 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8357 (mtpp) REVERT: C 505 MET cc_start: 0.8416 (tpp) cc_final: 0.8085 (mmt) REVERT: D 158 ASN cc_start: 0.8267 (m110) cc_final: 0.7858 (m-40) REVERT: D 333 LYS cc_start: 0.7368 (mttt) cc_final: 0.7059 (mttm) REVERT: D 426 THR cc_start: 0.8081 (m) cc_final: 0.7841 (m) REVERT: D 505 MET cc_start: 0.8450 (tpp) cc_final: 0.8059 (mmt) REVERT: E 32 TRP cc_start: 0.8043 (m100) cc_final: 0.7701 (m100) REVERT: E 158 ASN cc_start: 0.8273 (m110) cc_final: 0.8005 (m110) REVERT: E 351 ASN cc_start: 0.8534 (m-40) cc_final: 0.8323 (m-40) REVERT: E 505 MET cc_start: 0.8129 (mmt) cc_final: 0.7826 (mmt) REVERT: E 610 GLU cc_start: 0.7135 (tp30) cc_final: 0.6664 (mm-30) REVERT: F 41 MET cc_start: 0.8835 (mmt) cc_final: 0.8512 (mmt) REVERT: F 121 ASP cc_start: 0.7917 (t0) cc_final: 0.7681 (t0) REVERT: F 333 LYS cc_start: 0.7858 (mmmm) cc_final: 0.7127 (mttm) REVERT: F 334 MET cc_start: 0.8323 (tpp) cc_final: 0.7953 (ttm) REVERT: F 410 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7791 (tpp-160) REVERT: F 643 GLU cc_start: 0.6781 (pt0) cc_final: 0.6415 (pt0) outliers start: 33 outliers final: 30 residues processed: 283 average time/residue: 0.4584 time to fit residues: 204.0221 Evaluate side-chains 279 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 248 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 0.0060 chunk 339 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 47 optimal weight: 0.0000 chunk 88 optimal weight: 0.4980 chunk 319 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092722 restraints weight = 42100.903| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.18 r_work: 0.2946 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31578 Z= 0.157 Angle : 0.500 10.933 42918 Z= 0.248 Chirality : 0.041 0.227 4884 Planarity : 0.004 0.045 5598 Dihedral : 6.790 162.183 4392 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.39 % Allowed : 14.52 % Favored : 84.09 % 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: 4056 helix: 0.52 (0.15), residues: 1392 sheet: -2.01 (0.18), residues: 744 loop : -1.02 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 162 HIS 0.007 0.000 HIS E 463 PHE 0.022 0.001 PHE E 595 TYR 0.021 0.001 TYR A 607 ARG 0.007 0.000 ARG B 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6501.62 seconds wall clock time: 118 minutes 6.14 seconds (7086.14 seconds total)