Starting phenix.real_space_refine on Sat Aug 8 05:16:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xiq_66912/08_2026/9xiq_66912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xiq_66912/08_2026/9xiq_66912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xiq_66912/08_2026/9xiq_66912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xiq_66912/08_2026/9xiq_66912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xiq_66912/08_2026/9xiq_66912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xiq_66912/08_2026/9xiq_66912.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 90 5.16 5 C 16128 2.51 5 N 4542 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25446 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4210 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 4195 Chain: "B" Number of atoms: 4210 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 4195 Chain: "C" Number of atoms: 4210 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 4195 Chain: "D" Number of atoms: 4210 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 4195 Chain: "E" Number of atoms: 4210 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 4195 Chain: "F" Number of atoms: 4210 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 516, 4162 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 4195 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.91, per 1000 atoms: 0.39 Number of scatterers: 25446 At special positions: 0 Unit cell: (168.1, 161.54, 89.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 18 15.00 O 4668 8.00 N 4542 7.00 C 16128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 199 " distance=2.01 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 199 " distance=2.05 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 196 " distance=2.05 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 199 " distance=2.01 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 199 " distance=2.05 Simple disulfide: pdb=" SG CYS C 156 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 156 " - pdb=" SG CYS C 199 " distance=2.01 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 199 " distance=2.05 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 199 " distance=2.01 Simple disulfide: pdb=" SG CYS D 196 " - pdb=" SG CYS D 199 " distance=2.05 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 199 " distance=2.01 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 199 " distance=2.05 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 196 " distance=2.05 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 199 " distance=2.01 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 199 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.05 Conformation dependent library (CDL) restraints added in 1.8 seconds 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 30 sheets defined 59.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 1 through 3 No H-bonds generated for 'chain 'A' and resid 1 through 3' Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.646A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 41 through 53 removed outlier: 3.825A pdb=" N HIS A 53 " --> pdb=" O MET A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 86 through 101 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 119 through 136 removed outlier: 3.563A pdb=" N ARG A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.999A pdb=" N LEU A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 296 removed outlier: 3.594A pdb=" N LEU A 296 " --> pdb=" O ILE A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.507A pdb=" N LYS A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 362 through 374 removed outlier: 4.307A pdb=" N ARG A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.599A pdb=" N GLU A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 removed outlier: 3.600A pdb=" N ILE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 481 removed outlier: 3.635A pdb=" N VAL A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 473 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 515 removed outlier: 3.603A pdb=" N ARG A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 3 No H-bonds generated for 'chain 'B' and resid 1 through 3' Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.602A pdb=" N GLU B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 41 through 53 removed outlier: 3.829A pdb=" N HIS B 53 " --> pdb=" O MET B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 119 through 136 removed outlier: 3.561A pdb=" N ARG B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 249 through 254 removed outlier: 4.017A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 293 through 296 removed outlier: 3.603A pdb=" N LEU B 296 " --> pdb=" O ILE B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.504A pdb=" N LYS B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 362 through 374 removed outlier: 4.343A pdb=" N ARG B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 397 Processing helix chain 'B' and resid 408 through 418 Processing helix chain 'B' and resid 425 through 436 removed outlier: 4.587A pdb=" N GLU B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 434 " --> pdb=" O ARG B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 460 removed outlier: 3.605A pdb=" N ILE B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 479 removed outlier: 3.645A pdb=" N VAL B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 473 " --> pdb=" O MET B 469 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS B 479 " --> pdb=" O GLU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 515 removed outlier: 3.579A pdb=" N ARG B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 3 No H-bonds generated for 'chain 'C' and resid 1 through 3' Processing helix chain 'C' and resid 4 through 11 Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.596A pdb=" N GLU C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 41 through 53 removed outlier: 3.842A pdb=" N HIS C 53 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 119 through 136 removed outlier: 3.548A pdb=" N ARG C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 167 through 182 removed outlier: 3.523A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 210 Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'C' and resid 249 through 254 removed outlier: 4.041A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 296 removed outlier: 3.643A pdb=" N LEU C 296 " --> pdb=" O ILE C 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 293 through 296' Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 333 through 340 removed outlier: 3.603A pdb=" N LEU C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 362 through 374 removed outlier: 4.357A pdb=" N ARG C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 397 Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'C' and resid 425 through 436 removed outlier: 4.585A pdb=" N GLU C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 434 " --> pdb=" O ARG C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 460 removed outlier: 3.618A pdb=" N ILE C 449 " --> pdb=" O SER C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 481 removed outlier: 3.711A pdb=" N VAL C 470 " --> pdb=" O ASN C 466 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS C 479 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS C 480 " --> pdb=" O GLU C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 515 removed outlier: 3.572A pdb=" N ARG C 490 " --> pdb=" O ASP C 486 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 3 No H-bonds generated for 'chain 'D' and resid 1 through 3' Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.646A pdb=" N GLU D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.825A pdb=" N HIS D 53 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 119 through 136 removed outlier: 3.564A pdb=" N ARG D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'D' and resid 167 through 182 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 249 through 254 removed outlier: 3.998A pdb=" N LEU D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 266 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 296 removed outlier: 3.595A pdb=" N LEU D 296 " --> pdb=" O ILE D 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 293 through 296' Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 333 through 340 removed outlier: 3.505A pdb=" N LYS D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 351 Processing helix chain 'D' and resid 362 through 374 removed outlier: 4.293A pdb=" N ARG D 368 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR D 370 " --> pdb=" O GLU D 366 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 373 " --> pdb=" O ILE D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'D' and resid 425 through 436 removed outlier: 4.600A pdb=" N GLU D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET D 433 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY D 434 " --> pdb=" O ARG D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 460 removed outlier: 3.598A pdb=" N ILE D 449 " --> pdb=" O SER D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 481 removed outlier: 3.635A pdb=" N VAL D 470 " --> pdb=" O ASN D 466 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 473 " --> pdb=" O MET D 469 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS D 480 " --> pdb=" O GLU D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 515 removed outlier: 3.604A pdb=" N ARG D 490 " --> pdb=" O ASP D 486 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN D 498 " --> pdb=" O ARG D 494 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 3 No H-bonds generated for 'chain 'E' and resid 1 through 3' Processing helix chain 'E' and resid 4 through 11 Processing helix chain 'E' and resid 12 through 20 Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.602A pdb=" N GLU E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 Processing helix chain 'E' and resid 41 through 53 removed outlier: 3.830A pdb=" N HIS E 53 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 119 through 136 removed outlier: 3.566A pdb=" N ARG E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 167 through 182 Processing helix chain 'E' and resid 196 through 210 Processing helix chain 'E' and resid 213 through 221 Processing helix chain 'E' and resid 249 through 254 removed outlier: 4.017A pdb=" N LEU E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 266 Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 293 through 296 removed outlier: 3.600A pdb=" N LEU E 296 " --> pdb=" O ILE E 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 293 through 296' Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 333 through 340 removed outlier: 3.637A pdb=" N LEU E 339 " --> pdb=" O GLU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 351 Processing helix chain 'E' and resid 362 through 374 removed outlier: 4.362A pdb=" N ARG E 368 " --> pdb=" O SER E 364 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE E 369 " --> pdb=" O ASP E 365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP E 373 " --> pdb=" O ILE E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 397 Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'E' and resid 425 through 436 removed outlier: 4.598A pdb=" N GLU E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY E 434 " --> pdb=" O ARG E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 460 removed outlier: 3.605A pdb=" N ILE E 449 " --> pdb=" O SER E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 479 removed outlier: 3.646A pdb=" N VAL E 470 " --> pdb=" O ASN E 466 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU E 473 " --> pdb=" O MET E 469 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS E 479 " --> pdb=" O GLU E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 515 removed outlier: 3.578A pdb=" N ARG E 490 " --> pdb=" O ASP E 486 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN E 498 " --> pdb=" O ARG E 494 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN E 510 " --> pdb=" O GLU E 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 3 No H-bonds generated for 'chain 'F' and resid 1 through 3' Processing helix chain 'F' and resid 4 through 11 Processing helix chain 'F' and resid 12 through 20 Processing helix chain 'F' and resid 25 through 35 removed outlier: 3.596A pdb=" N GLU F 34 " --> pdb=" O ARG F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 41 through 53 removed outlier: 3.842A pdb=" N HIS F 53 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 73 Processing helix chain 'F' and resid 86 through 101 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 119 through 136 removed outlier: 3.548A pdb=" N ARG F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 166 Processing helix chain 'F' and resid 167 through 182 removed outlier: 3.523A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 210 Processing helix chain 'F' and resid 213 through 221 Processing helix chain 'F' and resid 249 through 254 removed outlier: 4.039A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 278 through 283 Processing helix chain 'F' and resid 293 through 296 removed outlier: 3.642A pdb=" N LEU F 296 " --> pdb=" O ILE F 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 293 through 296' Processing helix chain 'F' and resid 298 through 311 Processing helix chain 'F' and resid 333 through 340 removed outlier: 3.605A pdb=" N LEU F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 351 Processing helix chain 'F' and resid 362 through 374 removed outlier: 4.324A pdb=" N ARG F 368 " --> pdb=" O SER F 364 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE F 369 " --> pdb=" O ASP F 365 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR F 370 " --> pdb=" O GLU F 366 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP F 373 " --> pdb=" O ILE F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 397 Processing helix chain 'F' and resid 408 through 418 Processing helix chain 'F' and resid 425 through 436 removed outlier: 4.589A pdb=" N GLU F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU F 432 " --> pdb=" O ALA F 428 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY F 434 " --> pdb=" O ARG F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 460 removed outlier: 3.618A pdb=" N ILE F 449 " --> pdb=" O SER F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 481 removed outlier: 3.684A pdb=" N VAL F 470 " --> pdb=" O ASN F 466 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS F 479 " --> pdb=" O GLU F 475 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS F 480 " --> pdb=" O GLU F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 515 removed outlier: 3.581A pdb=" N ARG F 490 " --> pdb=" O ASP F 486 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN F 498 " --> pdb=" O ARG F 494 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 removed outlier: 4.122A pdb=" N LEU A 142 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 removed outlier: 6.304A pdb=" N ILE A 109 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 355 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 111 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 314 Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 382 removed outlier: 7.075A pdb=" N HIS A 381 " --> pdb=" O ILE A 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 24 removed outlier: 4.133A pdb=" N LEU B 142 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 59 Processing sheet with id=AA8, first strand: chain 'B' and resid 237 through 240 removed outlier: 6.297A pdb=" N ILE B 109 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B 355 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 111 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AB1, first strand: chain 'B' and resid 381 through 382 removed outlier: 7.124A pdb=" N HIS B 381 " --> pdb=" O ILE B 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 24 removed outlier: 4.160A pdb=" N LEU C 142 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 59 Processing sheet with id=AB4, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=AB5, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AB6, first strand: chain 'C' and resid 381 through 382 removed outlier: 7.142A pdb=" N HIS C 381 " --> pdb=" O ILE C 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 22 through 24 removed outlier: 4.122A pdb=" N LEU D 142 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 55 through 59 Processing sheet with id=AB9, first strand: chain 'D' and resid 237 through 240 removed outlier: 6.305A pdb=" N ILE D 109 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE D 355 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU D 111 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 312 through 314 Processing sheet with id=AC2, first strand: chain 'D' and resid 381 through 382 removed outlier: 7.077A pdb=" N HIS D 381 " --> pdb=" O ILE D 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 22 through 24 removed outlier: 4.133A pdb=" N LEU E 142 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 55 through 59 Processing sheet with id=AC5, first strand: chain 'E' and resid 237 through 240 removed outlier: 6.289A pdb=" N ILE E 109 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE E 355 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU E 111 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 312 through 314 Processing sheet with id=AC7, first strand: chain 'E' and resid 381 through 382 removed outlier: 7.124A pdb=" N HIS E 381 " --> pdb=" O ILE E 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 22 through 24 removed outlier: 4.161A pdb=" N LEU F 142 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 55 through 59 Processing sheet with id=AD1, first strand: chain 'F' and resid 237 through 240 Processing sheet with id=AD2, first strand: chain 'F' and resid 312 through 314 Processing sheet with id=AD3, first strand: chain 'F' and resid 381 through 382 removed outlier: 7.149A pdb=" N HIS F 381 " --> pdb=" O ILE F 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 1241 hydrogen bonds defined for protein. 3468 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: 5.35 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 8664 1.36 - 1.49: 6073 1.49 - 1.62: 11111 1.62 - 1.75: 12 1.75 - 1.88: 156 Bond restraints: 26016 Sorted by residual: bond pdb=" N3B ANP C 701 " pdb=" PG ANP C 701 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.82e+01 bond pdb=" N3B ANP D 701 " pdb=" PG ANP D 701 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N3B ANP F 701 " pdb=" PG ANP F 701 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" N3B ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" N3B ANP B 701 " pdb=" PG ANP B 701 " ideal model delta sigma weight residual 1.795 1.632 0.163 2.00e-02 2.50e+03 6.64e+01 ... (remaining 26011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 35000 3.54 - 7.08: 164 7.08 - 10.62: 32 10.62 - 14.16: 0 14.16 - 17.70: 6 Bond angle restraints: 35202 Sorted by residual: angle pdb=" CA CYS D 196 " pdb=" CB CYS D 196 " pdb=" SG CYS D 196 " ideal model delta sigma weight residual 114.40 132.10 -17.70 2.30e+00 1.89e-01 5.92e+01 angle pdb=" CA CYS A 196 " pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " ideal model delta sigma weight residual 114.40 132.04 -17.64 2.30e+00 1.89e-01 5.88e+01 angle pdb=" CA CYS E 196 " pdb=" CB CYS E 196 " pdb=" SG CYS E 196 " ideal model delta sigma weight residual 114.40 131.95 -17.55 2.30e+00 1.89e-01 5.82e+01 angle pdb=" CA CYS B 196 " pdb=" CB CYS B 196 " pdb=" SG CYS B 196 " ideal model delta sigma weight residual 114.40 131.92 -17.52 2.30e+00 1.89e-01 5.80e+01 angle pdb=" CA CYS F 196 " pdb=" CB CYS F 196 " pdb=" SG CYS F 196 " ideal model delta sigma weight residual 114.40 131.80 -17.40 2.30e+00 1.89e-01 5.73e+01 ... (remaining 35197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.33: 14655 29.33 - 58.65: 1390 58.65 - 87.98: 141 87.98 - 117.31: 20 117.31 - 146.63: 6 Dihedral angle restraints: 16212 sinusoidal: 7032 harmonic: 9180 Sorted by residual: dihedral pdb=" CB CYS F 196 " pdb=" SG CYS F 196 " pdb=" SG CYS F 199 " pdb=" CB CYS F 199 " ideal model delta sinusoidal sigma weight residual 93.00 25.20 67.80 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CB CYS C 196 " pdb=" SG CYS C 196 " pdb=" SG CYS C 199 " pdb=" CB CYS C 199 " ideal model delta sinusoidal sigma weight residual 93.00 25.27 67.73 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " pdb=" SG CYS A 199 " pdb=" CB CYS A 199 " ideal model delta sinusoidal sigma weight residual 93.00 25.28 67.72 1 1.00e+01 1.00e-02 5.96e+01 ... (remaining 16209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3508 0.083 - 0.166: 284 0.166 - 0.249: 6 0.249 - 0.333: 0 0.333 - 0.416: 6 Chirality restraints: 3804 Sorted by residual: chirality pdb=" C3' ANP D 701 " pdb=" C2' ANP D 701 " pdb=" C4' ANP D 701 " pdb=" O3' ANP D 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.77 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" C3' ANP B 701 " pdb=" C2' ANP B 701 " pdb=" C4' ANP B 701 " pdb=" O3' ANP B 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.77 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C3' ANP F 701 " pdb=" C2' ANP F 701 " pdb=" C4' ANP F 701 " pdb=" O3' ANP F 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.77 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 3801 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 104 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO F 105 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 105 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 105 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 104 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 105 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 105 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 105 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 104 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO E 105 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 105 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 105 " 0.030 5.00e-02 4.00e+02 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2934 2.75 - 3.29: 24942 3.29 - 3.82: 43523 3.82 - 4.36: 53574 4.36 - 4.90: 89443 Nonbonded interactions: 214416 Sorted by model distance: nonbonded pdb=" NH2BARG E 200 " pdb=" OD1 ASP F 233 " model vdw 2.209 3.120 nonbonded pdb=" NH2BARG B 200 " pdb=" OD1 ASP C 233 " model vdw 2.212 3.120 nonbonded pdb=" NH2BARG C 200 " pdb=" OD1 ASP D 233 " model vdw 2.215 3.120 nonbonded pdb=" OD1 ASP A 233 " pdb=" NH2BARG F 200 " model vdw 2.215 3.120 nonbonded pdb=" NH2BARG D 200 " pdb=" OD1 ASP E 233 " model vdw 2.220 3.120 ... (remaining 214411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 135 or resid 137 through 199 or resid 201 throug \ h 350 or resid 352 through 377 or resid 379 through 446 or resid 448 through 491 \ or resid 493 through 701)) selection = (chain 'B' and (resid 0 through 135 or resid 137 through 199 or resid 201 throug \ h 350 or resid 352 through 377 or resid 379 through 446 or resid 448 through 491 \ or resid 493 through 701)) selection = (chain 'C' and (resid 0 through 135 or resid 137 through 199 or resid 201 throug \ h 350 or resid 352 through 377 or resid 379 through 446 or resid 448 through 491 \ or resid 493 through 701)) selection = (chain 'D' and (resid 0 through 135 or resid 137 through 199 or resid 201 throug \ h 350 or resid 352 through 377 or resid 379 through 446 or resid 448 through 491 \ or resid 493 through 701)) selection = (chain 'E' and (resid 0 through 135 or resid 137 through 199 or resid 201 throug \ h 350 or resid 352 through 377 or resid 379 through 446 or resid 448 through 491 \ or resid 493 through 701)) selection = (chain 'F' and (resid 0 through 135 or resid 137 through 199 or resid 201 throug \ h 350 or resid 352 through 377 or resid 379 through 446 or resid 448 through 491 \ or resid 493 through 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 29.570 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 26034 Z= 0.221 Angle : 0.737 17.699 35238 Z= 0.352 Chirality : 0.045 0.416 3804 Planarity : 0.005 0.054 4578 Dihedral : 20.875 146.634 10254 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.30 % Allowed : 34.87 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3120 helix: -0.00 (0.13), residues: 1548 sheet: 0.54 (0.29), residues: 336 loop : -1.02 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 69 TYR 0.014 0.001 TYR A 344 PHE 0.016 0.001 PHE E 300 TRP 0.004 0.001 TRP E 21 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (26016) covalent geometry : angle 0.68831 / 0.33 (35202) SS BOND : bond 0.01890 / 1.18 ( 18) SS BOND : angle 8.30946 / 5.10 ( 36) hydrogen bonds : bond 0.26345 / 17.49 ( 1241) hydrogen bonds : angle 8.28836 / 5.85 ( 3468) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 1.051 Fit side-chains REVERT: C 352 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8449 (m) REVERT: C 471 MET cc_start: 0.8439 (mpp) cc_final: 0.7784 (mtt) REVERT: E 320 GLN cc_start: 0.6771 (mt0) cc_final: 0.6564 (pt0) REVERT: F 352 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8461 (m) outliers start: 52 outliers final: 48 residues processed: 340 average time/residue: 0.6551 time to fit residues: 258.8348 Evaluate side-chains 326 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 276 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 399 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.0870 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 202 GLN A 472 ASN B 202 GLN B 309 GLN B 320 GLN B 332 ASN B 472 ASN C 320 GLN C 472 ASN D 113 HIS D 202 GLN D 472 ASN E 309 GLN E 472 ASN F 320 GLN F 472 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104272 restraints weight = 114034.583| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.98 r_work: 0.2993 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26034 Z= 0.150 Angle : 0.747 20.374 35238 Z= 0.368 Chirality : 0.043 0.231 3804 Planarity : 0.005 0.052 4578 Dihedral : 12.594 127.262 3824 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.28 % Allowed : 33.52 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3120 helix: 0.67 (0.13), residues: 1584 sheet: 0.38 (0.29), residues: 330 loop : -0.76 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 69 TYR 0.012 0.001 TYR D 259 PHE 0.015 0.001 PHE B 300 TRP 0.003 0.001 TRP D 21 HIS 0.006 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (26016) covalent geometry : angle 0.67070 / 0.33 (35202) SS BOND : bond 0.02508 / 1.61 ( 18) SS BOND : angle 10.28067 / 6.26 ( 36) hydrogen bonds : bond 0.04302 / 2.85 ( 1241) hydrogen bonds : angle 5.45842 / 3.84 ( 3468) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 340 time to evaluate : 1.023 Fit side-chains REVERT: A 309 GLN cc_start: 0.7952 (tt0) cc_final: 0.7741 (tt0) REVERT: A 476 GLU cc_start: 0.7693 (tp30) cc_final: 0.7401 (tp30) REVERT: B 471 MET cc_start: 0.8281 (mpp) cc_final: 0.7689 (mtt) REVERT: B 472 ASN cc_start: 0.8019 (m-40) cc_final: 0.7597 (t0) REVERT: B 476 GLU cc_start: 0.7697 (tp30) cc_final: 0.7486 (tp30) REVERT: B 503 GLU cc_start: 0.7671 (tp30) cc_final: 0.7280 (tt0) REVERT: B 510 ASN cc_start: 0.7112 (m110) cc_final: 0.6622 (t0) REVERT: C 289 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7759 (tm-30) REVERT: C 471 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7370 (mtt) REVERT: C 476 GLU cc_start: 0.7602 (tp30) cc_final: 0.7362 (tp30) REVERT: C 503 GLU cc_start: 0.7747 (tp30) cc_final: 0.7443 (tp30) REVERT: D 309 GLN cc_start: 0.7936 (tt0) cc_final: 0.7715 (tt0) REVERT: D 476 GLU cc_start: 0.7693 (tp30) cc_final: 0.7407 (tp30) REVERT: E 471 MET cc_start: 0.8279 (mpp) cc_final: 0.7690 (mtt) REVERT: E 476 GLU cc_start: 0.7687 (tp30) cc_final: 0.7453 (tp30) REVERT: E 503 GLU cc_start: 0.7667 (tp30) cc_final: 0.7286 (tt0) REVERT: F 289 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7721 (tm-30) REVERT: F 472 ASN cc_start: 0.7967 (m-40) cc_final: 0.7732 (m-40) REVERT: F 476 GLU cc_start: 0.7621 (tp30) cc_final: 0.7374 (tp30) REVERT: F 510 ASN cc_start: 0.6998 (m110) cc_final: 0.6656 (t0) outliers start: 78 outliers final: 41 residues processed: 407 average time/residue: 0.6658 time to fit residues: 313.7080 Evaluate side-chains 326 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 409 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 0.0170 chunk 216 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 171 optimal weight: 0.0170 chunk 136 optimal weight: 7.9990 chunk 283 optimal weight: 0.9980 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN B 113 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN C 472 ASN D 113 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN E 113 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 GLN E 332 ASN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN F 510 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101923 restraints weight = 115145.823| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.95 r_work: 0.2959 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26034 Z= 0.175 Angle : 0.758 20.233 35238 Z= 0.376 Chirality : 0.044 0.205 3804 Planarity : 0.005 0.051 4578 Dihedral : 11.726 117.898 3790 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.69 % Allowed : 34.35 % Favored : 60.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3120 helix: 0.77 (0.13), residues: 1584 sheet: 0.06 (0.29), residues: 330 loop : -0.93 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 349 TYR 0.017 0.002 TYR D 344 PHE 0.009 0.001 PHE E 318 TRP 0.004 0.001 TRP F 21 HIS 0.011 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 (26016) covalent geometry : angle 0.68256 / 0.34 (35202) SS BOND : bond 0.02538 / 1.62 ( 18) SS BOND : angle 10.35202 / 6.30 ( 36) hydrogen bonds : bond 0.04130 / 2.74 ( 1241) hydrogen bonds : angle 5.24523 / 3.69 ( 3468) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 323 time to evaluate : 0.905 Fit side-chains REVERT: A 179 ARG cc_start: 0.7842 (ttm110) cc_final: 0.7440 (mtm-85) REVERT: A 303 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: A 476 GLU cc_start: 0.7826 (tp30) cc_final: 0.7417 (tp30) REVERT: B 399 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7016 (mt) REVERT: B 471 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7858 (mtt) REVERT: B 472 ASN cc_start: 0.8045 (m-40) cc_final: 0.7591 (t0) REVERT: B 476 GLU cc_start: 0.7702 (tp30) cc_final: 0.7399 (tp30) REVERT: B 498 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7267 (mm-40) REVERT: B 503 GLU cc_start: 0.7739 (tp30) cc_final: 0.7516 (tp30) REVERT: C 30 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7874 (mtm110) REVERT: C 113 HIS cc_start: 0.7482 (p-80) cc_final: 0.7216 (t-90) REVERT: C 303 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: C 471 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7303 (mtt) REVERT: C 476 GLU cc_start: 0.7613 (tp30) cc_final: 0.7292 (tp30) REVERT: C 503 GLU cc_start: 0.7742 (tp30) cc_final: 0.7288 (tp30) REVERT: D 179 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7435 (mtm-85) REVERT: D 303 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6882 (m-30) REVERT: D 476 GLU cc_start: 0.7832 (tp30) cc_final: 0.7420 (tp30) REVERT: E 314 LYS cc_start: 0.7125 (tppt) cc_final: 0.6696 (mptp) REVERT: E 399 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7004 (mt) REVERT: E 471 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7861 (mtt) REVERT: E 472 ASN cc_start: 0.8056 (m-40) cc_final: 0.7599 (t0) REVERT: E 476 GLU cc_start: 0.7723 (tp30) cc_final: 0.7397 (tp30) REVERT: F 30 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7891 (mtm110) REVERT: F 113 HIS cc_start: 0.7539 (p-80) cc_final: 0.7256 (t-90) REVERT: F 303 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: F 476 GLU cc_start: 0.7669 (tp30) cc_final: 0.7273 (tp30) REVERT: F 510 ASN cc_start: 0.6839 (m-40) cc_final: 0.6624 (t0) outliers start: 89 outliers final: 41 residues processed: 390 average time/residue: 0.6793 time to fit residues: 304.2580 Evaluate side-chains 339 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 303 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 409 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 71 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 293 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 HIS B 332 ASN C 113 HIS ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN D 113 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN F 113 HIS ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.101732 restraints weight = 116174.681| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.99 r_work: 0.2928 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 26034 Z= 0.197 Angle : 0.781 20.253 35238 Z= 0.387 Chirality : 0.045 0.211 3804 Planarity : 0.005 0.050 4578 Dihedral : 10.735 102.084 3779 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.03 % Allowed : 33.22 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 3120 helix: 0.80 (0.13), residues: 1572 sheet: -0.10 (0.29), residues: 330 loop : -0.96 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 372 TYR 0.015 0.002 TYR A 344 PHE 0.028 0.002 PHE B 300 TRP 0.004 0.001 TRP F 21 HIS 0.013 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.19 (26016) covalent geometry : angle 0.70646 / 0.35 (35202) SS BOND : bond 0.02618 / 1.67 ( 18) SS BOND : angle 10.41923 / 6.34 ( 36) hydrogen bonds : bond 0.04073 / 2.70 ( 1241) hydrogen bonds : angle 5.17147 / 3.64 ( 3468) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 320 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6825 (m-30) REVERT: A 335 GLU cc_start: 0.7131 (tp30) cc_final: 0.6511 (tt0) REVERT: A 367 VAL cc_start: 0.8479 (t) cc_final: 0.8268 (p) REVERT: A 471 MET cc_start: 0.8261 (mmp) cc_final: 0.7809 (mtt) REVERT: B 303 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6953 (m-30) REVERT: B 399 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.6921 (mt) REVERT: B 466 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7376 (p0) REVERT: B 471 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7792 (mtt) REVERT: B 472 ASN cc_start: 0.8014 (m-40) cc_final: 0.7542 (t0) REVERT: B 476 GLU cc_start: 0.7653 (tp30) cc_final: 0.7259 (tp30) REVERT: B 498 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7318 (mm-40) REVERT: C 303 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7007 (m-30) REVERT: C 471 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7250 (mtt) REVERT: C 472 ASN cc_start: 0.8034 (m-40) cc_final: 0.7741 (m-40) REVERT: C 476 GLU cc_start: 0.7589 (tp30) cc_final: 0.7185 (tp30) REVERT: C 503 GLU cc_start: 0.7712 (tp30) cc_final: 0.7493 (tp30) REVERT: D 303 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6797 (m-30) REVERT: D 335 GLU cc_start: 0.7133 (tp30) cc_final: 0.6492 (tt0) REVERT: D 367 VAL cc_start: 0.8487 (t) cc_final: 0.8266 (p) REVERT: D 471 MET cc_start: 0.8254 (mmp) cc_final: 0.7801 (mtt) REVERT: E 303 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6960 (m-30) REVERT: E 314 LYS cc_start: 0.7104 (tppt) cc_final: 0.6668 (mptp) REVERT: E 399 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6916 (mt) REVERT: E 466 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7378 (p0) REVERT: E 471 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7842 (mtt) REVERT: E 472 ASN cc_start: 0.8002 (m-40) cc_final: 0.7534 (t0) REVERT: E 476 GLU cc_start: 0.7651 (tp30) cc_final: 0.7223 (tp30) REVERT: E 498 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7272 (mm-40) REVERT: F 303 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: F 472 ASN cc_start: 0.7999 (m-40) cc_final: 0.7705 (m-40) REVERT: F 476 GLU cc_start: 0.7553 (tp30) cc_final: 0.7150 (tp30) REVERT: F 510 ASN cc_start: 0.7003 (m-40) cc_final: 0.6666 (t0) outliers start: 98 outliers final: 41 residues processed: 397 average time/residue: 0.6824 time to fit residues: 309.6735 Evaluate side-chains 343 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain E residue 498 GLN Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 303 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 409 LEU Chi-restraints excluded: chain F residue 420 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 23 optimal weight: 4.9990 chunk 137 optimal weight: 0.0070 chunk 153 optimal weight: 0.0670 chunk 118 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 297 optimal weight: 7.9990 chunk 74 optimal weight: 0.2980 chunk 271 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 202 GLN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN D 113 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS E 202 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN F 202 GLN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106532 restraints weight = 113666.377| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.98 r_work: 0.3006 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26034 Z= 0.124 Angle : 0.697 20.059 35238 Z= 0.346 Chirality : 0.042 0.217 3804 Planarity : 0.004 0.049 4578 Dihedral : 9.270 89.985 3775 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.83 % Allowed : 34.57 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3120 helix: 1.00 (0.13), residues: 1590 sheet: -0.24 (0.28), residues: 342 loop : -0.91 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.014 0.001 TYR E 259 PHE 0.026 0.001 PHE B 300 TRP 0.004 0.001 TRP F 393 HIS 0.012 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (26016) covalent geometry : angle 0.61594 / 0.31 (35202) SS BOND : bond 0.02425 / 1.56 ( 18) SS BOND : angle 10.25350 / 6.23 ( 36) hydrogen bonds : bond 0.03394 / 2.25 ( 1241) hydrogen bonds : angle 4.92370 / 3.46 ( 3468) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 346 time to evaluate : 0.819 Fit side-chains REVERT: A 149 THR cc_start: 0.7670 (m) cc_final: 0.7318 (p) REVERT: A 179 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7416 (mtm-85) REVERT: A 297 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7184 (t70) REVERT: A 342 ASN cc_start: 0.5732 (t0) cc_final: 0.5490 (t0) REVERT: A 367 VAL cc_start: 0.8420 (t) cc_final: 0.8200 (p) REVERT: A 469 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7522 (ptm) REVERT: A 471 MET cc_start: 0.8279 (mmp) cc_final: 0.7878 (mtt) REVERT: A 476 GLU cc_start: 0.7706 (tp30) cc_final: 0.7249 (tp30) REVERT: B 151 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.6174 (mp0) REVERT: B 349 ARG cc_start: 0.8040 (tpt-90) cc_final: 0.7748 (tmt90) REVERT: B 350 ASP cc_start: 0.7805 (m-30) cc_final: 0.7545 (m-30) REVERT: B 466 ASN cc_start: 0.7605 (p0) cc_final: 0.7279 (p0) REVERT: B 471 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7802 (mtt) REVERT: B 472 ASN cc_start: 0.8009 (m-40) cc_final: 0.7048 (t0) REVERT: B 476 GLU cc_start: 0.7700 (tp30) cc_final: 0.7440 (mp0) REVERT: B 498 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7259 (mm-40) REVERT: B 503 GLU cc_start: 0.7591 (tp30) cc_final: 0.7364 (tp30) REVERT: C 30 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7782 (mtm110) REVERT: C 297 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7377 (t70) REVERT: C 471 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7192 (mtt) REVERT: C 476 GLU cc_start: 0.7630 (tp30) cc_final: 0.7122 (tp30) REVERT: C 490 ARG cc_start: 0.7154 (tpp80) cc_final: 0.6726 (mmt90) REVERT: C 498 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7281 (mm-40) REVERT: D 179 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7424 (mtm-85) REVERT: D 367 VAL cc_start: 0.8456 (t) cc_final: 0.8249 (p) REVERT: D 469 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7532 (ptm) REVERT: D 471 MET cc_start: 0.8267 (mmp) cc_final: 0.7871 (mtt) REVERT: D 476 GLU cc_start: 0.7720 (tp30) cc_final: 0.7256 (tp30) REVERT: E 314 LYS cc_start: 0.7005 (tppt) cc_final: 0.6677 (mptp) REVERT: E 335 GLU cc_start: 0.7129 (tp30) cc_final: 0.6599 (tt0) REVERT: E 466 ASN cc_start: 0.7630 (p0) cc_final: 0.7303 (p0) REVERT: E 471 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7821 (mtt) REVERT: E 472 ASN cc_start: 0.8011 (m-40) cc_final: 0.7044 (t0) REVERT: E 476 GLU cc_start: 0.7709 (tp30) cc_final: 0.7435 (mp0) REVERT: F 30 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7787 (mtm110) REVERT: F 297 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7374 (t70) REVERT: F 476 GLU cc_start: 0.7644 (tp30) cc_final: 0.7168 (tp30) REVERT: F 490 ARG cc_start: 0.7168 (tpp80) cc_final: 0.6734 (mmt90) outliers start: 66 outliers final: 26 residues processed: 398 average time/residue: 0.6829 time to fit residues: 312.9431 Evaluate side-chains 328 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 293 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 297 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 301 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN C 330 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN F 330 HIS F 472 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104574 restraints weight = 123274.428| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.07 r_work: 0.2998 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26034 Z= 0.144 Angle : 0.724 20.098 35238 Z= 0.360 Chirality : 0.043 0.273 3804 Planarity : 0.005 0.047 4578 Dihedral : 9.370 87.917 3768 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.49 % Allowed : 34.76 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3120 helix: 1.09 (0.13), residues: 1590 sheet: -0.29 (0.28), residues: 342 loop : -1.02 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.015 0.001 TYR D 344 PHE 0.027 0.001 PHE E 300 TRP 0.004 0.001 TRP F 393 HIS 0.014 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (26016) covalent geometry : angle 0.64574 / 0.32 (35202) SS BOND : bond 0.02517 / 1.60 ( 18) SS BOND : angle 10.29592 / 6.26 ( 36) hydrogen bonds : bond 0.03515 / 2.33 ( 1241) hydrogen bonds : angle 4.87054 / 3.42 ( 3468) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 312 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 THR cc_start: 0.7728 (m) cc_final: 0.7381 (p) REVERT: A 179 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7491 (mtm-85) REVERT: A 332 ASN cc_start: 0.8063 (m-40) cc_final: 0.7591 (m110) REVERT: A 367 VAL cc_start: 0.8451 (t) cc_final: 0.8243 (p) REVERT: A 466 ASN cc_start: 0.7913 (p0) cc_final: 0.7711 (p0) REVERT: A 471 MET cc_start: 0.8331 (mmp) cc_final: 0.7931 (mtt) REVERT: B 466 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7304 (p0) REVERT: B 471 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7828 (mtt) REVERT: B 472 ASN cc_start: 0.8063 (m-40) cc_final: 0.7096 (t0) REVERT: B 476 GLU cc_start: 0.7788 (tp30) cc_final: 0.7509 (mp0) REVERT: B 498 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7322 (mm-40) REVERT: B 503 GLU cc_start: 0.7613 (tp30) cc_final: 0.7397 (tp30) REVERT: B 513 GLN cc_start: 0.5630 (tp40) cc_final: 0.5245 (mt0) REVERT: C 30 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7853 (mtm110) REVERT: C 297 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7423 (t70) REVERT: C 303 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: C 471 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7401 (mtt) REVERT: C 476 GLU cc_start: 0.7686 (tp30) cc_final: 0.7263 (tp30) REVERT: C 490 ARG cc_start: 0.7187 (tpp80) cc_final: 0.6755 (mmt90) REVERT: D 149 THR cc_start: 0.7747 (m) cc_final: 0.7393 (p) REVERT: D 179 ARG cc_start: 0.7820 (ttm110) cc_final: 0.7500 (mtm-85) REVERT: D 332 ASN cc_start: 0.8074 (m-40) cc_final: 0.7598 (m110) REVERT: D 367 VAL cc_start: 0.8469 (t) cc_final: 0.8255 (p) REVERT: D 471 MET cc_start: 0.8317 (mmp) cc_final: 0.7917 (mtt) REVERT: E 314 LYS cc_start: 0.7048 (tppt) cc_final: 0.6753 (mptp) REVERT: E 335 GLU cc_start: 0.7181 (tp30) cc_final: 0.6656 (tt0) REVERT: E 442 GLU cc_start: 0.8159 (tt0) cc_final: 0.7949 (tt0) REVERT: E 466 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7304 (p0) REVERT: E 471 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7821 (mtt) REVERT: E 472 ASN cc_start: 0.8040 (m-40) cc_final: 0.7085 (t0) REVERT: E 476 GLU cc_start: 0.7787 (tp30) cc_final: 0.7541 (mp0) REVERT: F 30 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7854 (mtm110) REVERT: F 297 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7423 (t70) REVERT: F 303 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6907 (m-30) REVERT: F 476 GLU cc_start: 0.7706 (tp30) cc_final: 0.7265 (tp30) REVERT: F 490 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6764 (mmt90) outliers start: 57 outliers final: 29 residues processed: 351 average time/residue: 0.6605 time to fit residues: 266.1138 Evaluate side-chains 327 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain E residue 510 ASN Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 297 ASP Chi-restraints excluded: chain F residue 303 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 142 optimal weight: 0.9980 chunk 234 optimal weight: 5.9990 chunk 198 optimal weight: 0.5980 chunk 98 optimal weight: 0.0030 chunk 46 optimal weight: 0.2980 chunk 210 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.105933 restraints weight = 120593.155| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.07 r_work: 0.2977 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26034 Z= 0.131 Angle : 0.712 19.955 35238 Z= 0.353 Chirality : 0.042 0.255 3804 Planarity : 0.005 0.047 4578 Dihedral : 9.362 89.953 3768 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.27 % Allowed : 34.76 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3120 helix: 1.15 (0.13), residues: 1590 sheet: -0.32 (0.28), residues: 342 loop : -0.97 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 349 TYR 0.014 0.001 TYR D 344 PHE 0.027 0.001 PHE E 300 TRP 0.004 0.001 TRP F 393 HIS 0.013 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (26016) covalent geometry : angle 0.63233 / 0.32 (35202) SS BOND : bond 0.02484 / 1.59 ( 18) SS BOND : angle 10.25631 / 6.23 ( 36) hydrogen bonds : bond 0.03345 / 2.22 ( 1241) hydrogen bonds : angle 4.79615 / 3.37 ( 3468) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 325 time to evaluate : 1.016 Fit side-chains REVERT: A 149 THR cc_start: 0.7674 (m) cc_final: 0.7318 (p) REVERT: A 179 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7459 (mtm-85) REVERT: A 297 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7236 (t70) REVERT: A 342 ASN cc_start: 0.5680 (t0) cc_final: 0.5438 (t0) REVERT: A 367 VAL cc_start: 0.8433 (t) cc_final: 0.8221 (p) REVERT: A 471 MET cc_start: 0.8265 (mmp) cc_final: 0.7896 (mtt) REVERT: A 476 GLU cc_start: 0.7737 (tp30) cc_final: 0.7377 (mp0) REVERT: B 350 ASP cc_start: 0.7775 (m-30) cc_final: 0.7497 (m-30) REVERT: B 466 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7261 (p0) REVERT: B 471 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7759 (mtt) REVERT: B 472 ASN cc_start: 0.7975 (m-40) cc_final: 0.7031 (t0) REVERT: B 476 GLU cc_start: 0.7689 (tp30) cc_final: 0.7413 (mp0) REVERT: B 498 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7301 (mm-40) REVERT: B 513 GLN cc_start: 0.5592 (tp40) cc_final: 0.5204 (mt0) REVERT: C 30 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7825 (mtm110) REVERT: C 113 HIS cc_start: 0.7570 (p90) cc_final: 0.7227 (t-90) REVERT: C 297 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7388 (t70) REVERT: C 471 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7341 (mtt) REVERT: C 476 GLU cc_start: 0.7621 (tp30) cc_final: 0.7095 (tp30) REVERT: C 490 ARG cc_start: 0.7195 (tpp80) cc_final: 0.6748 (mmt90) REVERT: D 149 THR cc_start: 0.7689 (m) cc_final: 0.7340 (p) REVERT: D 179 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7450 (mtm-85) REVERT: D 367 VAL cc_start: 0.8447 (t) cc_final: 0.8225 (p) REVERT: D 471 MET cc_start: 0.8253 (mmp) cc_final: 0.7887 (mtt) REVERT: D 476 GLU cc_start: 0.7753 (tp30) cc_final: 0.7378 (mp0) REVERT: E 314 LYS cc_start: 0.7013 (tppt) cc_final: 0.6733 (mptp) REVERT: E 335 GLU cc_start: 0.7213 (tp30) cc_final: 0.6581 (tt0) REVERT: E 350 ASP cc_start: 0.7746 (m-30) cc_final: 0.7370 (m-30) REVERT: E 466 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7258 (p0) REVERT: E 471 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7746 (mtt) REVERT: E 472 ASN cc_start: 0.8023 (m-40) cc_final: 0.7051 (t0) REVERT: E 476 GLU cc_start: 0.7770 (tp30) cc_final: 0.7444 (mp0) REVERT: E 498 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7338 (mm-40) REVERT: E 509 LYS cc_start: 0.6604 (tttp) cc_final: 0.6342 (tttm) REVERT: F 30 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7822 (mtm110) REVERT: F 113 HIS cc_start: 0.7570 (p90) cc_final: 0.7227 (t-90) REVERT: F 297 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7386 (t70) REVERT: F 433 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.5475 (mpt) REVERT: F 490 ARG cc_start: 0.7160 (tpp80) cc_final: 0.6734 (mmt90) REVERT: F 503 GLU cc_start: 0.7541 (tp30) cc_final: 0.7308 (tp30) outliers start: 51 outliers final: 25 residues processed: 364 average time/residue: 0.6652 time to fit residues: 278.2492 Evaluate side-chains 334 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 297 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 409 LEU Chi-restraints excluded: chain F residue 433 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 298 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 281 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 110 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105827 restraints weight = 109864.989| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.99 r_work: 0.3014 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26034 Z= 0.137 Angle : 0.720 19.973 35238 Z= 0.356 Chirality : 0.043 0.302 3804 Planarity : 0.005 0.047 4578 Dihedral : 9.360 89.912 3768 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.12 % Allowed : 34.65 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3120 helix: 1.16 (0.13), residues: 1590 sheet: -0.33 (0.29), residues: 342 loop : -0.97 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 349 TYR 0.013 0.001 TYR D 344 PHE 0.028 0.001 PHE E 300 TRP 0.004 0.001 TRP F 393 HIS 0.013 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 (26016) covalent geometry : angle 0.64103 / 0.32 (35202) SS BOND : bond 0.02513 / 1.60 ( 18) SS BOND : angle 10.26288 / 6.24 ( 36) hydrogen bonds : bond 0.03391 / 2.25 ( 1241) hydrogen bonds : angle 4.79943 / 3.37 ( 3468) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 319 time to evaluate : 1.077 Fit side-chains REVERT: A 149 THR cc_start: 0.7765 (m) cc_final: 0.7444 (p) REVERT: A 179 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7512 (mtm-85) REVERT: A 332 ASN cc_start: 0.8051 (m-40) cc_final: 0.7581 (m110) REVERT: A 342 ASN cc_start: 0.5764 (t0) cc_final: 0.5496 (t0) REVERT: A 367 VAL cc_start: 0.8444 (t) cc_final: 0.8237 (p) REVERT: A 469 MET cc_start: 0.8012 (ptm) cc_final: 0.7606 (ptm) REVERT: A 471 MET cc_start: 0.8258 (mmp) cc_final: 0.7910 (mtt) REVERT: A 476 GLU cc_start: 0.7782 (tp30) cc_final: 0.7443 (mp0) REVERT: B 49 MET cc_start: 0.9295 (ttp) cc_final: 0.8786 (ttp) REVERT: B 314 LYS cc_start: 0.7155 (tppt) cc_final: 0.6710 (mptp) REVERT: B 466 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7293 (p0) REVERT: B 471 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7765 (mtt) REVERT: B 472 ASN cc_start: 0.8026 (m-40) cc_final: 0.7249 (t0) REVERT: B 476 GLU cc_start: 0.7741 (tp30) cc_final: 0.7483 (mp0) REVERT: B 498 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7377 (mm-40) REVERT: B 513 GLN cc_start: 0.5605 (tp40) cc_final: 0.5224 (mt0) REVERT: C 30 ARG cc_start: 0.8247 (ttm110) cc_final: 0.7856 (mtm110) REVERT: C 113 HIS cc_start: 0.7600 (p90) cc_final: 0.7279 (t-90) REVERT: C 297 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7398 (t70) REVERT: C 471 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7379 (mtt) REVERT: C 476 GLU cc_start: 0.7753 (tp30) cc_final: 0.7545 (mp0) REVERT: C 490 ARG cc_start: 0.7222 (tpp80) cc_final: 0.6777 (mmt90) REVERT: D 149 THR cc_start: 0.7765 (m) cc_final: 0.7449 (p) REVERT: D 179 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7509 (mtm-85) REVERT: D 332 ASN cc_start: 0.8053 (m-40) cc_final: 0.7585 (m110) REVERT: D 367 VAL cc_start: 0.8463 (t) cc_final: 0.8254 (p) REVERT: D 469 MET cc_start: 0.8009 (ptm) cc_final: 0.7610 (ptm) REVERT: D 471 MET cc_start: 0.8236 (mmp) cc_final: 0.7902 (mtt) REVERT: D 476 GLU cc_start: 0.7796 (tp30) cc_final: 0.7440 (mp0) REVERT: E 49 MET cc_start: 0.9299 (ttp) cc_final: 0.8794 (ttp) REVERT: E 314 LYS cc_start: 0.7054 (tppt) cc_final: 0.6793 (mptp) REVERT: E 335 GLU cc_start: 0.7214 (tp30) cc_final: 0.6600 (tt0) REVERT: E 350 ASP cc_start: 0.7715 (m-30) cc_final: 0.7332 (m-30) REVERT: E 442 GLU cc_start: 0.8176 (tt0) cc_final: 0.7962 (tt0) REVERT: E 466 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7336 (p0) REVERT: E 471 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7745 (mtt) REVERT: E 472 ASN cc_start: 0.8025 (m-40) cc_final: 0.7088 (t0) REVERT: E 476 GLU cc_start: 0.7746 (tp30) cc_final: 0.7506 (mp0) REVERT: E 498 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7424 (mm-40) REVERT: E 509 LYS cc_start: 0.6742 (tttp) cc_final: 0.6466 (tttm) REVERT: F 30 ARG cc_start: 0.8247 (ttm110) cc_final: 0.7857 (mtm110) REVERT: F 113 HIS cc_start: 0.7615 (p90) cc_final: 0.7279 (t-90) REVERT: F 297 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7408 (t70) REVERT: F 433 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.5503 (mpt) REVERT: F 471 MET cc_start: 0.8242 (mpp) cc_final: 0.7345 (mtt) REVERT: F 490 ARG cc_start: 0.7187 (tpp80) cc_final: 0.6773 (mmt90) REVERT: F 503 GLU cc_start: 0.7567 (tp30) cc_final: 0.7309 (tp30) REVERT: F 513 GLN cc_start: 0.5581 (tp40) cc_final: 0.5275 (mt0) outliers start: 47 outliers final: 26 residues processed: 355 average time/residue: 0.6466 time to fit residues: 265.8068 Evaluate side-chains 337 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 303 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 297 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 409 LEU Chi-restraints excluded: chain F residue 433 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 47 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 303 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN E 113 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104220 restraints weight = 117595.354| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.99 r_work: 0.2995 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26034 Z= 0.155 Angle : 0.748 20.018 35238 Z= 0.370 Chirality : 0.044 0.310 3804 Planarity : 0.005 0.047 4578 Dihedral : 9.427 88.188 3768 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.00 % Allowed : 35.02 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3120 helix: 1.15 (0.13), residues: 1578 sheet: -0.37 (0.29), residues: 342 loop : -0.93 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 349 TYR 0.013 0.001 TYR D 344 PHE 0.029 0.001 PHE E 300 TRP 0.004 0.001 TRP E 393 HIS 0.013 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (26016) covalent geometry : angle 0.67194 / 0.33 (35202) SS BOND : bond 0.02569 / 1.64 ( 18) SS BOND : angle 10.31555 / 6.27 ( 36) hydrogen bonds : bond 0.03541 / 2.35 ( 1241) hydrogen bonds : angle 4.85889 / 3.41 ( 3468) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 149 THR cc_start: 0.7774 (m) cc_final: 0.7455 (p) REVERT: A 179 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7523 (mtm-85) REVERT: A 332 ASN cc_start: 0.8130 (m-40) cc_final: 0.7656 (m110) REVERT: A 367 VAL cc_start: 0.8484 (t) cc_final: 0.8280 (p) REVERT: A 466 ASN cc_start: 0.7873 (p0) cc_final: 0.7659 (p0) REVERT: A 471 MET cc_start: 0.8324 (mmp) cc_final: 0.7928 (mtt) REVERT: A 476 GLU cc_start: 0.7819 (tp30) cc_final: 0.7388 (tp30) REVERT: B 466 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7370 (p0) REVERT: B 471 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7828 (mtt) REVERT: B 472 ASN cc_start: 0.8047 (m-40) cc_final: 0.7253 (t0) REVERT: B 476 GLU cc_start: 0.7781 (tp30) cc_final: 0.7520 (mp0) REVERT: B 498 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7338 (mm-40) REVERT: B 513 GLN cc_start: 0.5663 (tp40) cc_final: 0.5293 (mt0) REVERT: C 113 HIS cc_start: 0.7673 (p90) cc_final: 0.7320 (t-90) REVERT: C 297 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7413 (t70) REVERT: C 471 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7242 (mtt) REVERT: C 490 ARG cc_start: 0.7250 (tpp80) cc_final: 0.6803 (mmt90) REVERT: D 149 THR cc_start: 0.7807 (m) cc_final: 0.7476 (p) REVERT: D 179 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7528 (mtm-85) REVERT: D 332 ASN cc_start: 0.8150 (m-40) cc_final: 0.7682 (m110) REVERT: D 367 VAL cc_start: 0.8474 (t) cc_final: 0.8268 (p) REVERT: D 466 ASN cc_start: 0.7855 (p0) cc_final: 0.7630 (p0) REVERT: D 471 MET cc_start: 0.8312 (mmp) cc_final: 0.7919 (mtt) REVERT: E 314 LYS cc_start: 0.7056 (tppt) cc_final: 0.6785 (mptp) REVERT: E 335 GLU cc_start: 0.7229 (tp30) cc_final: 0.6600 (tt0) REVERT: E 442 GLU cc_start: 0.8202 (tt0) cc_final: 0.7980 (tt0) REVERT: E 466 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7415 (p0) REVERT: E 471 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7827 (mtt) REVERT: E 472 ASN cc_start: 0.8041 (m-40) cc_final: 0.7087 (t0) REVERT: E 476 GLU cc_start: 0.7787 (tp30) cc_final: 0.7547 (mp0) REVERT: F 113 HIS cc_start: 0.7671 (p90) cc_final: 0.7322 (t-90) REVERT: F 297 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7405 (t70) REVERT: F 433 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.5556 (mpt) REVERT: F 471 MET cc_start: 0.8234 (mpp) cc_final: 0.7295 (mtt) REVERT: F 490 ARG cc_start: 0.7190 (tpp80) cc_final: 0.6772 (mmt90) REVERT: F 503 GLU cc_start: 0.7598 (tp30) cc_final: 0.7327 (tp30) REVERT: F 513 GLN cc_start: 0.5595 (tp40) cc_final: 0.5290 (mt0) outliers start: 44 outliers final: 28 residues processed: 342 average time/residue: 0.6833 time to fit residues: 270.0578 Evaluate side-chains 328 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 297 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 409 LEU Chi-restraints excluded: chain F residue 433 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 193 optimal weight: 4.9990 chunk 197 optimal weight: 0.0970 chunk 300 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 250 optimal weight: 0.0170 chunk 228 optimal weight: 0.0070 chunk 256 optimal weight: 4.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN E 113 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106798 restraints weight = 111434.703| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.95 r_work: 0.3024 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26034 Z= 0.125 Angle : 0.719 19.994 35238 Z= 0.354 Chirality : 0.043 0.296 3804 Planarity : 0.005 0.047 4578 Dihedral : 9.388 89.995 3768 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.70 % Allowed : 35.06 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 3120 helix: 1.18 (0.13), residues: 1590 sheet: -0.37 (0.28), residues: 342 loop : -0.94 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 349 TYR 0.012 0.001 TYR B 344 PHE 0.029 0.001 PHE E 300 TRP 0.005 0.001 TRP C 393 HIS 0.013 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (26016) covalent geometry : angle 0.63977 / 0.32 (35202) SS BOND : bond 0.02499 / 1.60 ( 18) SS BOND : angle 10.27082 / 6.24 ( 36) hydrogen bonds : bond 0.03290 / 2.19 ( 1241) hydrogen bonds : angle 4.81067 / 3.38 ( 3468) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 1.005 Fit side-chains REVERT: A 149 THR cc_start: 0.7735 (m) cc_final: 0.7410 (p) REVERT: A 179 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7506 (mtm-85) REVERT: A 332 ASN cc_start: 0.8100 (m-40) cc_final: 0.7625 (m110) REVERT: A 342 ASN cc_start: 0.5780 (t0) cc_final: 0.5501 (t0) REVERT: A 367 VAL cc_start: 0.8443 (t) cc_final: 0.8236 (p) REVERT: A 466 ASN cc_start: 0.7844 (p0) cc_final: 0.7642 (p0) REVERT: A 471 MET cc_start: 0.8250 (mmp) cc_final: 0.7842 (mtt) REVERT: A 476 GLU cc_start: 0.7733 (tp30) cc_final: 0.7378 (mp0) REVERT: B 49 MET cc_start: 0.9269 (ttp) cc_final: 0.8683 (ttp) REVERT: B 350 ASP cc_start: 0.7705 (m-30) cc_final: 0.7344 (m-30) REVERT: B 442 GLU cc_start: 0.8086 (tt0) cc_final: 0.7861 (mt-10) REVERT: B 466 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7326 (p0) REVERT: B 471 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7676 (mtt) REVERT: B 472 ASN cc_start: 0.7976 (m-40) cc_final: 0.7201 (t0) REVERT: B 476 GLU cc_start: 0.7707 (tp30) cc_final: 0.7422 (mp0) REVERT: B 498 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7307 (mm-40) REVERT: B 513 GLN cc_start: 0.5679 (tp40) cc_final: 0.5304 (mt0) REVERT: C 30 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7873 (mtm110) REVERT: C 113 HIS cc_start: 0.7554 (p90) cc_final: 0.7262 (t-90) REVERT: C 297 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7354 (t70) REVERT: C 471 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7272 (mtt) REVERT: D 149 THR cc_start: 0.7757 (m) cc_final: 0.7427 (p) REVERT: D 179 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7499 (mtm-85) REVERT: D 332 ASN cc_start: 0.8087 (m-40) cc_final: 0.7628 (m110) REVERT: D 367 VAL cc_start: 0.8459 (t) cc_final: 0.8242 (p) REVERT: D 466 ASN cc_start: 0.7834 (p0) cc_final: 0.7628 (p0) REVERT: D 471 MET cc_start: 0.8229 (mmp) cc_final: 0.7826 (mtt) REVERT: D 476 GLU cc_start: 0.7741 (tp30) cc_final: 0.7372 (mp0) REVERT: E 49 MET cc_start: 0.9272 (ttp) cc_final: 0.8689 (ttp) REVERT: E 335 GLU cc_start: 0.7221 (tp30) cc_final: 0.6599 (tt0) REVERT: E 350 ASP cc_start: 0.7731 (m-30) cc_final: 0.7355 (m-30) REVERT: E 466 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7330 (p0) REVERT: E 471 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7673 (mtt) REVERT: E 472 ASN cc_start: 0.7988 (m-40) cc_final: 0.7049 (t0) REVERT: E 476 GLU cc_start: 0.7697 (tp30) cc_final: 0.7442 (mp0) REVERT: E 509 LYS cc_start: 0.6757 (tttp) cc_final: 0.6454 (tttm) REVERT: F 30 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7875 (mtm110) REVERT: F 113 HIS cc_start: 0.7555 (p90) cc_final: 0.7264 (t-90) REVERT: F 297 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7361 (t70) REVERT: F 433 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.5511 (mpt) REVERT: F 471 MET cc_start: 0.8207 (mpp) cc_final: 0.7379 (mtt) REVERT: F 490 ARG cc_start: 0.7146 (tpp80) cc_final: 0.6743 (mmt90) REVERT: F 503 GLU cc_start: 0.7525 (tp30) cc_final: 0.7253 (tp30) REVERT: F 513 GLN cc_start: 0.5599 (tp40) cc_final: 0.5299 (mt0) outliers start: 36 outliers final: 21 residues processed: 332 average time/residue: 0.6484 time to fit residues: 249.6574 Evaluate side-chains 320 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 297 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 409 LEU Chi-restraints excluded: chain F residue 433 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 141 optimal weight: 0.9980 chunk 24 optimal weight: 0.0050 chunk 9 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 281 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN E 113 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105433 restraints weight = 117476.284| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.02 r_work: 0.2994 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26034 Z= 0.139 Angle : 0.731 19.922 35238 Z= 0.360 Chirality : 0.043 0.294 3804 Planarity : 0.005 0.047 4578 Dihedral : 9.405 89.785 3768 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.67 % Allowed : 35.02 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3120 helix: 1.14 (0.13), residues: 1590 sheet: -0.38 (0.29), residues: 342 loop : -0.94 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 349 TYR 0.013 0.001 TYR D 344 PHE 0.028 0.001 PHE E 300 TRP 0.005 0.001 TRP C 393 HIS 0.013 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (26016) covalent geometry : angle 0.65404 / 0.32 (35202) SS BOND : bond 0.02512 / 1.60 ( 18) SS BOND : angle 10.26986 / 6.24 ( 36) hydrogen bonds : bond 0.03401 / 2.26 ( 1241) hydrogen bonds : angle 4.81085 / 3.38 ( 3468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9383.27 seconds wall clock time: 160 minutes 28.23 seconds (9628.23 seconds total)