Starting phenix.real_space_refine on Fri Jun 20 15:48:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yag_39098/06_2025/8yag_39098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yag_39098/06_2025/8yag_39098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yag_39098/06_2025/8yag_39098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yag_39098/06_2025/8yag_39098.map" model { file = "/net/cci-nas-00/data/ceres_data/8yag_39098/06_2025/8yag_39098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yag_39098/06_2025/8yag_39098.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.060 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 Zn 16 6.06 5 S 80 5.16 5 C 14984 2.51 5 N 4304 2.21 5 O 4576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23960 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2993 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2993 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2993 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2993 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2993 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2993 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2993 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2993 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.34, per 1000 atoms: 0.64 Number of scatterers: 23960 At special positions: 0 Unit cell: (136.85, 136.85, 104.55, 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) Zn 16 29.99 S 80 16.00 O 4576 8.00 N 4304 7.00 C 14984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.04 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.04 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.04 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.04 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.04 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.04 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: 6.52 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 271 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 42.6% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.593A pdb=" N PHE A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.631A pdb=" N PHE A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY A 112 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.678A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 354 through 363 removed outlier: 4.134A pdb=" N ILE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.535A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 removed outlier: 3.527A pdb=" N LEU A 413 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.594A pdb=" N PHE B 99 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.631A pdb=" N PHE B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 293 through 304 removed outlier: 3.679A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 354 through 363 removed outlier: 4.134A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.535A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 removed outlier: 3.527A pdb=" N LEU B 413 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.593A pdb=" N PHE C 99 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.631A pdb=" N PHE C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY C 112 " --> pdb=" O TYR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 171 through 179 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 190 through 204 Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.679A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 322 Processing helix chain 'C' and resid 325 through 336 Processing helix chain 'C' and resid 354 through 363 removed outlier: 4.134A pdb=" N ILE C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 373 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.535A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 removed outlier: 3.527A pdb=" N LEU C 413 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.594A pdb=" N PHE D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.631A pdb=" N PHE D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 171 through 179 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 293 through 304 removed outlier: 3.679A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 354 through 363 removed outlier: 4.134A pdb=" N ILE D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.535A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 414 removed outlier: 3.527A pdb=" N LEU D 413 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.594A pdb=" N PHE E 99 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.632A pdb=" N PHE E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY E 112 " --> pdb=" O TYR E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 276 through 287 Processing helix chain 'E' and resid 293 through 304 removed outlier: 3.679A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 Processing helix chain 'E' and resid 325 through 336 Processing helix chain 'E' and resid 354 through 363 removed outlier: 4.134A pdb=" N ILE E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 375 through 383 removed outlier: 3.534A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 414 removed outlier: 3.527A pdb=" N LEU E 413 " --> pdb=" O ASN E 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 100 removed outlier: 3.594A pdb=" N PHE F 99 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 removed outlier: 3.632A pdb=" N PHE F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY F 112 " --> pdb=" O TYR F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 Processing helix chain 'F' and resid 171 through 179 Processing helix chain 'F' and resid 182 through 186 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 276 through 287 Processing helix chain 'F' and resid 293 through 304 removed outlier: 3.679A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 Processing helix chain 'F' and resid 325 through 336 Processing helix chain 'F' and resid 354 through 363 removed outlier: 4.133A pdb=" N ILE F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 373 Processing helix chain 'F' and resid 375 through 383 removed outlier: 3.535A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 414 removed outlier: 3.526A pdb=" N LEU F 413 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 100 removed outlier: 3.592A pdb=" N PHE G 99 " --> pdb=" O SER G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 120 removed outlier: 3.631A pdb=" N PHE G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY G 112 " --> pdb=" O TYR G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 171 through 179 Processing helix chain 'G' and resid 182 through 186 Processing helix chain 'G' and resid 190 through 204 Processing helix chain 'G' and resid 230 through 244 Processing helix chain 'G' and resid 254 through 265 Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 293 through 304 removed outlier: 3.679A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 322 Processing helix chain 'G' and resid 325 through 336 Processing helix chain 'G' and resid 354 through 363 removed outlier: 4.134A pdb=" N ILE G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 375 through 383 removed outlier: 3.534A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 414 removed outlier: 3.527A pdb=" N LEU G 413 " --> pdb=" O ASN G 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.594A pdb=" N PHE H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.632A pdb=" N PHE H 106 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY H 112 " --> pdb=" O TYR H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 Processing helix chain 'H' and resid 171 through 179 Processing helix chain 'H' and resid 182 through 186 Processing helix chain 'H' and resid 190 through 204 Processing helix chain 'H' and resid 230 through 244 Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 276 through 287 Processing helix chain 'H' and resid 293 through 304 removed outlier: 3.679A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 322 Processing helix chain 'H' and resid 325 through 336 Processing helix chain 'H' and resid 354 through 363 removed outlier: 4.133A pdb=" N ILE H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 373 Processing helix chain 'H' and resid 375 through 383 removed outlier: 3.535A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 414 removed outlier: 3.526A pdb=" N LEU H 413 " --> pdb=" O ASN H 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG A 37 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 53 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG A 47 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG A 37 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 13.687A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 13.357A pdb=" N ARG A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N LEU A 25 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ARG A 73 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS A 27 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N PHE A 31 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 418 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.273A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP A 81 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.521A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG B 37 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 53 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 47 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG B 37 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 13.687A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 13.357A pdb=" N ARG B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N LEU B 25 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ARG B 73 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS B 27 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N PHE B 31 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 418 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.273A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP B 81 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.521A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG C 37 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 53 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG C 47 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG C 37 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 13.687A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 13.357A pdb=" N ARG C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N LEU C 25 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ARG C 73 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS C 27 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N PHE C 31 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 418 " --> pdb=" O PHE C 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 84 removed outlier: 6.273A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.521A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG D 37 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 53 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG D 47 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG D 37 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 13.687A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.357A pdb=" N ARG D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N LEU D 25 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ARG D 73 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS D 27 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N PHE D 31 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL D 418 " --> pdb=" O PHE D 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.273A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.522A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.601A pdb=" N ARG E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN E 53 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG E 47 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE E 51 " --> pdb=" O ARG E 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.601A pdb=" N ARG E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 13.687A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 13.358A pdb=" N ARG E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N LEU E 25 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ARG E 73 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N CYS E 27 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL E 418 " --> pdb=" O PHE E 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.273A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 209 through 212 removed outlier: 6.522A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.601A pdb=" N ARG F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN F 53 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG F 47 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE F 51 " --> pdb=" O ARG F 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.601A pdb=" N ARG F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 13.687A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 13.357A pdb=" N ARG F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.331A pdb=" N LEU F 25 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ARG F 73 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS F 27 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL F 418 " --> pdb=" O PHE F 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.273A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.522A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN G 53 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG G 47 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE G 51 " --> pdb=" O ARG G 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.602A pdb=" N ARG G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 13.687A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 13.358A pdb=" N ARG G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N LEU G 25 " --> pdb=" O ARG G 71 " (cutoff:3.500A) removed outlier: 10.672A pdb=" N ARG G 73 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS G 27 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N PHE G 31 " --> pdb=" O PRO G 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL G 418 " --> pdb=" O PHE G 425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.273A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 209 through 212 removed outlier: 6.521A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.601A pdb=" N ARG H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN H 53 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG H 47 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE H 51 " --> pdb=" O ARG H 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.601A pdb=" N ARG H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 13.687A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 13.357A pdb=" N ARG H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N LEU H 25 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N ARG H 73 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS H 27 " --> pdb=" O ARG H 73 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL H 418 " --> pdb=" O PHE H 425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.273A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 209 through 212 removed outlier: 6.522A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2832 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: 8.73 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4160 1.32 - 1.44: 6241 1.44 - 1.57: 13871 1.57 - 1.69: 0 1.69 - 1.82: 144 Bond restraints: 24416 Sorted by residual: bond pdb=" C PRO F 134 " pdb=" O PRO F 134 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.26e-02 6.30e+03 1.36e+01 bond pdb=" CX KCX G 210 " pdb=" OQ1 KCX G 210 " ideal model delta sigma weight residual 1.250 1.323 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C PRO B 134 " pdb=" O PRO B 134 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.26e-02 6.30e+03 1.30e+01 bond pdb=" C PRO D 134 " pdb=" O PRO D 134 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.26e-02 6.30e+03 1.30e+01 bond pdb=" C PRO H 134 " pdb=" O PRO H 134 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.26e-02 6.30e+03 1.30e+01 ... (remaining 24411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 32063 1.65 - 3.31: 883 3.31 - 4.96: 125 4.96 - 6.62: 25 6.62 - 8.27: 16 Bond angle restraints: 33112 Sorted by residual: angle pdb=" N VAL H 347 " pdb=" CA VAL H 347 " pdb=" C VAL H 347 " ideal model delta sigma weight residual 110.42 104.72 5.70 9.60e-01 1.09e+00 3.53e+01 angle pdb=" N VAL B 347 " pdb=" CA VAL B 347 " pdb=" C VAL B 347 " ideal model delta sigma weight residual 110.42 104.78 5.64 9.60e-01 1.09e+00 3.46e+01 angle pdb=" N VAL C 347 " pdb=" CA VAL C 347 " pdb=" C VAL C 347 " ideal model delta sigma weight residual 110.42 104.78 5.64 9.60e-01 1.09e+00 3.45e+01 angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 110.42 104.78 5.64 9.60e-01 1.09e+00 3.45e+01 angle pdb=" N VAL D 347 " pdb=" CA VAL D 347 " pdb=" C VAL D 347 " ideal model delta sigma weight residual 110.42 104.79 5.63 9.60e-01 1.09e+00 3.44e+01 ... (remaining 33107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 12749 16.72 - 33.44: 1257 33.44 - 50.16: 346 50.16 - 66.88: 104 66.88 - 83.60: 24 Dihedral angle restraints: 14480 sinusoidal: 5576 harmonic: 8904 Sorted by residual: dihedral pdb=" CB CYS F 27 " pdb=" SG CYS F 27 " pdb=" SG CYS F 75 " pdb=" CB CYS F 75 " ideal model delta sinusoidal sigma weight residual -86.00 -121.81 35.81 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CB CYS E 27 " pdb=" SG CYS E 27 " pdb=" SG CYS E 75 " pdb=" CB CYS E 75 " ideal model delta sinusoidal sigma weight residual -86.00 -121.81 35.81 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CB CYS H 27 " pdb=" SG CYS H 27 " pdb=" SG CYS H 75 " pdb=" CB CYS H 75 " ideal model delta sinusoidal sigma weight residual -86.00 -121.80 35.80 1 1.00e+01 1.00e-02 1.81e+01 ... (remaining 14477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2808 0.051 - 0.103: 696 0.103 - 0.154: 152 0.154 - 0.206: 9 0.206 - 0.257: 23 Chirality restraints: 3688 Sorted by residual: chirality pdb=" CA VAL H 347 " pdb=" N VAL H 347 " pdb=" C VAL H 347 " pdb=" CB VAL H 347 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA VAL D 347 " pdb=" N VAL D 347 " pdb=" C VAL D 347 " pdb=" CB VAL D 347 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA VAL B 347 " pdb=" N VAL B 347 " pdb=" C VAL B 347 " pdb=" CB VAL B 347 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3685 not shown) Planarity restraints: 4392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 353 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C ASN D 353 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN D 353 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA D 354 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 353 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C ASN B 353 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN B 353 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA B 354 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 353 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ASN H 353 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN H 353 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA H 354 " 0.011 2.00e-02 2.50e+03 ... (remaining 4389 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 40 2.42 - 3.04: 13930 3.04 - 3.66: 34831 3.66 - 4.28: 56993 4.28 - 4.90: 93467 Nonbonded interactions: 199261 Sorted by model distance: nonbonded pdb=" SD MET F 345 " pdb=" ND2 ASN F 353 " model vdw 1.802 3.480 nonbonded pdb=" SD MET H 345 " pdb=" ND2 ASN H 353 " model vdw 1.802 3.480 nonbonded pdb=" SD MET G 345 " pdb=" ND2 ASN G 353 " model vdw 1.802 3.480 nonbonded pdb=" SD MET A 345 " pdb=" ND2 ASN A 353 " model vdw 1.802 3.480 nonbonded pdb=" SD MET D 345 " pdb=" ND2 ASN D 353 " model vdw 1.802 3.480 ... (remaining 199256 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 62.530 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.130 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:15.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24448 Z= 0.290 Angle : 0.666 8.273 33128 Z= 0.423 Chirality : 0.051 0.257 3688 Planarity : 0.004 0.039 4392 Dihedral : 15.226 83.599 8824 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 13.44 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3136 helix: 0.86 (0.14), residues: 1280 sheet: 0.78 (0.28), residues: 376 loop : -0.96 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 289 HIS 0.005 0.001 HIS B 251 PHE 0.007 0.001 PHE H 122 TYR 0.011 0.001 TYR B 333 ARG 0.002 0.000 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.17837 ( 1032) hydrogen bonds : angle 5.20440 ( 2832) metal coordination : bond 0.00304 ( 24) SS BOND : bond 0.00626 ( 8) SS BOND : angle 0.81206 ( 16) covalent geometry : bond 0.00450 (24416) covalent geometry : angle 0.66630 (33112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 2.970 Fit side-chains REVERT: A 259 LYS cc_start: 0.8484 (tttt) cc_final: 0.8271 (ttpt) REVERT: B 259 LYS cc_start: 0.8471 (tttt) cc_final: 0.8257 (ttpt) REVERT: C 259 LYS cc_start: 0.8481 (tttt) cc_final: 0.8273 (ttpt) REVERT: D 259 LYS cc_start: 0.8466 (tttt) cc_final: 0.8251 (ttpt) REVERT: E 37 ARG cc_start: 0.7239 (mtp-110) cc_final: 0.6748 (mtm180) REVERT: E 71 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7502 (mtt-85) REVERT: E 73 ARG cc_start: 0.8485 (mmt-90) cc_final: 0.8243 (mmt-90) REVERT: F 37 ARG cc_start: 0.7226 (mtp-110) cc_final: 0.6738 (mtm180) REVERT: F 71 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7481 (mtt-85) REVERT: G 37 ARG cc_start: 0.7237 (mtp-110) cc_final: 0.6748 (mtm180) REVERT: G 71 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7502 (mtt-85) REVERT: G 73 ARG cc_start: 0.8468 (mmt-90) cc_final: 0.8229 (mmt-90) REVERT: H 37 ARG cc_start: 0.7228 (mtp-110) cc_final: 0.6739 (mtm180) REVERT: H 71 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7481 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 1.8567 time to fit residues: 842.3961 Evaluate side-chains 285 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS B 176 HIS C 176 HIS D 176 HIS E 26 HIS E 176 HIS E 286 HIS F 26 HIS F 176 HIS F 286 HIS G 26 HIS G 176 HIS G 286 HIS H 26 HIS H 176 HIS H 286 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112747 restraints weight = 21657.725| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.25 r_work: 0.3180 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24448 Z= 0.154 Angle : 0.561 5.471 33128 Z= 0.311 Chirality : 0.048 0.145 3688 Planarity : 0.005 0.042 4392 Dihedral : 5.630 58.213 3504 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.42 % Allowed : 13.32 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3136 helix: 1.16 (0.14), residues: 1280 sheet: 1.23 (0.28), residues: 384 loop : -1.02 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 289 HIS 0.007 0.001 HIS B 251 PHE 0.010 0.002 PHE G 122 TYR 0.016 0.002 TYR H 244 ARG 0.003 0.000 ARG H 109 Details of bonding type rmsd hydrogen bonds : bond 0.06319 ( 1032) hydrogen bonds : angle 4.19686 ( 2832) metal coordination : bond 0.00345 ( 24) SS BOND : bond 0.00918 ( 8) SS BOND : angle 1.55618 ( 16) covalent geometry : bond 0.00331 (24416) covalent geometry : angle 0.55992 (33112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 2.452 Fit side-chains REVERT: A 259 LYS cc_start: 0.8695 (tttt) cc_final: 0.8444 (ttmt) REVERT: A 312 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5820 (mm-30) REVERT: B 259 LYS cc_start: 0.8696 (tttt) cc_final: 0.8442 (ttmt) REVERT: C 259 LYS cc_start: 0.8691 (tttt) cc_final: 0.8446 (ttmt) REVERT: C 312 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5818 (mm-30) REVERT: D 222 LYS cc_start: 0.8272 (tttm) cc_final: 0.8071 (tttm) REVERT: D 259 LYS cc_start: 0.8693 (tttt) cc_final: 0.8444 (ttmt) REVERT: E 71 ARG cc_start: 0.8283 (mtt90) cc_final: 0.7775 (mtt-85) REVERT: E 391 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: F 71 ARG cc_start: 0.8287 (mtt90) cc_final: 0.7818 (mtt-85) REVERT: F 278 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: F 362 GLU cc_start: 0.7944 (tt0) cc_final: 0.7737 (mt-10) REVERT: F 391 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: G 71 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7776 (mtt-85) REVERT: G 391 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: H 71 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7813 (mtt-85) REVERT: H 278 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: H 391 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7738 (mt-10) outliers start: 59 outliers final: 8 residues processed: 321 average time/residue: 1.6425 time to fit residues: 590.5587 Evaluate side-chains 293 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 277 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 391 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 235 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 194 optimal weight: 0.0970 chunk 296 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 30 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS C 26 HIS D 26 HIS E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113088 restraints weight = 21916.247| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.22 r_work: 0.3170 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24448 Z= 0.152 Angle : 0.553 5.346 33128 Z= 0.306 Chirality : 0.048 0.144 3688 Planarity : 0.005 0.044 4392 Dihedral : 5.835 57.562 3504 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.30 % Allowed : 13.24 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3136 helix: 1.19 (0.14), residues: 1280 sheet: 1.70 (0.30), residues: 304 loop : -1.05 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 289 HIS 0.007 0.001 HIS B 251 PHE 0.010 0.002 PHE E 122 TYR 0.015 0.002 TYR F 244 ARG 0.002 0.000 ARG D 199 Details of bonding type rmsd hydrogen bonds : bond 0.06160 ( 1032) hydrogen bonds : angle 4.14243 ( 2832) metal coordination : bond 0.00333 ( 24) SS BOND : bond 0.00903 ( 8) SS BOND : angle 1.27636 ( 16) covalent geometry : bond 0.00330 (24416) covalent geometry : angle 0.55206 (33112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 2.490 Fit side-chains REVERT: A 259 LYS cc_start: 0.8729 (tttt) cc_final: 0.8523 (ttmt) REVERT: A 312 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5937 (mm-30) REVERT: B 259 LYS cc_start: 0.8760 (tttt) cc_final: 0.8555 (ttmt) REVERT: B 312 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5903 (mm-30) REVERT: C 259 LYS cc_start: 0.8747 (tttt) cc_final: 0.8538 (ttmt) REVERT: C 312 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5921 (mm-30) REVERT: D 312 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5945 (mm-30) REVERT: E 37 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7019 (mtm180) REVERT: E 71 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7909 (mtt-85) REVERT: E 326 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7277 (mm-40) REVERT: F 37 ARG cc_start: 0.7487 (mtm110) cc_final: 0.7000 (mtm180) REVERT: F 71 ARG cc_start: 0.8357 (mtt90) cc_final: 0.7918 (mtt-85) REVERT: F 73 ARG cc_start: 0.8578 (mmt-90) cc_final: 0.8295 (mmt-90) REVERT: F 326 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7285 (mm-40) REVERT: G 37 ARG cc_start: 0.7479 (mtm110) cc_final: 0.6998 (mtm180) REVERT: G 71 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7911 (mtt-85) REVERT: G 326 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7265 (mm-40) REVERT: H 37 ARG cc_start: 0.7494 (mtm110) cc_final: 0.7004 (mtm180) REVERT: H 71 ARG cc_start: 0.8350 (mtt90) cc_final: 0.7911 (mtt-85) REVERT: H 73 ARG cc_start: 0.8572 (mmt-90) cc_final: 0.8290 (mmt-90) REVERT: H 326 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7253 (mm-40) outliers start: 56 outliers final: 14 residues processed: 299 average time/residue: 1.7055 time to fit residues: 569.4410 Evaluate side-chains 284 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 326 GLN Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 326 GLN Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 326 GLN Chi-restraints excluded: chain H residue 401 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 169 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 195 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 189 optimal weight: 0.0270 chunk 162 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS C 26 HIS D 26 HIS E 26 HIS F 26 HIS F 251 HIS G 26 HIS G 251 HIS H 26 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110053 restraints weight = 21621.774| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.21 r_work: 0.3140 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24448 Z= 0.205 Angle : 0.622 6.039 33128 Z= 0.347 Chirality : 0.051 0.152 3688 Planarity : 0.005 0.052 4392 Dihedral : 6.645 58.814 3504 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.21 % Allowed : 13.81 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3136 helix: 0.98 (0.14), residues: 1280 sheet: 1.28 (0.30), residues: 336 loop : -1.09 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 289 HIS 0.009 0.002 HIS F 251 PHE 0.013 0.002 PHE F 122 TYR 0.018 0.003 TYR E 244 ARG 0.003 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.07300 ( 1032) hydrogen bonds : angle 4.27994 ( 2832) metal coordination : bond 0.00434 ( 24) SS BOND : bond 0.01113 ( 8) SS BOND : angle 1.45527 ( 16) covalent geometry : bond 0.00459 (24416) covalent geometry : angle 0.62107 (33112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 2.761 Fit side-chains REVERT: A 312 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5928 (mm-30) REVERT: B 259 LYS cc_start: 0.8777 (tttt) cc_final: 0.8572 (ttmt) REVERT: B 312 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5939 (mm-30) REVERT: C 312 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5931 (mm-30) REVERT: D 312 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5941 (mm-30) REVERT: E 37 ARG cc_start: 0.7547 (mtm110) cc_final: 0.7089 (mtm180) REVERT: E 71 ARG cc_start: 0.8362 (mtt90) cc_final: 0.7883 (mtt-85) REVERT: F 37 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7074 (mtm180) REVERT: F 71 ARG cc_start: 0.8371 (mtt90) cc_final: 0.7890 (mtt-85) REVERT: G 37 ARG cc_start: 0.7537 (mtm110) cc_final: 0.7085 (mtm180) REVERT: G 71 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7882 (mtt-85) REVERT: H 37 ARG cc_start: 0.7542 (mtm110) cc_final: 0.7081 (mtm180) REVERT: H 71 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7875 (mtt-85) outliers start: 54 outliers final: 20 residues processed: 293 average time/residue: 1.8186 time to fit residues: 596.9851 Evaluate side-chains 277 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 401 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 23 optimal weight: 0.2980 chunk 236 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 0.1980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS C 26 HIS D 26 HIS E 26 HIS E 251 HIS F 26 HIS G 26 HIS H 26 HIS H 251 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112905 restraints weight = 21892.891| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.24 r_work: 0.3181 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24448 Z= 0.130 Angle : 0.523 5.788 33128 Z= 0.287 Chirality : 0.046 0.146 3688 Planarity : 0.004 0.046 4392 Dihedral : 6.602 86.525 3504 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.05 % Allowed : 13.57 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3136 helix: 1.21 (0.14), residues: 1280 sheet: 1.60 (0.30), residues: 304 loop : -1.07 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 289 HIS 0.007 0.001 HIS G 251 PHE 0.008 0.001 PHE C 229 TYR 0.013 0.002 TYR E 244 ARG 0.002 0.000 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.05458 ( 1032) hydrogen bonds : angle 4.04095 ( 2832) metal coordination : bond 0.00276 ( 24) SS BOND : bond 0.00830 ( 8) SS BOND : angle 1.31296 ( 16) covalent geometry : bond 0.00274 (24416) covalent geometry : angle 0.52184 (33112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 2.653 Fit side-chains REVERT: A 312 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5862 (mm-30) REVERT: B 259 LYS cc_start: 0.8699 (tttt) cc_final: 0.8461 (ttmt) REVERT: B 312 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5835 (mm-30) REVERT: C 312 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5866 (mm-30) REVERT: D 312 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5848 (mm-30) REVERT: E 37 ARG cc_start: 0.7442 (mtm110) cc_final: 0.6976 (mtm180) REVERT: E 71 ARG cc_start: 0.8352 (mtt90) cc_final: 0.7873 (mtt-85) REVERT: E 326 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7329 (mm-40) REVERT: F 37 ARG cc_start: 0.7435 (mtm110) cc_final: 0.6968 (mtm180) REVERT: F 71 ARG cc_start: 0.8337 (mtt90) cc_final: 0.7851 (mtt-85) REVERT: F 326 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7309 (mm-40) REVERT: G 37 ARG cc_start: 0.7429 (mtm110) cc_final: 0.6974 (mtm180) REVERT: G 71 ARG cc_start: 0.8353 (mtt90) cc_final: 0.7876 (mtt-85) REVERT: G 326 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7324 (mm-40) REVERT: H 37 ARG cc_start: 0.7423 (mtm110) cc_final: 0.6950 (mtm180) REVERT: H 71 ARG cc_start: 0.8330 (mtt90) cc_final: 0.7845 (mtt-85) REVERT: H 326 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7272 (mm-40) outliers start: 50 outliers final: 7 residues processed: 292 average time/residue: 1.6442 time to fit residues: 539.1499 Evaluate side-chains 269 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain E residue 326 GLN Chi-restraints excluded: chain F residue 326 GLN Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain H residue 326 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 95 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 271 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS C 26 HIS D 26 HIS E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112684 restraints weight = 21733.332| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.23 r_work: 0.3177 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24448 Z= 0.131 Angle : 0.522 5.484 33128 Z= 0.286 Chirality : 0.046 0.146 3688 Planarity : 0.004 0.046 4392 Dihedral : 6.240 89.868 3504 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.93 % Allowed : 13.36 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3136 helix: 1.27 (0.14), residues: 1280 sheet: 1.00 (0.28), residues: 384 loop : -1.00 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 289 HIS 0.007 0.001 HIS F 251 PHE 0.007 0.001 PHE H 122 TYR 0.013 0.002 TYR G 244 ARG 0.002 0.000 ARG B 201 Details of bonding type rmsd hydrogen bonds : bond 0.05529 ( 1032) hydrogen bonds : angle 4.00592 ( 2832) metal coordination : bond 0.00269 ( 24) SS BOND : bond 0.00818 ( 8) SS BOND : angle 1.32030 ( 16) covalent geometry : bond 0.00277 (24416) covalent geometry : angle 0.52106 (33112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 2.490 Fit side-chains REVERT: A 115 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: A 312 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5857 (mm-30) REVERT: B 115 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: B 259 LYS cc_start: 0.8695 (tttt) cc_final: 0.8460 (ttmt) REVERT: B 312 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.5848 (mm-30) REVERT: C 115 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: C 312 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5873 (mm-30) REVERT: D 115 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: D 312 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5858 (mm-30) REVERT: E 37 ARG cc_start: 0.7409 (mtm110) cc_final: 0.6921 (mtm180) REVERT: E 71 ARG cc_start: 0.8342 (mtt90) cc_final: 0.7869 (mtt-85) REVERT: E 326 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7375 (mm-40) REVERT: F 37 ARG cc_start: 0.7404 (mtm110) cc_final: 0.6912 (mtm180) REVERT: F 47 ARG cc_start: 0.8388 (mtt-85) cc_final: 0.8175 (mtt90) REVERT: F 71 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7891 (mtt-85) REVERT: F 326 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7290 (mm-40) REVERT: G 37 ARG cc_start: 0.7396 (mtm110) cc_final: 0.6889 (mtm180) REVERT: G 47 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8180 (mtt90) REVERT: G 71 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7875 (mtt-85) REVERT: G 326 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7373 (mm-40) REVERT: H 37 ARG cc_start: 0.7408 (mtm110) cc_final: 0.6917 (mtm180) REVERT: H 47 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.8077 (mtt90) REVERT: H 71 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7841 (mtt-85) REVERT: H 326 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7285 (mm-40) outliers start: 47 outliers final: 13 residues processed: 287 average time/residue: 1.7561 time to fit residues: 565.5135 Evaluate side-chains 284 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 326 GLN Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 326 GLN Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 326 GLN Chi-restraints excluded: chain H residue 401 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 223 optimal weight: 4.9990 chunk 228 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS C 26 HIS D 26 HIS E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109210 restraints weight = 21703.290| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.26 r_work: 0.3132 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24448 Z= 0.212 Angle : 0.632 6.169 33128 Z= 0.351 Chirality : 0.051 0.155 3688 Planarity : 0.005 0.055 4392 Dihedral : 5.892 56.553 3504 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.80 % Allowed : 13.44 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3136 helix: 0.98 (0.14), residues: 1280 sheet: 1.56 (0.31), residues: 304 loop : -1.14 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 289 HIS 0.008 0.002 HIS B 251 PHE 0.013 0.002 PHE G 122 TYR 0.018 0.003 TYR G 244 ARG 0.003 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.07387 ( 1032) hydrogen bonds : angle 4.26070 ( 2832) metal coordination : bond 0.00467 ( 24) SS BOND : bond 0.01089 ( 8) SS BOND : angle 1.68658 ( 16) covalent geometry : bond 0.00478 (24416) covalent geometry : angle 0.63120 (33112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 2.466 Fit side-chains REVERT: A 312 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5762 (mm-30) REVERT: B 259 LYS cc_start: 0.8633 (tttt) cc_final: 0.8400 (ttmt) REVERT: B 312 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5781 (mm-30) REVERT: C 312 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5775 (mm-30) REVERT: D 312 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5785 (mm-30) REVERT: E 37 ARG cc_start: 0.7433 (mtm110) cc_final: 0.6929 (mtm180) REVERT: E 71 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7785 (mtt-85) REVERT: E 326 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7298 (mm-40) REVERT: F 37 ARG cc_start: 0.7430 (mtm110) cc_final: 0.6926 (mtm180) REVERT: F 71 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7783 (mtt-85) REVERT: F 326 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7293 (mm-40) REVERT: G 37 ARG cc_start: 0.7395 (mtm110) cc_final: 0.6912 (mtm180) REVERT: G 71 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7784 (mtt-85) REVERT: G 326 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7287 (mm-40) REVERT: H 37 ARG cc_start: 0.7423 (mtm110) cc_final: 0.6931 (mtm180) REVERT: H 71 ARG cc_start: 0.8307 (mtt90) cc_final: 0.7775 (mtt-85) REVERT: H 326 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7321 (mm-40) outliers start: 44 outliers final: 26 residues processed: 282 average time/residue: 1.6707 time to fit residues: 529.3383 Evaluate side-chains 281 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 326 GLN Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 326 GLN Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 326 GLN Chi-restraints excluded: chain H residue 401 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 224 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 303 optimal weight: 0.7980 chunk 273 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 274 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS C 26 HIS D 26 HIS E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109991 restraints weight = 21632.225| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.25 r_work: 0.3143 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24448 Z= 0.187 Angle : 0.601 6.728 33128 Z= 0.333 Chirality : 0.050 0.148 3688 Planarity : 0.005 0.050 4392 Dihedral : 5.782 46.423 3504 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.09 % Allowed : 13.98 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3136 helix: 1.00 (0.14), residues: 1280 sheet: 1.54 (0.32), residues: 304 loop : -1.14 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 289 HIS 0.008 0.002 HIS B 251 PHE 0.011 0.002 PHE F 122 TYR 0.016 0.002 TYR G 244 ARG 0.002 0.000 ARG F 320 Details of bonding type rmsd hydrogen bonds : bond 0.06803 ( 1032) hydrogen bonds : angle 4.20858 ( 2832) metal coordination : bond 0.00396 ( 24) SS BOND : bond 0.01029 ( 8) SS BOND : angle 1.64793 ( 16) covalent geometry : bond 0.00416 (24416) covalent geometry : angle 0.60022 (33112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 2.724 Fit side-chains REVERT: A 312 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5793 (mm-30) REVERT: B 259 LYS cc_start: 0.8656 (tttt) cc_final: 0.8392 (ttmt) REVERT: B 312 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5778 (mm-30) REVERT: B 391 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: C 312 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5804 (mm-30) REVERT: D 312 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5785 (mm-30) REVERT: D 391 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: E 37 ARG cc_start: 0.7429 (mtm110) cc_final: 0.6916 (mtm180) REVERT: E 71 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7795 (mtt-85) REVERT: E 326 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7320 (mm-40) REVERT: F 37 ARG cc_start: 0.7421 (mtm110) cc_final: 0.6907 (mtm180) REVERT: F 71 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7786 (mtt-85) REVERT: F 326 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7287 (mm-40) REVERT: G 37 ARG cc_start: 0.7413 (mtm110) cc_final: 0.6906 (mtm180) REVERT: G 71 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7791 (mtt-85) REVERT: G 326 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7313 (mm-40) REVERT: H 37 ARG cc_start: 0.7426 (mtm110) cc_final: 0.6915 (mtm180) REVERT: H 71 ARG cc_start: 0.8306 (mtt90) cc_final: 0.7775 (mtt-85) REVERT: H 326 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7325 (mm-40) outliers start: 51 outliers final: 27 residues processed: 280 average time/residue: 1.9084 time to fit residues: 598.0593 Evaluate side-chains 287 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 326 GLN Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 326 GLN Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 326 GLN Chi-restraints excluded: chain H residue 401 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 84 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 chunk 242 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 128 optimal weight: 0.4980 chunk 137 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 162 optimal weight: 0.0870 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS C 26 HIS D 26 HIS E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114796 restraints weight = 22057.039| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.21 r_work: 0.3210 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24448 Z= 0.105 Angle : 0.491 6.640 33128 Z= 0.266 Chirality : 0.045 0.146 3688 Planarity : 0.004 0.045 4392 Dihedral : 5.197 56.699 3504 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.02 % Allowed : 14.96 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3136 helix: 1.37 (0.15), residues: 1280 sheet: 0.91 (0.28), residues: 384 loop : -0.96 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 289 HIS 0.007 0.001 HIS G 251 PHE 0.006 0.001 PHE H 357 TYR 0.010 0.001 TYR C 333 ARG 0.003 0.000 ARG D 201 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 1032) hydrogen bonds : angle 3.91572 ( 2832) metal coordination : bond 0.00159 ( 24) SS BOND : bond 0.00699 ( 8) SS BOND : angle 1.29546 ( 16) covalent geometry : bond 0.00212 (24416) covalent geometry : angle 0.49047 (33112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 2.499 Fit side-chains REVERT: B 259 LYS cc_start: 0.8772 (tttt) cc_final: 0.8569 (ttmt) REVERT: E 37 ARG cc_start: 0.7467 (mtm110) cc_final: 0.6977 (mtm180) REVERT: E 71 ARG cc_start: 0.8339 (mtt90) cc_final: 0.7883 (mtt-85) REVERT: F 37 ARG cc_start: 0.7462 (mtm110) cc_final: 0.6976 (mtm180) REVERT: F 71 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7922 (mtt-85) REVERT: G 37 ARG cc_start: 0.7445 (mtm110) cc_final: 0.6968 (mtm180) REVERT: G 71 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7894 (mtt-85) REVERT: H 37 ARG cc_start: 0.7455 (mtm110) cc_final: 0.6964 (mtm180) REVERT: H 71 ARG cc_start: 0.8339 (mtt90) cc_final: 0.7917 (mtt-85) REVERT: H 73 ARG cc_start: 0.8593 (mmt-90) cc_final: 0.8355 (mmt-90) outliers start: 25 outliers final: 11 residues processed: 282 average time/residue: 1.6642 time to fit residues: 529.0862 Evaluate side-chains 271 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 260 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 401 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 262 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 121 optimal weight: 0.0000 chunk 274 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS C 26 HIS D 26 HIS E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111154 restraints weight = 21851.492| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.21 r_work: 0.3156 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24448 Z= 0.167 Angle : 0.576 6.343 33128 Z= 0.317 Chirality : 0.049 0.147 3688 Planarity : 0.005 0.048 4392 Dihedral : 5.373 47.039 3504 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.90 % Allowed : 15.16 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3136 helix: 1.19 (0.14), residues: 1280 sheet: 0.98 (0.28), residues: 384 loop : -1.02 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 289 HIS 0.007 0.001 HIS B 251 PHE 0.010 0.002 PHE G 122 TYR 0.015 0.002 TYR F 244 ARG 0.002 0.000 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.06418 ( 1032) hydrogen bonds : angle 4.10891 ( 2832) metal coordination : bond 0.00359 ( 24) SS BOND : bond 0.00916 ( 8) SS BOND : angle 1.58461 ( 16) covalent geometry : bond 0.00367 (24416) covalent geometry : angle 0.57522 (33112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 263 time to evaluate : 2.753 Fit side-chains REVERT: A 391 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: B 259 LYS cc_start: 0.8774 (tttt) cc_final: 0.8561 (ttmt) REVERT: E 37 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7043 (mtm180) REVERT: E 71 ARG cc_start: 0.8379 (mtt90) cc_final: 0.7881 (mtt-85) REVERT: F 37 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7030 (mtm180) REVERT: F 71 ARG cc_start: 0.8377 (mtt90) cc_final: 0.7912 (mtt-85) REVERT: G 37 ARG cc_start: 0.7501 (mtm110) cc_final: 0.7025 (mtm180) REVERT: G 71 ARG cc_start: 0.8379 (mtt90) cc_final: 0.7917 (mtt-85) REVERT: H 37 ARG cc_start: 0.7516 (mtm110) cc_final: 0.7037 (mtm180) REVERT: H 71 ARG cc_start: 0.8368 (mtt90) cc_final: 0.7898 (mtt-85) outliers start: 22 outliers final: 19 residues processed: 274 average time/residue: 1.7468 time to fit residues: 535.6644 Evaluate side-chains 275 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 401 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 115 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 263 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 299 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 247 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS C 26 HIS D 26 HIS E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112579 restraints weight = 21890.620| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.23 r_work: 0.3174 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24448 Z= 0.135 Angle : 0.536 6.922 33128 Z= 0.293 Chirality : 0.047 0.146 3688 Planarity : 0.004 0.046 4392 Dihedral : 5.199 50.185 3504 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.70 % Allowed : 15.41 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3136 helix: 1.26 (0.14), residues: 1280 sheet: 0.94 (0.28), residues: 384 loop : -0.99 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 289 HIS 0.007 0.001 HIS G 251 PHE 0.007 0.002 PHE A 229 TYR 0.013 0.002 TYR G 244 ARG 0.002 0.000 ARG B 201 Details of bonding type rmsd hydrogen bonds : bond 0.05575 ( 1032) hydrogen bonds : angle 4.01787 ( 2832) metal coordination : bond 0.00280 ( 24) SS BOND : bond 0.00824 ( 8) SS BOND : angle 1.49002 ( 16) covalent geometry : bond 0.00287 (24416) covalent geometry : angle 0.53506 (33112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19756.69 seconds wall clock time: 344 minutes 57.31 seconds (20697.31 seconds total)