Starting phenix.real_space_refine on Fri Sep 19 06:36:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yag_39098/09_2025/8yag_39098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yag_39098/09_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_39098/09_2025/8yag_39098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yag_39098/09_2025/8yag_39098.map" model { file = "/net/cci-nas-00/data/ceres_data/8yag_39098/09_2025/8yag_39098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yag_39098/09_2025/8yag_39098.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.78, per 1000 atoms: 0.24 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: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.01 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: 5.22 Time building geometry restraints manager: 2.38 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.550 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG E 298 TYR 0.011 0.001 TYR B 333 PHE 0.007 0.001 PHE H 122 TRP 0.004 0.001 TRP C 289 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00450 (24416) covalent geometry : angle 0.66630 (33112) SS BOND : bond 0.00626 ( 8) SS BOND : angle 0.81206 ( 16) hydrogen bonds : bond 0.17837 ( 1032) hydrogen bonds : angle 5.20440 ( 2832) metal coordination : bond 0.00304 ( 24) *********************** 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 : 1.011 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: 0.9353 time to fit residues: 422.1353 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 : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.141080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113399 restraints weight = 21599.959| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.25 r_work: 0.3188 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24448 Z= 0.143 Angle : 0.547 5.568 33128 Z= 0.303 Chirality : 0.047 0.144 3688 Planarity : 0.005 0.041 4392 Dihedral : 5.490 56.453 3504 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.38 % Allowed : 13.52 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 3136 helix: 1.21 (0.14), residues: 1280 sheet: 1.23 (0.28), residues: 384 loop : -1.00 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.016 0.002 TYR H 244 PHE 0.009 0.002 PHE G 122 TRP 0.008 0.002 TRP F 289 HIS 0.006 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00306 (24416) covalent geometry : angle 0.54623 (33112) SS BOND : bond 0.00870 ( 8) SS BOND : angle 1.61164 ( 16) hydrogen bonds : bond 0.05946 ( 1032) hydrogen bonds : angle 4.15869 ( 2832) metal coordination : bond 0.00347 ( 24) *********************** 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 362 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 1.113 Fit side-chains REVERT: A 115 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: A 222 LYS cc_start: 0.8241 (tttm) cc_final: 0.8040 (tttm) REVERT: A 259 LYS cc_start: 0.8693 (tttt) cc_final: 0.8453 (ttmt) REVERT: A 312 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5781 (mm-30) REVERT: B 115 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: B 259 LYS cc_start: 0.8695 (tttt) cc_final: 0.8452 (ttmt) REVERT: C 115 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: C 259 LYS cc_start: 0.8692 (tttt) cc_final: 0.8458 (ttmt) REVERT: C 312 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5796 (mm-30) REVERT: D 115 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: D 259 LYS cc_start: 0.8690 (tttt) cc_final: 0.8452 (ttmt) REVERT: E 71 ARG cc_start: 0.8260 (mtt90) cc_final: 0.7759 (mtt-85) REVERT: E 391 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: F 71 ARG cc_start: 0.8272 (mtt90) cc_final: 0.7768 (mtt-85) REVERT: F 278 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: G 71 ARG cc_start: 0.8259 (mtt90) cc_final: 0.7760 (mtt-85) REVERT: H 71 ARG cc_start: 0.8269 (mtt90) cc_final: 0.7766 (mtt-85) REVERT: H 278 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7440 (tt0) outliers start: 58 outliers final: 4 residues processed: 323 average time/residue: 0.7702 time to fit residues: 277.5255 Evaluate side-chains 293 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 280 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 115 GLU 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 G residue 104 ILE Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 278 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 109 optimal weight: 8.9990 chunk 309 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.138264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111019 restraints weight = 21962.834| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.22 r_work: 0.3142 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24448 Z= 0.208 Angle : 0.629 5.891 33128 Z= 0.352 Chirality : 0.051 0.150 3688 Planarity : 0.005 0.055 4392 Dihedral : 6.461 56.425 3504 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.21 % Allowed : 13.69 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.14), residues: 3136 helix: 0.99 (0.14), residues: 1280 sheet: 1.61 (0.31), residues: 304 loop : -1.14 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 73 TYR 0.019 0.003 TYR G 244 PHE 0.013 0.002 PHE F 122 TRP 0.011 0.002 TRP G 289 HIS 0.008 0.002 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00469 (24416) covalent geometry : angle 0.62836 (33112) SS BOND : bond 0.01115 ( 8) SS BOND : angle 1.48770 ( 16) hydrogen bonds : bond 0.07402 ( 1032) hydrogen bonds : angle 4.32109 ( 2832) metal coordination : bond 0.00437 ( 24) *********************** 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 322 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 0.943 Fit side-chains REVERT: A 259 LYS cc_start: 0.8768 (tttt) cc_final: 0.8551 (ttmt) REVERT: A 312 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5903 (mm-30) REVERT: B 312 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5925 (mm-30) REVERT: C 259 LYS cc_start: 0.8763 (tttt) cc_final: 0.8548 (ttmt) REVERT: C 312 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5905 (mm-30) REVERT: D 312 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5927 (mm-30) REVERT: E 37 ARG cc_start: 0.7527 (mtm110) cc_final: 0.7081 (mtm180) REVERT: E 71 ARG cc_start: 0.8357 (mtt90) cc_final: 0.7868 (mtt-85) REVERT: E 225 ASP cc_start: 0.7312 (p0) cc_final: 0.7053 (p0) REVERT: F 37 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7066 (mtm180) REVERT: F 71 ARG cc_start: 0.8359 (mtt90) cc_final: 0.7904 (mtt-85) REVERT: F 225 ASP cc_start: 0.7313 (p0) cc_final: 0.7055 (p0) REVERT: G 37 ARG cc_start: 0.7514 (mtm110) cc_final: 0.7072 (mtm180) REVERT: G 71 ARG cc_start: 0.8355 (mtt90) cc_final: 0.7869 (mtt-85) REVERT: G 225 ASP cc_start: 0.7321 (p0) cc_final: 0.7063 (p0) REVERT: H 37 ARG cc_start: 0.7529 (mtm110) cc_final: 0.7081 (mtm180) REVERT: H 71 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7893 (mtt-85) REVERT: H 225 ASP cc_start: 0.7326 (p0) cc_final: 0.7069 (p0) outliers start: 54 outliers final: 14 residues processed: 290 average time/residue: 0.8184 time to fit residues: 264.9317 Evaluate side-chains 275 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 257 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 401 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 305 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.135293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107178 restraints weight = 21545.445| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.26 r_work: 0.3102 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 24448 Z= 0.322 Angle : 0.770 7.152 33128 Z= 0.433 Chirality : 0.059 0.172 3688 Planarity : 0.007 0.064 4392 Dihedral : 6.726 66.599 3504 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.54 % Allowed : 13.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.14), residues: 3136 helix: 0.59 (0.14), residues: 1280 sheet: 1.08 (0.30), residues: 336 loop : -1.25 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 201 TYR 0.022 0.004 TYR E 244 PHE 0.019 0.003 PHE F 122 TRP 0.014 0.003 TRP E 289 HIS 0.011 0.002 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00751 (24416) covalent geometry : angle 0.76899 (33112) SS BOND : bond 0.01491 ( 8) SS BOND : angle 1.95819 ( 16) hydrogen bonds : bond 0.09190 ( 1032) hydrogen bonds : angle 4.54651 ( 2832) metal coordination : bond 0.00632 ( 24) *********************** 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 312 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 0.800 Fit side-chains REVERT: A 259 LYS cc_start: 0.8611 (tttt) cc_final: 0.8375 (ttmt) REVERT: C 259 LYS cc_start: 0.8629 (tttt) cc_final: 0.8387 (ttmt) REVERT: E 37 ARG cc_start: 0.7464 (mtm110) cc_final: 0.6942 (mtm180) REVERT: E 50 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6539 (mmp-170) REVERT: E 71 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7763 (mtt-85) REVERT: E 225 ASP cc_start: 0.7308 (p0) cc_final: 0.7067 (p0) REVERT: F 37 ARG cc_start: 0.7473 (mtm110) cc_final: 0.6953 (mtm180) REVERT: F 50 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7023 (mtp180) REVERT: F 71 ARG cc_start: 0.8292 (mtt90) cc_final: 0.7764 (mtt-85) REVERT: F 225 ASP cc_start: 0.7328 (p0) cc_final: 0.7096 (p0) REVERT: G 37 ARG cc_start: 0.7463 (mtm110) cc_final: 0.6946 (mtm180) REVERT: G 50 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.6511 (mmp-170) REVERT: G 71 ARG cc_start: 0.8288 (mtt90) cc_final: 0.7764 (mtt-85) REVERT: G 225 ASP cc_start: 0.7309 (p0) cc_final: 0.7067 (p0) REVERT: H 37 ARG cc_start: 0.7473 (mtm110) cc_final: 0.6950 (mtm180) REVERT: H 50 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7013 (mtp180) REVERT: H 71 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7756 (mtt-85) REVERT: H 225 ASP cc_start: 0.7340 (p0) cc_final: 0.7087 (p0) outliers start: 62 outliers final: 21 residues processed: 288 average time/residue: 0.8047 time to fit residues: 258.1181 Evaluate side-chains 258 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 401 MET Chi-restraints excluded: chain F residue 50 ARG 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 327 ASP 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 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 401 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 21 optimal weight: 1.9990 chunk 240 optimal weight: 0.0040 chunk 226 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 287 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.141051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113954 restraints weight = 21878.814| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.24 r_work: 0.3197 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 24448 Z= 0.111 Angle : 0.501 5.493 33128 Z= 0.274 Chirality : 0.045 0.148 3688 Planarity : 0.004 0.046 4392 Dihedral : 5.510 51.785 3504 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.39 % Allowed : 13.98 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.15), residues: 3136 helix: 1.16 (0.15), residues: 1280 sheet: 1.49 (0.31), residues: 304 loop : -1.12 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 34 TYR 0.011 0.001 TYR E 244 PHE 0.006 0.001 PHE F 229 TRP 0.007 0.001 TRP F 289 HIS 0.007 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00226 (24416) covalent geometry : angle 0.50028 (33112) SS BOND : bond 0.00801 ( 8) SS BOND : angle 1.33327 ( 16) hydrogen bonds : bond 0.04890 ( 1032) hydrogen bonds : angle 4.01615 ( 2832) metal coordination : bond 0.00163 ( 24) *********************** 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 297 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.907 Fit side-chains REVERT: A 259 LYS cc_start: 0.8698 (tttt) cc_final: 0.8463 (ttmt) REVERT: C 259 LYS cc_start: 0.8737 (tttt) cc_final: 0.8499 (ttmt) REVERT: E 37 ARG cc_start: 0.7453 (mtm110) cc_final: 0.6974 (mtm180) REVERT: E 71 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7872 (mtt-85) REVERT: E 225 ASP cc_start: 0.7181 (p0) cc_final: 0.6930 (p0) REVERT: F 37 ARG cc_start: 0.7447 (mtm110) cc_final: 0.6966 (mtm180) REVERT: F 71 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7865 (mtt-85) REVERT: F 225 ASP cc_start: 0.7182 (p0) cc_final: 0.6914 (p0) REVERT: G 37 ARG cc_start: 0.7442 (mtm110) cc_final: 0.6965 (mtm180) REVERT: G 71 ARG cc_start: 0.8332 (mtt90) cc_final: 0.7875 (mtt-85) REVERT: G 225 ASP cc_start: 0.7193 (p0) cc_final: 0.6941 (p0) REVERT: H 37 ARG cc_start: 0.7444 (mtm110) cc_final: 0.6959 (mtm180) REVERT: H 71 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7861 (mtt-85) REVERT: H 225 ASP cc_start: 0.7193 (p0) cc_final: 0.6942 (p0) outliers start: 34 outliers final: 9 residues processed: 282 average time/residue: 0.8319 time to fit residues: 261.7330 Evaluate side-chains 265 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 256 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain F residue 401 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 142 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 294 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 237 optimal weight: 0.0050 chunk 56 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.138134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110373 restraints weight = 21808.026| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.26 r_work: 0.3147 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1815 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 : 0.580 5.696 33128 Z= 0.321 Chirality : 0.049 0.148 3688 Planarity : 0.005 0.047 4392 Dihedral : 5.694 48.516 3504 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.84 % Allowed : 13.61 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 3136 helix: 1.07 (0.14), residues: 1280 sheet: 1.50 (0.31), residues: 304 loop : -1.12 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 320 TYR 0.015 0.002 TYR E 244 PHE 0.010 0.002 PHE H 122 TRP 0.009 0.002 TRP E 289 HIS 0.007 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00377 (24416) covalent geometry : angle 0.57867 (33112) SS BOND : bond 0.00967 ( 8) SS BOND : angle 1.60173 ( 16) hydrogen bonds : bond 0.06556 ( 1032) hydrogen bonds : angle 4.16053 ( 2832) metal coordination : bond 0.00357 ( 24) *********************** 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 304 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.900 Fit side-chains REVERT: A 259 LYS cc_start: 0.8681 (tttt) cc_final: 0.8407 (ttmt) REVERT: A 312 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5834 (mm-30) REVERT: B 312 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5822 (mm-30) REVERT: C 259 LYS cc_start: 0.8691 (tttt) cc_final: 0.8428 (ttmt) REVERT: C 312 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5851 (mm-30) REVERT: D 312 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.5834 (mm-30) REVERT: E 37 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6906 (mtm180) REVERT: E 71 ARG cc_start: 0.8321 (mtt90) cc_final: 0.7819 (mtt-85) REVERT: E 225 ASP cc_start: 0.7257 (p0) cc_final: 0.6994 (p0) REVERT: E 326 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7379 (mm-40) REVERT: F 37 ARG cc_start: 0.7409 (mtm110) cc_final: 0.6906 (mtm180) REVERT: F 71 ARG cc_start: 0.8329 (mtt90) cc_final: 0.7829 (mtt-85) REVERT: F 225 ASP cc_start: 0.7278 (p0) cc_final: 0.7024 (p0) REVERT: F 326 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7395 (mm-40) REVERT: G 37 ARG cc_start: 0.7398 (mtm110) cc_final: 0.6899 (mtm180) REVERT: G 71 ARG cc_start: 0.8325 (mtt90) cc_final: 0.7823 (mtt-85) REVERT: G 225 ASP cc_start: 0.7264 (p0) cc_final: 0.7002 (p0) REVERT: G 326 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7370 (mm-40) REVERT: H 37 ARG cc_start: 0.7416 (mtm110) cc_final: 0.6914 (mtm180) REVERT: H 71 ARG cc_start: 0.8321 (mtt90) cc_final: 0.7821 (mtt-85) REVERT: H 225 ASP cc_start: 0.7288 (p0) cc_final: 0.7033 (p0) REVERT: H 326 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7392 (mm-40) outliers start: 45 outliers final: 20 residues processed: 280 average time/residue: 0.7670 time to fit residues: 240.6845 Evaluate side-chains 287 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 27 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 259 LYS 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 F residue 124 SER Chi-restraints excluded: chain F residue 326 GLN Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 326 GLN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 245 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 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 = 0.3568 r_free = 0.3568 target = 0.136641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108762 restraints weight = 21617.997| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.26 r_work: 0.3124 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24448 Z= 0.227 Angle : 0.659 8.514 33128 Z= 0.366 Chirality : 0.052 0.161 3688 Planarity : 0.006 0.055 4392 Dihedral : 5.965 55.384 3504 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.48 % Allowed : 14.22 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.14), residues: 3136 helix: 0.87 (0.14), residues: 1280 sheet: 1.47 (0.32), residues: 304 loop : -1.18 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 298 TYR 0.017 0.003 TYR F 244 PHE 0.013 0.003 PHE H 122 TRP 0.011 0.002 TRP E 289 HIS 0.015 0.002 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00514 (24416) covalent geometry : angle 0.65821 (33112) SS BOND : bond 0.01152 ( 8) SS BOND : angle 1.83744 ( 16) hydrogen bonds : bond 0.07713 ( 1032) hydrogen bonds : angle 4.31886 ( 2832) metal coordination : bond 0.00468 ( 24) *********************** 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 296 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 1.113 Fit side-chains REVERT: A 259 LYS cc_start: 0.8631 (tttt) cc_final: 0.8368 (ttmt) REVERT: C 259 LYS cc_start: 0.8648 (tttt) cc_final: 0.8383 (ttmt) REVERT: E 37 ARG cc_start: 0.7423 (mtm110) cc_final: 0.6902 (mtm180) REVERT: E 71 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7814 (mtt-85) REVERT: E 225 ASP cc_start: 0.7241 (p0) cc_final: 0.6977 (p0) REVERT: F 37 ARG cc_start: 0.7422 (mtm110) cc_final: 0.6901 (mtm180) REVERT: F 71 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7808 (mtt-85) REVERT: F 225 ASP cc_start: 0.7206 (p0) cc_final: 0.6947 (p0) REVERT: F 326 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7346 (mm-40) REVERT: G 37 ARG cc_start: 0.7403 (mtm110) cc_final: 0.6885 (mtm180) REVERT: G 71 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7814 (mtt-85) REVERT: G 225 ASP cc_start: 0.7247 (p0) cc_final: 0.6982 (p0) REVERT: H 37 ARG cc_start: 0.7435 (mtm110) cc_final: 0.6915 (mtm180) REVERT: H 71 ARG cc_start: 0.8303 (mtt90) cc_final: 0.7802 (mtt-85) REVERT: H 225 ASP cc_start: 0.7226 (p0) cc_final: 0.6967 (p0) REVERT: H 326 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7348 (mm-40) outliers start: 36 outliers final: 22 residues processed: 280 average time/residue: 0.8828 time to fit residues: 275.4322 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 : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain 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 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 184 optimal weight: 0.1980 chunk 300 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 101 optimal weight: 0.4980 chunk 250 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.139522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112204 restraints weight = 21823.941| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.23 r_work: 0.3170 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24448 Z= 0.134 Angle : 0.539 6.985 33128 Z= 0.295 Chirality : 0.047 0.148 3688 Planarity : 0.005 0.048 4392 Dihedral : 5.373 46.773 3504 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.48 % Allowed : 14.22 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.15), residues: 3136 helix: 1.15 (0.14), residues: 1280 sheet: 1.47 (0.32), residues: 304 loop : -1.11 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 201 TYR 0.013 0.002 TYR E 244 PHE 0.007 0.002 PHE D 229 TRP 0.008 0.001 TRP F 289 HIS 0.013 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00284 (24416) covalent geometry : angle 0.53763 (33112) SS BOND : bond 0.00843 ( 8) SS BOND : angle 1.49723 ( 16) hydrogen bonds : bond 0.05582 ( 1032) hydrogen bonds : angle 4.06362 ( 2832) metal coordination : bond 0.00248 ( 24) *********************** 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 308 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 1.002 Fit side-chains REVERT: A 259 LYS cc_start: 0.8708 (tttt) cc_final: 0.8474 (ttmt) REVERT: C 259 LYS cc_start: 0.8710 (tttt) cc_final: 0.8479 (ttmt) REVERT: E 37 ARG cc_start: 0.7432 (mtm110) cc_final: 0.6927 (mtm180) REVERT: E 71 ARG cc_start: 0.8336 (mtt90) cc_final: 0.7844 (mtt-85) REVERT: E 225 ASP cc_start: 0.7239 (p0) cc_final: 0.6986 (p0) REVERT: F 37 ARG cc_start: 0.7427 (mtm110) cc_final: 0.6920 (mtm180) REVERT: F 71 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7855 (mtt-85) REVERT: F 225 ASP cc_start: 0.7264 (p0) cc_final: 0.7013 (p0) REVERT: G 37 ARG cc_start: 0.7417 (mtm110) cc_final: 0.6913 (mtm180) REVERT: G 71 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7853 (mtt-85) REVERT: G 225 ASP cc_start: 0.7244 (p0) cc_final: 0.6990 (p0) REVERT: H 37 ARG cc_start: 0.7435 (mtm110) cc_final: 0.6926 (mtm180) REVERT: H 71 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7854 (mtt-85) REVERT: H 225 ASP cc_start: 0.7252 (p0) cc_final: 0.7004 (p0) REVERT: H 326 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7409 (mm-40) outliers start: 36 outliers final: 24 residues processed: 293 average time/residue: 0.8287 time to fit residues: 270.9833 Evaluate side-chains 288 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 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 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 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 151 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 217 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 81 optimal weight: 0.0000 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.143054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116273 restraints weight = 22244.176| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.23 r_work: 0.3231 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1822 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= 0.094 Angle : 0.473 6.798 33128 Z= 0.255 Chirality : 0.044 0.146 3688 Planarity : 0.004 0.044 4392 Dihedral : 4.753 44.547 3504 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.82 % Allowed : 15.25 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3136 helix: 1.26 (0.14), residues: 1328 sheet: 0.63 (0.29), residues: 344 loop : -0.99 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 201 TYR 0.009 0.001 TYR A 333 PHE 0.005 0.001 PHE C 299 TRP 0.006 0.001 TRP H 289 HIS 0.011 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00186 (24416) covalent geometry : angle 0.47269 (33112) SS BOND : bond 0.00652 ( 8) SS BOND : angle 1.23486 ( 16) hydrogen bonds : bond 0.04095 ( 1032) hydrogen bonds : angle 3.81184 ( 2832) metal coordination : bond 0.00109 ( 24) *********************** 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 303 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 283 time to evaluate : 0.950 Fit side-chains REVERT: A 259 LYS cc_start: 0.8735 (tttt) cc_final: 0.8495 (ttmt) REVERT: A 312 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5550 (tp30) REVERT: C 259 LYS cc_start: 0.8736 (tttt) cc_final: 0.8498 (ttmt) REVERT: E 37 ARG cc_start: 0.7372 (mtm110) cc_final: 0.6858 (mtm180) REVERT: E 47 ARG cc_start: 0.8361 (mtt-85) cc_final: 0.8078 (mtt90) REVERT: E 50 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7648 (mtp180) REVERT: E 71 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7830 (mtt-85) REVERT: E 131 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7861 (mm-30) REVERT: E 225 ASP cc_start: 0.7152 (p0) cc_final: 0.6885 (p0) REVERT: F 37 ARG cc_start: 0.7370 (mtm110) cc_final: 0.6858 (mtm180) REVERT: F 71 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7839 (mtt-85) REVERT: F 131 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7875 (mm-30) REVERT: F 225 ASP cc_start: 0.7146 (p0) cc_final: 0.6894 (p0) REVERT: G 37 ARG cc_start: 0.7353 (mtm110) cc_final: 0.6845 (mtm180) REVERT: G 50 ARG cc_start: 0.7876 (mtp180) cc_final: 0.7651 (mtp180) REVERT: G 71 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7834 (mtt-85) REVERT: G 131 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7866 (mm-30) REVERT: G 225 ASP cc_start: 0.7156 (p0) cc_final: 0.6886 (p0) REVERT: H 37 ARG cc_start: 0.7363 (mtm110) cc_final: 0.6845 (mtm180) REVERT: H 71 ARG cc_start: 0.8303 (mtt90) cc_final: 0.7836 (mtt-85) REVERT: H 131 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7861 (mm-30) REVERT: H 225 ASP cc_start: 0.7158 (p0) cc_final: 0.6906 (p0) outliers start: 20 outliers final: 11 residues processed: 294 average time/residue: 0.7879 time to fit residues: 259.4591 Evaluate side-chains 282 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 271 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 27 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 208 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 chunk 210 optimal weight: 0.7980 chunk 203 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 308 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.139969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112493 restraints weight = 21913.202| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.24 r_work: 0.3180 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24448 Z= 0.131 Angle : 0.527 6.530 33128 Z= 0.288 Chirality : 0.046 0.146 3688 Planarity : 0.004 0.043 4392 Dihedral : 4.934 37.094 3504 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.49 % Allowed : 15.45 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3136 helix: 1.38 (0.14), residues: 1280 sheet: 0.91 (0.28), residues: 384 loop : -0.95 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 201 TYR 0.013 0.002 TYR E 244 PHE 0.007 0.001 PHE A 229 TRP 0.008 0.002 TRP H 289 HIS 0.013 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00277 (24416) covalent geometry : angle 0.52652 (33112) SS BOND : bond 0.00795 ( 8) SS BOND : angle 1.45100 ( 16) hydrogen bonds : bond 0.05446 ( 1032) hydrogen bonds : angle 3.95319 ( 2832) metal coordination : bond 0.00259 ( 24) ********************** 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 290 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 278 time to evaluate : 1.049 Fit side-chains REVERT: A 259 LYS cc_start: 0.8699 (tttt) cc_final: 0.8454 (ttmt) REVERT: C 259 LYS cc_start: 0.8701 (tttt) cc_final: 0.8454 (ttmt) REVERT: E 71 ARG cc_start: 0.8295 (mtt90) cc_final: 0.7804 (mtt-85) REVERT: E 225 ASP cc_start: 0.7211 (p0) cc_final: 0.6944 (p0) REVERT: F 71 ARG cc_start: 0.8304 (mtt90) cc_final: 0.7819 (mtt-85) REVERT: F 225 ASP cc_start: 0.7236 (p0) cc_final: 0.6986 (p0) REVERT: G 71 ARG cc_start: 0.8298 (mtt90) cc_final: 0.7807 (mtt-85) REVERT: G 225 ASP cc_start: 0.7211 (p0) cc_final: 0.6941 (p0) REVERT: H 71 ARG cc_start: 0.8304 (mtt90) cc_final: 0.7822 (mtt-85) REVERT: H 225 ASP cc_start: 0.7222 (p0) cc_final: 0.6973 (p0) outliers start: 12 outliers final: 11 residues processed: 290 average time/residue: 0.8457 time to fit residues: 274.4739 Evaluate side-chains 282 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 271 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 27 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 168 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.137483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109647 restraints weight = 21628.276| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.26 r_work: 0.3138 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24448 Z= 0.199 Angle : 0.623 7.069 33128 Z= 0.344 Chirality : 0.051 0.151 3688 Planarity : 0.005 0.051 4392 Dihedral : 5.261 30.903 3504 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.94 % Allowed : 14.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.15), residues: 3136 helix: 1.10 (0.14), residues: 1280 sheet: 1.56 (0.32), residues: 304 loop : -1.11 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 298 TYR 0.017 0.002 TYR G 244 PHE 0.012 0.002 PHE F 122 TRP 0.010 0.002 TRP H 289 HIS 0.015 0.002 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00447 (24416) covalent geometry : angle 0.62198 (33112) SS BOND : bond 0.01057 ( 8) SS BOND : angle 1.73158 ( 16) hydrogen bonds : bond 0.07087 ( 1032) hydrogen bonds : angle 4.18711 ( 2832) metal coordination : bond 0.00419 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8953.84 seconds wall clock time: 152 minutes 52.21 seconds (9172.21 seconds total)