Starting phenix.real_space_refine on Fri May 23 06:37:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yag_39098/05_2025/8yag_39098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yag_39098/05_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_39098/05_2025/8yag_39098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yag_39098/05_2025/8yag_39098.map" model { file = "/net/cci-nas-00/data/ceres_data/8yag_39098/05_2025/8yag_39098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yag_39098/05_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.19, per 1000 atoms: 0.59 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: 6.27 Conformation dependent library (CDL) restraints added in 3.4 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: 3.12 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: 7.90 Time building geometry restraints manager: 7.09 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: 0.20 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 56.990 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.110 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.370 ------------------------------------------------------------------------------- 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 : 2.964 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: 1.8197 time to fit residues: 825.9954 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 : 2.550 ------------------------------------------------------------------------------- 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 : 2.842 Fit side-chains REVERT: A 259 LYS cc_start: 0.8694 (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: 0.8695 (tttt) cc_final: 0.8441 (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: 0.5817 (mm-30) REVERT: D 222 LYS cc_start: 0.8273 (tttm) cc_final: 0.8072 (tttm) REVERT: D 259 LYS cc_start: 0.8692 (tttt) cc_final: 0.8444 (ttmt) REVERT: E 71 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7776 (mtt-85) REVERT: E 391 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: F 71 ARG cc_start: 0.8288 (mtt90) cc_final: 0.7818 (mtt-85) REVERT: F 278 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: F 362 GLU cc_start: 0.7943 (tt0) cc_final: 0.7737 (mt-10) REVERT: F 391 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: G 71 ARG cc_start: 0.8283 (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: 0.8281 (mtt90) cc_final: 0.7813 (mtt-85) REVERT: H 278 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7458 (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: 1.6581 time to fit residues: 596.4824 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 : 2.580 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113088 restraints weight = 21915.785| |-----------------------------------------------------------------------------| 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 0.00332 ( 24) SS BOND : bond 0.00903 ( 8) SS BOND : angle 1.27633 ( 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 : 2.451 Fit side-chains REVERT: A 259 LYS cc_start: 0.8729 (tttt) cc_final: 0.8523 (ttmt) REVERT: A 312 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5935 (mm-30) REVERT: B 259 LYS cc_start: 0.8759 (tttt) cc_final: 0.8555 (ttmt) REVERT: B 312 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5900 (mm-30) REVERT: C 259 LYS cc_start: 0.8747 (tttt) cc_final: 0.8537 (ttmt) REVERT: C 312 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5919 (mm-30) REVERT: D 312 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5942 (mm-30) REVERT: E 37 ARG cc_start: 0.7496 (mtm110) cc_final: 0.7009 (mtm180) REVERT: E 71 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7906 (mtt-85) REVERT: E 326 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7278 (mm-40) REVERT: F 37 ARG cc_start: 0.7481 (mtm110) cc_final: 0.6992 (mtm180) REVERT: F 71 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7915 (mtt-85) REVERT: F 73 ARG cc_start: 0.8576 (mmt-90) cc_final: 0.8293 (mmt-90) REVERT: F 326 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7287 (mm-40) REVERT: G 37 ARG cc_start: 0.7472 (mtm110) cc_final: 0.6990 (mtm180) REVERT: G 71 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7907 (mtt-85) REVERT: G 326 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7267 (mm-40) REVERT: H 37 ARG cc_start: 0.7488 (mtm110) cc_final: 0.6997 (mtm180) REVERT: H 71 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7907 (mtt-85) REVERT: H 73 ARG cc_start: 0.8570 (mmt-90) cc_final: 0.8287 (mmt-90) REVERT: H 326 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7255 (mm-40) outliers start: 56 outliers final: 14 residues processed: 299 average time/residue: 1.7362 time to fit residues: 581.3041 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 : 2.595 ------------------------------------------------------------------------------- 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: 0.0980 chunk 70 optimal weight: 5.9990 overall best weight: 2.5642 ------------------------------------------------------------------------------- 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 H 26 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111105 restraints weight = 21653.607| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.24 r_work: 0.3159 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24448 Z= 0.168 Angle : 0.573 5.572 33128 Z= 0.318 Chirality : 0.049 0.144 3688 Planarity : 0.005 0.046 4392 Dihedral : 6.520 59.797 3504 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.17 % Allowed : 13.65 % Favored : 84.18 % 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: 0.19 (0.14), residues: 3136 helix: 1.11 (0.14), residues: 1280 sheet: 1.66 (0.30), residues: 304 loop : -1.06 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 289 HIS 0.007 0.001 HIS F 251 PHE 0.011 0.002 PHE G 122 TYR 0.016 0.002 TYR E 244 ARG 0.002 0.000 ARG B 199 Details of bonding type rmsd hydrogen bonds : bond 0.06503 ( 1032) hydrogen bonds : angle 4.17322 ( 2832) metal coordination : bond 0.00366 ( 24) SS BOND : bond 0.00990 ( 8) SS BOND : angle 1.30909 ( 16) covalent geometry : bond 0.00369 (24416) covalent geometry : angle 0.57205 (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 317 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 2.500 Fit side-chains REVERT: A 259 LYS cc_start: 0.8709 (tttt) cc_final: 0.8456 (ttmt) REVERT: A 312 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5863 (mm-30) REVERT: B 259 LYS cc_start: 0.8689 (tttt) cc_final: 0.8436 (ttmt) REVERT: B 312 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5832 (mm-30) REVERT: C 259 LYS cc_start: 0.8713 (tttt) cc_final: 0.8455 (ttmt) REVERT: C 312 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5857 (mm-30) REVERT: D 312 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5871 (mm-30) REVERT: E 37 ARG cc_start: 0.7443 (mtm110) cc_final: 0.6975 (mtm180) REVERT: E 71 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7829 (mtt-85) REVERT: E 131 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7831 (mm-30) REVERT: E 326 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7207 (mm-40) REVERT: F 37 ARG cc_start: 0.7436 (mtm110) cc_final: 0.6968 (mtm180) REVERT: F 71 ARG cc_start: 0.8329 (mtt90) cc_final: 0.7834 (mtt-85) REVERT: F 131 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: G 37 ARG cc_start: 0.7422 (mtm110) cc_final: 0.6961 (mtm180) REVERT: G 71 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7828 (mtt-85) REVERT: G 131 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: G 326 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7198 (mm-40) REVERT: H 37 ARG cc_start: 0.7448 (mtm110) cc_final: 0.6978 (mtm180) REVERT: H 71 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7822 (mtt-85) REVERT: H 131 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7829 (mm-30) outliers start: 53 outliers final: 19 residues processed: 293 average time/residue: 1.6523 time to fit residues: 542.0931 Evaluate side-chains 289 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 2.607 ------------------------------------------------------------------------------- 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 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 104 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 131 GLU 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 104 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 131 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 131 GLU Chi-restraints excluded: chain G residue 278 GLU 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 124 SER Chi-restraints excluded: chain H residue 131 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: 10.0000 chunk 236 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 G 251 HIS H 26 HIS H 251 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107947 restraints weight = 21626.113| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.26 r_work: 0.3114 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24448 Z= 0.274 Angle : 0.708 6.765 33128 Z= 0.398 Chirality : 0.055 0.175 3688 Planarity : 0.006 0.061 4392 Dihedral : 6.783 84.695 3504 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.17 % Allowed : 13.85 % 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: -0.17 (0.14), residues: 3136 helix: 0.74 (0.14), residues: 1280 sheet: 1.13 (0.30), residues: 336 loop : -1.16 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 289 HIS 0.011 0.002 HIS G 251 PHE 0.016 0.003 PHE F 122 TYR 0.020 0.003 TYR F 244 ARG 0.004 0.001 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.08503 ( 1032) hydrogen bonds : angle 4.44117 ( 2832) metal coordination : bond 0.00543 ( 24) SS BOND : bond 0.01323 ( 8) SS BOND : angle 1.82788 ( 16) covalent geometry : bond 0.00632 (24416) covalent geometry : angle 0.70696 (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 299 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 2.482 Fit side-chains REVERT: A 259 LYS cc_start: 0.8597 (tttt) cc_final: 0.8354 (ttmt) REVERT: B 259 LYS cc_start: 0.8594 (tttt) cc_final: 0.8349 (ttmt) REVERT: C 259 LYS cc_start: 0.8608 (tttt) cc_final: 0.8364 (ttmt) REVERT: E 37 ARG cc_start: 0.7452 (mtm110) cc_final: 0.6937 (mtm180) REVERT: E 50 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6484 (mmp-170) REVERT: E 71 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7768 (mtt-85) REVERT: E 307 ASP cc_start: 0.6675 (OUTLIER) cc_final: 0.6463 (t70) REVERT: F 37 ARG cc_start: 0.7446 (mtm110) cc_final: 0.6927 (mtm180) REVERT: F 71 ARG cc_start: 0.8295 (mtt90) cc_final: 0.7767 (mtt-85) REVERT: F 307 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6465 (t70) REVERT: G 37 ARG cc_start: 0.7445 (mtm110) cc_final: 0.6934 (mtm180) REVERT: G 50 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6479 (mmp-170) REVERT: G 71 ARG cc_start: 0.8296 (mtt90) cc_final: 0.7771 (mtt-85) REVERT: G 307 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6458 (t70) REVERT: H 37 ARG cc_start: 0.7438 (mtm110) cc_final: 0.6914 (mtm180) REVERT: H 50 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6450 (mmp-170) REVERT: H 71 ARG cc_start: 0.8288 (mtt90) cc_final: 0.7759 (mtt-85) REVERT: H 307 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6469 (t70) outliers start: 53 outliers final: 25 residues processed: 275 average time/residue: 1.6707 time to fit residues: 513.7238 Evaluate side-chains 265 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain E residue 50 ARG 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 307 ASP Chi-restraints excluded: chain E residue 380 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 307 ASP Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain G residue 50 ARG 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 307 ASP Chi-restraints excluded: chain G residue 380 GLU Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 50 ARG 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 307 ASP Chi-restraints excluded: chain H residue 380 GLU Chi-restraints excluded: chain H residue 401 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 95 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.138510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111052 restraints weight = 21654.186| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.23 r_work: 0.3154 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24448 Z= 0.161 Angle : 0.568 5.572 33128 Z= 0.315 Chirality : 0.048 0.149 3688 Planarity : 0.005 0.050 4392 Dihedral : 5.810 58.174 3504 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.89 % Allowed : 14.14 % 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: 0.02 (0.14), residues: 3136 helix: 1.00 (0.14), residues: 1280 sheet: 1.46 (0.32), residues: 304 loop : -1.16 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 289 HIS 0.007 0.001 HIS D 251 PHE 0.010 0.002 PHE C 229 TYR 0.015 0.002 TYR F 244 ARG 0.002 0.000 ARG C 199 Details of bonding type rmsd hydrogen bonds : bond 0.06295 ( 1032) hydrogen bonds : angle 4.17205 ( 2832) metal coordination : bond 0.00322 ( 24) SS BOND : bond 0.00950 ( 8) SS BOND : angle 1.59316 ( 16) covalent geometry : bond 0.00351 (24416) covalent geometry : angle 0.56686 (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 308 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 262 time to evaluate : 2.512 Fit side-chains REVERT: A 115 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: A 259 LYS cc_start: 0.8736 (tttt) cc_final: 0.8491 (ttmt) REVERT: B 115 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: B 259 LYS cc_start: 0.8723 (tttt) cc_final: 0.8480 (ttmt) REVERT: C 115 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: C 259 LYS cc_start: 0.8735 (tttt) cc_final: 0.8489 (ttmt) REVERT: D 115 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: E 37 ARG cc_start: 0.7482 (mtm110) cc_final: 0.7001 (mtm180) REVERT: E 71 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7877 (mtt-85) REVERT: E 326 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7387 (mm-40) REVERT: F 37 ARG cc_start: 0.7473 (mtm110) cc_final: 0.6989 (mtm180) REVERT: F 71 ARG cc_start: 0.8360 (mtt90) cc_final: 0.7840 (mtt-85) REVERT: G 37 ARG cc_start: 0.7470 (mtm110) cc_final: 0.6992 (mtm180) REVERT: G 71 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7881 (mtt-85) REVERT: G 326 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7374 (mm-40) REVERT: H 37 ARG cc_start: 0.7483 (mtm110) cc_final: 0.6999 (mtm180) REVERT: H 71 ARG cc_start: 0.8352 (mtt90) cc_final: 0.7834 (mtt-85) outliers start: 46 outliers final: 12 residues processed: 284 average time/residue: 1.7005 time to fit residues: 543.0761 Evaluate side-chains 276 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 258 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 326 GLN Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 104 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 223 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.137884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110083 restraints weight = 21799.072| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.26 r_work: 0.3142 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24448 Z= 0.178 Angle : 0.591 6.024 33128 Z= 0.329 Chirality : 0.049 0.149 3688 Planarity : 0.005 0.050 4392 Dihedral : 5.780 47.783 3504 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.48 % Allowed : 14.67 % Favored : 83.85 % 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: 0.02 (0.14), residues: 3136 helix: 0.98 (0.14), residues: 1280 sheet: 1.46 (0.32), residues: 304 loop : -1.14 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 289 HIS 0.007 0.001 HIS B 251 PHE 0.010 0.002 PHE H 122 TYR 0.016 0.002 TYR E 244 ARG 0.002 0.000 ARG F 298 Details of bonding type rmsd hydrogen bonds : bond 0.06741 ( 1032) hydrogen bonds : angle 4.21032 ( 2832) metal coordination : bond 0.00379 ( 24) SS BOND : bond 0.00995 ( 8) SS BOND : angle 1.64766 ( 16) covalent geometry : bond 0.00394 (24416) covalent geometry : angle 0.59019 (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 294 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 2.530 Fit side-chains REVERT: A 259 LYS cc_start: 0.8676 (tttt) cc_final: 0.8399 (ttmt) REVERT: B 259 LYS cc_start: 0.8687 (tttt) cc_final: 0.8411 (ttmt) REVERT: C 259 LYS cc_start: 0.8680 (tttt) cc_final: 0.8405 (ttmt) REVERT: E 37 ARG cc_start: 0.7429 (mtm110) cc_final: 0.6925 (mtm180) REVERT: E 71 ARG cc_start: 0.8326 (mtt90) cc_final: 0.7808 (mtt-85) REVERT: E 326 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7335 (mm-40) REVERT: F 37 ARG cc_start: 0.7422 (mtm110) cc_final: 0.6915 (mtm180) REVERT: F 71 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7810 (mtt-85) REVERT: F 326 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7300 (mm-40) REVERT: G 37 ARG cc_start: 0.7417 (mtm110) cc_final: 0.6918 (mtm180) REVERT: G 71 ARG cc_start: 0.8327 (mtt90) cc_final: 0.7811 (mtt-85) REVERT: G 326 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7329 (mm-40) REVERT: H 37 ARG cc_start: 0.7429 (mtm110) cc_final: 0.6924 (mtm180) REVERT: H 71 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7801 (mtt-85) REVERT: H 326 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7299 (mm-40) outliers start: 36 outliers final: 20 residues processed: 274 average time/residue: 1.7332 time to fit residues: 531.4574 Evaluate side-chains 278 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain D residue 104 ILE 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 326 GLN Chi-restraints excluded: chain F residue 401 MET 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 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: 6.9990 chunk 79 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 274 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.135677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107626 restraints weight = 21475.148| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.26 r_work: 0.3108 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 24448 Z= 0.283 Angle : 0.720 6.874 33128 Z= 0.405 Chirality : 0.056 0.178 3688 Planarity : 0.006 0.055 4392 Dihedral : 6.150 52.942 3504 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.56 % Allowed : 14.84 % Favored : 83.61 % 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 (0.14), residues: 3136 helix: 0.68 (0.14), residues: 1280 sheet: 1.17 (0.30), residues: 344 loop : -1.23 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP H 289 HIS 0.010 0.002 HIS B 251 PHE 0.016 0.003 PHE F 122 TYR 0.019 0.003 TYR F 244 ARG 0.004 0.001 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.08641 ( 1032) hydrogen bonds : angle 4.44876 ( 2832) metal coordination : bond 0.00544 ( 24) SS BOND : bond 0.01324 ( 8) SS BOND : angle 2.06857 ( 16) covalent geometry : bond 0.00652 (24416) covalent geometry : angle 0.71915 (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 286 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 2.937 Fit side-chains REVERT: A 115 GLU cc_start: 0.8642 (tt0) cc_final: 0.8423 (tt0) REVERT: A 259 LYS cc_start: 0.8597 (tttt) cc_final: 0.8353 (ttmt) REVERT: A 312 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5789 (mm-30) REVERT: B 115 GLU cc_start: 0.8659 (tt0) cc_final: 0.8444 (tt0) REVERT: B 259 LYS cc_start: 0.8591 (tttt) cc_final: 0.8344 (ttmt) REVERT: B 312 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5789 (mm-30) REVERT: C 115 GLU cc_start: 0.8652 (tt0) cc_final: 0.8438 (tt0) REVERT: C 259 LYS cc_start: 0.8601 (tttt) cc_final: 0.8355 (ttmt) REVERT: C 312 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5799 (mm-30) REVERT: D 115 GLU cc_start: 0.8657 (tt0) cc_final: 0.8444 (tt0) REVERT: D 312 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5788 (mm-30) REVERT: E 37 ARG cc_start: 0.7502 (mtm110) cc_final: 0.6993 (mtm180) REVERT: E 71 ARG cc_start: 0.8304 (mtt90) cc_final: 0.7792 (mtt-85) REVERT: F 37 ARG cc_start: 0.7490 (mtm110) cc_final: 0.6973 (mtm180) REVERT: F 71 ARG cc_start: 0.8304 (mtt90) cc_final: 0.7788 (mtt-85) REVERT: F 326 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7382 (mm-40) REVERT: G 37 ARG cc_start: 0.7477 (mtm110) cc_final: 0.6974 (mtm180) REVERT: G 71 ARG cc_start: 0.8306 (mtt90) cc_final: 0.7795 (mtt-85) REVERT: H 37 ARG cc_start: 0.7490 (mtm110) cc_final: 0.6974 (mtm180) REVERT: H 71 ARG cc_start: 0.8302 (mtt90) cc_final: 0.7786 (mtt-85) REVERT: H 326 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7390 (mm-40) outliers start: 38 outliers final: 21 residues processed: 266 average time/residue: 1.7497 time to fit residues: 520.1308 Evaluate side-chains 268 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 2.603 ------------------------------------------------------------------------------- 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 27 CYS 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 27 CYS Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 326 GLN Chi-restraints excluded: chain F residue 401 MET 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 278 GLU 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 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: 4.9990 chunk 252 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.137959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110215 restraints weight = 21777.635| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.26 r_work: 0.3144 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24448 Z= 0.171 Angle : 0.588 6.052 33128 Z= 0.326 Chirality : 0.049 0.149 3688 Planarity : 0.005 0.055 4392 Dihedral : 5.814 59.980 3504 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.72 % Allowed : 14.55 % Favored : 83.73 % 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: 0.92 (0.14), residues: 1280 sheet: 1.39 (0.32), residues: 304 loop : -1.18 (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 F 251 PHE 0.010 0.002 PHE C 229 TYR 0.016 0.002 TYR F 244 ARG 0.002 0.000 ARG C 199 Details of bonding type rmsd hydrogen bonds : bond 0.06560 ( 1032) hydrogen bonds : angle 4.21243 ( 2832) metal coordination : bond 0.00349 ( 24) SS BOND : bond 0.00972 ( 8) SS BOND : angle 1.70962 ( 16) covalent geometry : bond 0.00376 (24416) covalent geometry : angle 0.58693 (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 313 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 2.726 Fit side-chains REVERT: A 259 LYS cc_start: 0.8674 (tttt) cc_final: 0.8383 (ttmt) REVERT: A 312 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5771 (mm-30) REVERT: B 259 LYS cc_start: 0.8673 (tttt) cc_final: 0.8385 (ttmt) REVERT: B 312 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5769 (mm-30) REVERT: B 391 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: C 259 LYS cc_start: 0.8679 (tttt) cc_final: 0.8388 (ttmt) REVERT: C 312 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5786 (mm-30) REVERT: D 312 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5774 (mm-30) REVERT: E 37 ARG cc_start: 0.7470 (mtm110) cc_final: 0.6945 (mtm180) REVERT: E 71 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7806 (mtt-85) REVERT: F 37 ARG cc_start: 0.7461 (mtm110) cc_final: 0.6933 (mtm180) REVERT: F 71 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7804 (mtt-85) REVERT: G 37 ARG cc_start: 0.7420 (mtm110) cc_final: 0.6901 (mtm180) REVERT: G 71 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7812 (mtt-85) REVERT: H 37 ARG cc_start: 0.7468 (mtm110) cc_final: 0.6942 (mtm180) REVERT: H 71 ARG cc_start: 0.8312 (mtt90) cc_final: 0.7802 (mtt-85) outliers start: 42 outliers final: 22 residues processed: 289 average time/residue: 1.7017 time to fit residues: 553.4287 Evaluate side-chains 285 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 2.528 ------------------------------------------------------------------------------- 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 B residue 391 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 27 CYS 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 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 401 MET 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 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 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: 4.9990 chunk 172 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 252 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 274 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.140730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113576 restraints weight = 22050.285| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.24 r_work: 0.3193 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1780 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= 0.114 Angle : 0.505 5.713 33128 Z= 0.276 Chirality : 0.045 0.149 3688 Planarity : 0.005 0.051 4392 Dihedral : 5.050 45.510 3504 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.82 % Allowed : 15.61 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3136 helix: 1.27 (0.15), residues: 1280 sheet: 1.41 (0.31), residues: 304 loop : -1.05 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 289 HIS 0.013 0.001 HIS F 251 PHE 0.006 0.001 PHE F 357 TYR 0.011 0.001 TYR A 333 ARG 0.002 0.000 ARG D 201 Details of bonding type rmsd hydrogen bonds : bond 0.04971 ( 1032) hydrogen bonds : angle 3.95957 ( 2832) metal coordination : bond 0.00218 ( 24) SS BOND : bond 0.00752 ( 8) SS BOND : angle 1.40152 ( 16) covalent geometry : bond 0.00233 (24416) covalent geometry : angle 0.50403 (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 286 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 2.697 Fit side-chains REVERT: A 259 LYS cc_start: 0.8726 (tttt) cc_final: 0.8493 (ttmt) REVERT: A 312 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5809 (mm-30) REVERT: B 259 LYS cc_start: 0.8715 (tttt) cc_final: 0.8488 (ttmt) REVERT: B 312 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5800 (mm-30) REVERT: C 259 LYS cc_start: 0.8727 (tttt) cc_final: 0.8497 (ttmt) REVERT: C 312 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5821 (mm-30) REVERT: D 312 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5813 (mm-30) REVERT: E 37 ARG cc_start: 0.7420 (mtm110) cc_final: 0.6905 (mtm180) REVERT: E 71 ARG cc_start: 0.8324 (mtt90) cc_final: 0.7832 (mtt-85) REVERT: E 131 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7821 (mm-30) REVERT: F 37 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6886 (mtm180) REVERT: F 71 ARG cc_start: 0.8320 (mtt90) cc_final: 0.7823 (mtt-85) REVERT: F 131 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7813 (mm-30) REVERT: F 302 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6704 (mt-10) REVERT: G 37 ARG cc_start: 0.7394 (mtm110) cc_final: 0.6888 (mtm180) REVERT: G 71 ARG cc_start: 0.8336 (mtt90) cc_final: 0.7848 (mtt-85) REVERT: G 131 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7804 (mm-30) REVERT: G 302 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6727 (mt-10) REVERT: H 37 ARG cc_start: 0.7410 (mtm110) cc_final: 0.6887 (mtm180) REVERT: H 71 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7824 (mtt-85) REVERT: H 131 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7815 (mm-30) REVERT: H 302 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6696 (mt-10) outliers start: 20 outliers final: 8 residues processed: 274 average time/residue: 1.6108 time to fit residues: 495.3251 Evaluate side-chains 273 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 261 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 312 GLU 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 F residue 401 MET 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 115 optimal weight: 0.0050 chunk 131 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 299 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 247 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.136999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109044 restraints weight = 21605.877| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.26 r_work: 0.3129 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24448 Z= 0.217 Angle : 0.638 6.208 33128 Z= 0.356 Chirality : 0.052 0.156 3688 Planarity : 0.006 0.052 4392 Dihedral : 5.602 48.888 3504 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.27 % Allowed : 15.00 % Favored : 83.73 % 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: 0.02 (0.14), residues: 3136 helix: 0.97 (0.14), residues: 1280 sheet: 1.47 (0.32), residues: 304 loop : -1.13 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 289 HIS 0.016 0.002 HIS F 251 PHE 0.013 0.002 PHE F 122 TYR 0.017 0.003 TYR F 244 ARG 0.003 0.001 ARG F 298 Details of bonding type rmsd hydrogen bonds : bond 0.07495 ( 1032) hydrogen bonds : angle 4.26866 ( 2832) metal coordination : bond 0.00440 ( 24) SS BOND : bond 0.01112 ( 8) SS BOND : angle 1.84084 ( 16) covalent geometry : bond 0.00492 (24416) covalent geometry : angle 0.63664 (33112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17899.50 seconds wall clock time: 310 minutes 40.64 seconds (18640.64 seconds total)