Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 10:48:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b40_15835/10_2023/8b40_15835.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b40_15835/10_2023/8b40_15835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b40_15835/10_2023/8b40_15835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b40_15835/10_2023/8b40_15835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b40_15835/10_2023/8b40_15835.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b40_15835/10_2023/8b40_15835.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22484 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 259 5.16 5 C 25746 2.51 5 N 6447 2.21 5 O 7014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 102": "OD1" <-> "OD2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 102": "OD1" <-> "OD2" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 39466 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5638 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5638 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5638 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5638 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5638 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5638 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5638 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 14.92, per 1000 atoms: 0.38 Number of scatterers: 39466 At special positions: 0 Unit cell: (162.75, 162.75, 187.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 259 16.00 O 7014 8.00 N 6447 7.00 C 25746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 293 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 293 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS C 293 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 115 " - pdb=" SG CYS D 293 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 308 " distance=2.03 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 293 " distance=2.04 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: 11.66 Conformation dependent library (CDL) restraints added in 3.9 seconds 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9422 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 21 sheets defined 51.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 104 through 119 Processing helix chain 'A' and resid 121 through 148 Proline residue: A 128 - end of helix removed outlier: 4.574A pdb=" N TRP A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 168 removed outlier: 4.295A pdb=" N LYS A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 removed outlier: 4.287A pdb=" N THR A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 253 removed outlier: 4.102A pdb=" N GLU A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 287 removed outlier: 4.030A pdb=" N ALA A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 342 removed outlier: 4.782A pdb=" N LEU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 381 through 389 removed outlier: 4.111A pdb=" N SER A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 393 through 409 Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 507 through 513 removed outlier: 3.601A pdb=" N LEU A 513 " --> pdb=" O MET A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.573A pdb=" N VAL A 560 " --> pdb=" O PRO A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 677 through 682 removed outlier: 4.082A pdb=" N CYS A 682 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 705 Processing helix chain 'A' and resid 722 through 728 Processing helix chain 'A' and resid 745 through 751 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 785 through 791 Processing helix chain 'A' and resid 793 through 802 Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 121 through 148 Proline residue: B 128 - end of helix removed outlier: 4.607A pdb=" N TRP B 145 " --> pdb=" O CYS B 141 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 168 removed outlier: 4.235A pdb=" N LYS B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 removed outlier: 4.336A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.963A pdb=" N GLU B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 287 removed outlier: 4.025A pdb=" N ALA B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 342 removed outlier: 4.737A pdb=" N LEU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 367 through 381 Processing helix chain 'B' and resid 381 through 389 removed outlier: 4.136A pdb=" N SER B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS B 386 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 393 through 409 Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 507 through 513 removed outlier: 3.582A pdb=" N LEU B 513 " --> pdb=" O MET B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.539A pdb=" N VAL B 560 " --> pdb=" O PRO B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 588 Processing helix chain 'B' and resid 607 through 611 Processing helix chain 'B' and resid 629 through 634 removed outlier: 3.502A pdb=" N PHE B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 677 through 682 removed outlier: 4.066A pdb=" N CYS B 682 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 722 through 728 Processing helix chain 'B' and resid 745 through 751 Processing helix chain 'B' and resid 768 through 774 Processing helix chain 'B' and resid 785 through 791 Processing helix chain 'B' and resid 793 through 802 Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 121 through 148 Proline residue: C 128 - end of helix removed outlier: 4.585A pdb=" N TRP C 145 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 168 removed outlier: 4.292A pdb=" N LYS C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 removed outlier: 4.356A pdb=" N THR C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.954A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 287 removed outlier: 4.086A pdb=" N ALA C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 342 removed outlier: 4.910A pdb=" N LEU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 367 through 381 Processing helix chain 'C' and resid 381 through 389 removed outlier: 4.194A pdb=" N SER C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 392 No H-bonds generated for 'chain 'C' and resid 390 through 392' Processing helix chain 'C' and resid 393 through 409 Processing helix chain 'C' and resid 410 through 418 Processing helix chain 'C' and resid 437 through 443 Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 507 through 513 removed outlier: 3.521A pdb=" N LEU C 513 " --> pdb=" O MET C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 3.648A pdb=" N VAL C 560 " --> pdb=" O PRO C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 removed outlier: 3.513A pdb=" N LYS C 586 " --> pdb=" O ASN C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 611 Processing helix chain 'C' and resid 629 through 634 Processing helix chain 'C' and resid 653 through 659 Processing helix chain 'C' and resid 676 through 682 removed outlier: 4.183A pdb=" N CYS C 682 " --> pdb=" O LEU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 705 Processing helix chain 'C' and resid 722 through 728 Processing helix chain 'C' and resid 745 through 751 Processing helix chain 'C' and resid 768 through 774 removed outlier: 3.507A pdb=" N LEU C 771 " --> pdb=" O PRO C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 791 Processing helix chain 'C' and resid 793 through 802 Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 121 through 148 Proline residue: D 128 - end of helix removed outlier: 4.569A pdb=" N TRP D 145 " --> pdb=" O CYS D 141 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 168 removed outlier: 4.274A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 removed outlier: 4.319A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 4.083A pdb=" N GLU D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 253 " --> pdb=" O ARG D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 287 removed outlier: 4.082A pdb=" N ALA D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 342 Processing helix chain 'D' and resid 353 through 359 Processing helix chain 'D' and resid 367 through 381 Processing helix chain 'D' and resid 381 through 389 removed outlier: 4.200A pdb=" N SER D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS D 386 " --> pdb=" O PRO D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 392 No H-bonds generated for 'chain 'D' and resid 390 through 392' Processing helix chain 'D' and resid 393 through 409 Processing helix chain 'D' and resid 410 through 418 Processing helix chain 'D' and resid 437 through 443 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.507A pdb=" N ILE D 463 " --> pdb=" O PRO D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 493 Processing helix chain 'D' and resid 507 through 513 removed outlier: 3.549A pdb=" N LEU D 513 " --> pdb=" O MET D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 3.692A pdb=" N VAL D 560 " --> pdb=" O PRO D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 588 removed outlier: 3.586A pdb=" N LYS D 586 " --> pdb=" O ASN D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 611 Processing helix chain 'D' and resid 629 through 634 removed outlier: 3.622A pdb=" N PHE D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 659 Processing helix chain 'D' and resid 676 through 682 removed outlier: 4.168A pdb=" N CYS D 682 " --> pdb=" O LEU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 705 Processing helix chain 'D' and resid 722 through 728 removed outlier: 3.658A pdb=" N CYS D 728 " --> pdb=" O LEU D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 751 Processing helix chain 'D' and resid 768 through 774 Processing helix chain 'D' and resid 785 through 791 Processing helix chain 'D' and resid 793 through 802 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 104 through 119 Processing helix chain 'E' and resid 121 through 148 Proline residue: E 128 - end of helix removed outlier: 4.484A pdb=" N TRP E 145 " --> pdb=" O CYS E 141 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE E 146 " --> pdb=" O SER E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 168 removed outlier: 4.244A pdb=" N LYS E 154 " --> pdb=" O GLY E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 176 removed outlier: 4.297A pdb=" N THR E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 253 removed outlier: 4.087A pdb=" N GLU E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 285 removed outlier: 4.079A pdb=" N ALA E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 342 removed outlier: 4.874A pdb=" N LEU E 315 " --> pdb=" O THR E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 367 through 381 Processing helix chain 'E' and resid 381 through 389 removed outlier: 4.205A pdb=" N SER E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS E 386 " --> pdb=" O PRO E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 392 No H-bonds generated for 'chain 'E' and resid 390 through 392' Processing helix chain 'E' and resid 393 through 409 Processing helix chain 'E' and resid 410 through 418 Processing helix chain 'E' and resid 437 through 443 Processing helix chain 'E' and resid 460 through 466 removed outlier: 3.511A pdb=" N ILE E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 493 Processing helix chain 'E' and resid 507 through 513 removed outlier: 3.513A pdb=" N LEU E 513 " --> pdb=" O MET E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 563 removed outlier: 3.673A pdb=" N VAL E 560 " --> pdb=" O PRO E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 588 removed outlier: 3.554A pdb=" N LYS E 586 " --> pdb=" O ASN E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 611 Processing helix chain 'E' and resid 629 through 634 removed outlier: 3.621A pdb=" N PHE E 633 " --> pdb=" O GLU E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 659 Processing helix chain 'E' and resid 676 through 682 removed outlier: 4.226A pdb=" N CYS E 682 " --> pdb=" O LEU E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 705 Processing helix chain 'E' and resid 722 through 728 removed outlier: 3.724A pdb=" N CYS E 728 " --> pdb=" O LEU E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 745 through 751 Processing helix chain 'E' and resid 768 through 774 Processing helix chain 'E' and resid 785 through 791 Processing helix chain 'E' and resid 793 through 802 Processing helix chain 'F' and resid 22 through 50 removed outlier: 3.620A pdb=" N ASP F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 148 Proline residue: F 128 - end of helix removed outlier: 4.491A pdb=" N TRP F 145 " --> pdb=" O CYS F 141 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 removed outlier: 4.315A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 4.274A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 253 removed outlier: 4.133A pdb=" N GLU F 243 " --> pdb=" O LYS F 239 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 285 removed outlier: 4.043A pdb=" N ALA F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 342 removed outlier: 4.764A pdb=" N LEU F 315 " --> pdb=" O THR F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 359 Processing helix chain 'F' and resid 367 through 381 Processing helix chain 'F' and resid 381 through 389 removed outlier: 4.211A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS F 386 " --> pdb=" O PRO F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 392 No H-bonds generated for 'chain 'F' and resid 390 through 392' Processing helix chain 'F' and resid 393 through 409 Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 437 through 443 Processing helix chain 'F' and resid 460 through 466 Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 507 through 513 removed outlier: 3.571A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 removed outlier: 3.662A pdb=" N VAL F 560 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 588 removed outlier: 3.523A pdb=" N LYS F 586 " --> pdb=" O ASN F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'F' and resid 629 through 634 Processing helix chain 'F' and resid 653 through 659 Processing helix chain 'F' and resid 676 through 682 removed outlier: 4.217A pdb=" N CYS F 682 " --> pdb=" O LEU F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 Processing helix chain 'F' and resid 722 through 728 removed outlier: 3.619A pdb=" N CYS F 728 " --> pdb=" O LEU F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 745 through 751 Processing helix chain 'F' and resid 768 through 774 Processing helix chain 'F' and resid 785 through 791 Processing helix chain 'F' and resid 793 through 802 Processing helix chain 'G' and resid 22 through 49 Processing helix chain 'G' and resid 104 through 119 Processing helix chain 'G' and resid 121 through 148 Proline residue: G 128 - end of helix removed outlier: 4.562A pdb=" N TRP G 145 " --> pdb=" O CYS G 141 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE G 146 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 168 removed outlier: 4.289A pdb=" N LYS G 154 " --> pdb=" O GLY G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 176 removed outlier: 4.329A pdb=" N THR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 253 removed outlier: 4.056A pdb=" N GLU G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU G 253 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 287 removed outlier: 4.044A pdb=" N ALA G 282 " --> pdb=" O ALA G 278 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL G 287 " --> pdb=" O LEU G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 342 removed outlier: 4.853A pdb=" N LEU G 315 " --> pdb=" O THR G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 359 Processing helix chain 'G' and resid 367 through 381 Processing helix chain 'G' and resid 381 through 389 removed outlier: 4.196A pdb=" N SER G 385 " --> pdb=" O ASP G 381 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS G 386 " --> pdb=" O PRO G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 392 No H-bonds generated for 'chain 'G' and resid 390 through 392' Processing helix chain 'G' and resid 393 through 409 Processing helix chain 'G' and resid 410 through 418 Processing helix chain 'G' and resid 437 through 443 Processing helix chain 'G' and resid 460 through 466 Processing helix chain 'G' and resid 482 through 493 Processing helix chain 'G' and resid 507 through 513 removed outlier: 3.550A pdb=" N LEU G 513 " --> pdb=" O MET G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 563 removed outlier: 3.607A pdb=" N VAL G 560 " --> pdb=" O PRO G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 588 Processing helix chain 'G' and resid 607 through 611 Processing helix chain 'G' and resid 629 through 634 Processing helix chain 'G' and resid 653 through 659 Processing helix chain 'G' and resid 676 through 682 removed outlier: 4.143A pdb=" N CYS G 682 " --> pdb=" O LEU G 679 " (cutoff:3.500A) Processing helix chain 'G' and resid 699 through 705 Processing helix chain 'G' and resid 722 through 728 Processing helix chain 'G' and resid 745 through 751 Processing helix chain 'G' and resid 768 through 774 Processing helix chain 'G' and resid 785 through 791 Processing helix chain 'G' and resid 793 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 420 removed outlier: 5.941A pdb=" N LEU A 426 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LYS A 450 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU A 428 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLU A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 430 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU A 449 " --> pdb=" O CYS A 473 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS A 475 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 451 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU A 472 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LYS A 499 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 474 " --> pdb=" O LYS A 499 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A 547 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N HIS A 573 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 549 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET A 570 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL A 597 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 572 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 594 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 618 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 617 " --> pdb=" O LYS A 643 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 642 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU A 688 " --> pdb=" O SER A 712 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE A 711 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 757 " --> pdb=" O VAL A 783 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 459 removed outlier: 6.236A pdb=" N VAL A 457 " --> pdb=" O LYS A 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 419 through 420 removed outlier: 5.929A pdb=" N LEU B 426 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LYS B 450 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU B 428 " --> pdb=" O LYS B 450 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLU B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 430 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 449 " --> pdb=" O CYS B 473 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N HIS B 475 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 451 " --> pdb=" O HIS B 475 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 547 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS B 573 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 549 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET B 570 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL B 597 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 572 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 618 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B 617 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 642 " --> pdb=" O ARG B 664 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 688 " --> pdb=" O SER B 712 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE B 711 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 757 " --> pdb=" O VAL B 783 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 457 through 459 removed outlier: 6.254A pdb=" N VAL B 457 " --> pdb=" O LYS B 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AA8, first strand: chain 'C' and resid 419 through 420 removed outlier: 5.861A pdb=" N LEU C 426 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS C 450 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU C 428 " --> pdb=" O LYS C 450 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLU C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 430 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU C 449 " --> pdb=" O CYS C 473 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS C 475 " --> pdb=" O LEU C 449 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 451 " --> pdb=" O HIS C 475 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU C 472 " --> pdb=" O SER C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LYS C 499 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C 474 " --> pdb=" O LYS C 499 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 496 " --> pdb=" O TYR C 520 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL C 522 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C 498 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 519 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS C 550 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 521 " --> pdb=" O LYS C 550 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 595 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 572 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 618 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 642 " --> pdb=" O ARG C 664 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 666 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU C 688 " --> pdb=" O SER C 712 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE C 711 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 757 " --> pdb=" O VAL C 783 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 457 through 459 removed outlier: 6.265A pdb=" N VAL C 457 " --> pdb=" O LYS C 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 52 through 56 Processing sheet with id=AB2, first strand: chain 'D' and resid 419 through 420 removed outlier: 3.566A pdb=" N LEU D 428 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS D 450 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU D 449 " --> pdb=" O CYS D 473 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS D 475 " --> pdb=" O LEU D 449 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 451 " --> pdb=" O HIS D 475 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU D 472 " --> pdb=" O SER D 497 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LYS D 499 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU D 474 " --> pdb=" O LYS D 499 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU D 496 " --> pdb=" O TYR D 520 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL D 522 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL D 498 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU D 547 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N HIS D 573 " --> pdb=" O LEU D 547 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 549 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET D 570 " --> pdb=" O GLU D 593 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU D 595 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 572 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 597 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU D 688 " --> pdb=" O SER D 712 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE D 711 " --> pdb=" O LYS D 735 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU D 734 " --> pdb=" O ASP D 758 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 757 " --> pdb=" O VAL D 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 457 through 459 removed outlier: 6.197A pdb=" N VAL D 457 " --> pdb=" O LYS D 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AB5, first strand: chain 'E' and resid 419 through 420 removed outlier: 5.753A pdb=" N LEU E 426 " --> pdb=" O SER E 448 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS E 450 " --> pdb=" O LEU E 426 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU E 428 " --> pdb=" O LYS E 450 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU E 430 " --> pdb=" O GLU E 452 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU E 449 " --> pdb=" O CYS E 473 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N HIS E 475 " --> pdb=" O LEU E 449 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU E 451 " --> pdb=" O HIS E 475 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU E 472 " --> pdb=" O SER E 497 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LYS E 499 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU E 474 " --> pdb=" O LYS E 499 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU E 496 " --> pdb=" O TYR E 520 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL E 522 " --> pdb=" O LEU E 496 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL E 498 " --> pdb=" O VAL E 522 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU E 519 " --> pdb=" O SER E 548 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS E 550 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU E 521 " --> pdb=" O LYS E 550 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU E 547 " --> pdb=" O CYS E 571 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N HIS E 573 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE E 549 " --> pdb=" O HIS E 573 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET E 570 " --> pdb=" O GLU E 593 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU E 595 " --> pdb=" O MET E 570 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 572 " --> pdb=" O GLU E 595 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL E 597 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE E 666 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU E 688 " --> pdb=" O SER E 712 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE E 711 " --> pdb=" O LYS E 735 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU E 734 " --> pdb=" O ASP E 758 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU E 757 " --> pdb=" O VAL E 783 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 457 through 459 removed outlier: 6.188A pdb=" N VAL E 457 " --> pdb=" O LYS E 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AB8, first strand: chain 'F' and resid 419 through 420 removed outlier: 5.793A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU F 496 " --> pdb=" O TYR F 520 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL F 522 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL F 498 " --> pdb=" O VAL F 522 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU F 547 " --> pdb=" O CYS F 571 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N HIS F 573 " --> pdb=" O LEU F 547 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE F 549 " --> pdb=" O HIS F 573 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET F 570 " --> pdb=" O GLU F 593 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 595 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 572 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL F 597 " --> pdb=" O VAL F 572 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 642 " --> pdb=" O ARG F 664 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU F 688 " --> pdb=" O SER F 712 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE F 711 " --> pdb=" O LYS F 735 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU F 757 " --> pdb=" O VAL F 783 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 457 through 459 removed outlier: 6.229A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 52 through 56 Processing sheet with id=AC2, first strand: chain 'G' and resid 419 through 420 removed outlier: 5.871A pdb=" N LEU G 426 " --> pdb=" O SER G 448 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS G 450 " --> pdb=" O LEU G 426 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU G 428 " --> pdb=" O LYS G 450 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU G 452 " --> pdb=" O LEU G 428 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU G 430 " --> pdb=" O GLU G 452 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU G 449 " --> pdb=" O CYS G 473 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N HIS G 475 " --> pdb=" O LEU G 449 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU G 451 " --> pdb=" O HIS G 475 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU G 472 " --> pdb=" O SER G 497 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYS G 499 " --> pdb=" O LEU G 472 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU G 474 " --> pdb=" O LYS G 499 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU G 519 " --> pdb=" O SER G 548 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LYS G 550 " --> pdb=" O LEU G 519 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU G 521 " --> pdb=" O LYS G 550 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU G 547 " --> pdb=" O CYS G 571 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N HIS G 573 " --> pdb=" O LEU G 547 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE G 549 " --> pdb=" O HIS G 573 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU G 595 " --> pdb=" O MET G 570 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL G 572 " --> pdb=" O GLU G 595 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP G 618 " --> pdb=" O LEU G 594 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 642 " --> pdb=" O ARG G 664 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU G 688 " --> pdb=" O SER G 712 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE G 711 " --> pdb=" O LYS G 735 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU G 757 " --> pdb=" O VAL G 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 457 through 459 removed outlier: 6.255A pdb=" N VAL G 457 " --> pdb=" O LYS G 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 1779 hydrogen bonds defined for protein. 4461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.92 Time building geometry restraints manager: 12.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12243 1.34 - 1.46: 9119 1.46 - 1.58: 18580 1.58 - 1.70: 0 1.70 - 1.81: 392 Bond restraints: 40334 Sorted by residual: bond pdb=" CA ILE G 443 " pdb=" CB ILE G 443 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.02e+00 bond pdb=" CA ILE E 443 " pdb=" CB ILE E 443 " ideal model delta sigma weight residual 1.540 1.527 0.014 1.36e-02 5.41e+03 9.89e-01 bond pdb=" CA ILE C 443 " pdb=" CB ILE C 443 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.83e-01 bond pdb=" CA ILE B 443 " pdb=" CB ILE B 443 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.73e-01 bond pdb=" N PRO D 699 " pdb=" CA PRO D 699 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 7.55e-01 ... (remaining 40329 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.62: 1010 106.62 - 113.46: 22546 113.46 - 120.30: 14585 120.30 - 127.15: 15976 127.15 - 133.99: 406 Bond angle restraints: 54523 Sorted by residual: angle pdb=" N TYR G 343 " pdb=" CA TYR G 343 " pdb=" C TYR G 343 " ideal model delta sigma weight residual 114.62 109.88 4.74 1.14e+00 7.69e-01 1.73e+01 angle pdb=" N TYR F 343 " pdb=" CA TYR F 343 " pdb=" C TYR F 343 " ideal model delta sigma weight residual 114.62 109.93 4.69 1.14e+00 7.69e-01 1.70e+01 angle pdb=" N TYR C 343 " pdb=" CA TYR C 343 " pdb=" C TYR C 343 " ideal model delta sigma weight residual 114.75 109.90 4.85 1.26e+00 6.30e-01 1.48e+01 angle pdb=" N TYR D 343 " pdb=" CA TYR D 343 " pdb=" C TYR D 343 " ideal model delta sigma weight residual 114.75 110.14 4.61 1.26e+00 6.30e-01 1.34e+01 angle pdb=" N TYR E 343 " pdb=" CA TYR E 343 " pdb=" C TYR E 343 " ideal model delta sigma weight residual 114.75 110.43 4.32 1.26e+00 6.30e-01 1.18e+01 ... (remaining 54518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.84: 22463 13.84 - 27.67: 1480 27.67 - 41.51: 420 41.51 - 55.34: 82 55.34 - 69.18: 27 Dihedral angle restraints: 24472 sinusoidal: 10038 harmonic: 14434 Sorted by residual: dihedral pdb=" CA MET C 312 " pdb=" C MET C 312 " pdb=" N ALA C 313 " pdb=" CA ALA C 313 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET D 312 " pdb=" C MET D 312 " pdb=" N ALA D 313 " pdb=" CA ALA D 313 " ideal model delta harmonic sigma weight residual 180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA HIS D 310 " pdb=" C HIS D 310 " pdb=" N THR D 311 " pdb=" CA THR D 311 " ideal model delta harmonic sigma weight residual 180.00 -162.15 -17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 24469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3659 0.027 - 0.054: 1763 0.054 - 0.080: 515 0.080 - 0.107: 266 0.107 - 0.134: 69 Chirality restraints: 6272 Sorted by residual: chirality pdb=" CA TYR E 279 " pdb=" N TYR E 279 " pdb=" C TYR E 279 " pdb=" CB TYR E 279 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA TYR D 279 " pdb=" N TYR D 279 " pdb=" C TYR D 279 " pdb=" CB TYR D 279 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA TYR G 279 " pdb=" N TYR G 279 " pdb=" C TYR G 279 " pdb=" CB TYR G 279 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 6269 not shown) Planarity restraints: 6727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 321 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C PHE D 321 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE D 321 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS D 322 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 321 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C PHE C 321 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE C 321 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS C 322 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 321 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C PHE F 321 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE F 321 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS F 322 " -0.009 2.00e-02 2.50e+03 ... (remaining 6724 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 911 2.70 - 3.25: 41072 3.25 - 3.80: 66013 3.80 - 4.35: 85278 4.35 - 4.90: 137579 Nonbonded interactions: 330853 Sorted by model distance: nonbonded pdb=" O ARG G 637 " pdb=" OG SER G 661 " model vdw 2.149 2.440 nonbonded pdb=" O ARG F 637 " pdb=" OG SER F 661 " model vdw 2.153 2.440 nonbonded pdb=" O ARG C 637 " pdb=" OG SER C 661 " model vdw 2.153 2.440 nonbonded pdb=" O ARG A 637 " pdb=" OG SER A 661 " model vdw 2.169 2.440 nonbonded pdb=" OD2 ASP A 104 " pdb=" OH TYR B 108 " model vdw 2.176 2.440 ... (remaining 330848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.030 Extract box with map and model: 8.560 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 76.160 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.002 0.026 40334 Z= 0.139 Angle : 0.495 7.096 54523 Z= 0.277 Chirality : 0.037 0.134 6272 Planarity : 0.004 0.029 6727 Dihedral : 10.449 69.175 15008 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.74 % Rotamer: Outliers : 4.31 % Allowed : 7.54 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4788 helix: 0.31 (0.12), residues: 2268 sheet: -1.19 (0.20), residues: 700 loop : -0.37 (0.15), residues: 1820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 4 residues processed: 119 average time/residue: 0.1428 time to fit residues: 22.1174 Evaluate side-chains 58 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0490 time to fit residues: 1.0214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 5.9990 chunk 366 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 246 optimal weight: 0.0020 chunk 195 optimal weight: 6.9990 chunk 378 optimal weight: 0.0030 chunk 146 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 281 optimal weight: 0.5980 chunk 438 optimal weight: 5.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 375 HIS B 482 HIS B 573 HIS B 635 HIS ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40334 Z= 0.207 Angle : 0.629 8.590 54523 Z= 0.323 Chirality : 0.043 0.259 6272 Planarity : 0.004 0.028 6727 Dihedral : 4.437 23.017 5173 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: -0.31 (0.13), residues: 4788 helix: 0.48 (0.12), residues: 2338 sheet: -1.23 (0.19), residues: 714 loop : -0.49 (0.15), residues: 1736 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1364 time to fit residues: 14.1059 Evaluate side-chains 54 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 4.9990 chunk 136 optimal weight: 0.0270 chunk 365 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 439 optimal weight: 8.9990 chunk 474 optimal weight: 6.9990 chunk 391 optimal weight: 6.9990 chunk 435 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 352 optimal weight: 0.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40334 Z= 0.218 Angle : 0.624 7.883 54523 Z= 0.319 Chirality : 0.041 0.181 6272 Planarity : 0.004 0.030 6727 Dihedral : 4.545 23.927 5173 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.16 % Allowed : 1.88 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4788 helix: 0.19 (0.11), residues: 2394 sheet: -1.20 (0.20), residues: 700 loop : -0.83 (0.15), residues: 1694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.1298 time to fit residues: 11.5129 Evaluate side-chains 48 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 0.0060 chunk 330 optimal weight: 0.5980 chunk 228 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 440 optimal weight: 5.9990 chunk 466 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 417 optimal weight: 0.8980 chunk 125 optimal weight: 0.0050 overall best weight: 0.7012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40334 Z= 0.161 Angle : 0.595 7.119 54523 Z= 0.303 Chirality : 0.041 0.219 6272 Planarity : 0.003 0.029 6727 Dihedral : 4.464 24.353 5173 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 4788 helix: 0.42 (0.11), residues: 2275 sheet: -1.15 (0.20), residues: 700 loop : -0.77 (0.14), residues: 1813 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1255 time to fit residues: 10.9776 Evaluate side-chains 47 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 7.9990 chunk 265 optimal weight: 0.0060 chunk 6 optimal weight: 3.9990 chunk 347 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 398 optimal weight: 7.9990 chunk 322 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 419 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 739 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40334 Z= 0.254 Angle : 0.647 8.618 54523 Z= 0.329 Chirality : 0.043 0.395 6272 Planarity : 0.004 0.035 6727 Dihedral : 4.808 23.672 5173 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 4788 helix: 0.15 (0.11), residues: 2296 sheet: -1.49 (0.21), residues: 658 loop : -0.84 (0.14), residues: 1834 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1315 time to fit residues: 10.0655 Evaluate side-chains 43 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 2.9990 chunk 420 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 467 optimal weight: 4.9990 chunk 387 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 154 optimal weight: 0.8980 chunk 245 optimal weight: 0.0370 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40334 Z= 0.166 Angle : 0.591 8.180 54523 Z= 0.298 Chirality : 0.043 0.299 6272 Planarity : 0.003 0.031 6727 Dihedral : 4.605 24.869 5173 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.12), residues: 4788 helix: 0.24 (0.11), residues: 2289 sheet: -1.62 (0.20), residues: 672 loop : -0.85 (0.14), residues: 1827 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1337 time to fit residues: 10.5431 Evaluate side-chains 40 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 266 optimal weight: 0.3980 chunk 341 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 chunk 393 optimal weight: 0.0170 chunk 260 optimal weight: 3.9990 chunk 465 optimal weight: 0.5980 chunk 291 optimal weight: 6.9990 chunk 283 optimal weight: 0.0000 chunk 214 optimal weight: 0.9990 overall best weight: 0.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 40334 Z= 0.150 Angle : 0.590 8.483 54523 Z= 0.297 Chirality : 0.042 0.223 6272 Planarity : 0.003 0.033 6727 Dihedral : 4.379 24.537 5173 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -0.69 (0.12), residues: 4788 helix: 0.35 (0.11), residues: 2247 sheet: -1.60 (0.20), residues: 672 loop : -0.85 (0.14), residues: 1869 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1441 time to fit residues: 11.3010 Evaluate side-chains 42 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 9.9990 chunk 185 optimal weight: 0.5980 chunk 278 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 295 optimal weight: 1.9990 chunk 317 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 365 optimal weight: 0.0270 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40334 Z= 0.182 Angle : 0.606 9.389 54523 Z= 0.307 Chirality : 0.043 0.369 6272 Planarity : 0.004 0.035 6727 Dihedral : 4.449 22.697 5173 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -0.84 (0.12), residues: 4788 helix: 0.17 (0.11), residues: 2247 sheet: -1.63 (0.21), residues: 672 loop : -0.86 (0.14), residues: 1869 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1327 time to fit residues: 10.1972 Evaluate side-chains 45 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 0.9980 chunk 445 optimal weight: 8.9990 chunk 406 optimal weight: 3.9990 chunk 433 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 188 optimal weight: 0.0010 chunk 340 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 392 optimal weight: 0.9980 chunk 410 optimal weight: 10.0000 chunk 432 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40334 Z= 0.196 Angle : 0.626 10.089 54523 Z= 0.319 Chirality : 0.043 0.274 6272 Planarity : 0.004 0.036 6727 Dihedral : 4.545 22.655 5173 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4788 helix: 0.04 (0.11), residues: 2254 sheet: -1.60 (0.21), residues: 672 loop : -0.82 (0.14), residues: 1862 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1332 time to fit residues: 10.2262 Evaluate side-chains 42 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 2.9990 chunk 458 optimal weight: 0.9980 chunk 279 optimal weight: 0.4980 chunk 217 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 481 optimal weight: 4.9990 chunk 442 optimal weight: 0.0870 chunk 383 optimal weight: 0.0070 chunk 39 optimal weight: 6.9990 chunk 295 optimal weight: 0.0000 chunk 234 optimal weight: 3.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 HIS B 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40334 Z= 0.168 Angle : 0.657 17.443 54523 Z= 0.322 Chirality : 0.043 0.220 6272 Planarity : 0.003 0.033 6727 Dihedral : 4.557 23.053 5173 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.12), residues: 4788 helix: 0.06 (0.11), residues: 2254 sheet: -1.58 (0.21), residues: 672 loop : -0.79 (0.14), residues: 1862 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.497 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1213 time to fit residues: 9.7528 Evaluate side-chains 41 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 4.9990 chunk 408 optimal weight: 0.0010 chunk 117 optimal weight: 5.9990 chunk 353 optimal weight: 4.9990 chunk 56 optimal weight: 0.0050 chunk 106 optimal weight: 0.1980 chunk 383 optimal weight: 0.0170 chunk 160 optimal weight: 6.9990 chunk 394 optimal weight: 0.0870 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.0616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.086024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.073496 restraints weight = 55447.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.073814 restraints weight = 28796.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.073707 restraints weight = 23176.496| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 40334 Z= 0.158 Angle : 0.611 9.517 54523 Z= 0.309 Chirality : 0.043 0.188 6272 Planarity : 0.003 0.029 6727 Dihedral : 4.390 22.926 5173 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 4788 helix: 0.03 (0.11), residues: 2240 sheet: -1.47 (0.20), residues: 707 loop : -0.63 (0.15), residues: 1841 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2947.53 seconds wall clock time: 55 minutes 56.25 seconds (3356.25 seconds total)