Starting phenix.real_space_refine on Wed Feb 4 23:47:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i42_35162/02_2026/8i42_35162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i42_35162/02_2026/8i42_35162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i42_35162/02_2026/8i42_35162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i42_35162/02_2026/8i42_35162.map" model { file = "/net/cci-nas-00/data/ceres_data/8i42_35162/02_2026/8i42_35162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i42_35162/02_2026/8i42_35162.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 20 5.16 5 C 9350 2.51 5 N 2055 2.21 5 O 2595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14060 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "B" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "C" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "D" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "E" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "A" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 139 Chain: "B" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 139 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 139 Chain: "D" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 139 Chain: "E" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 139 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ALEU A 313 " occ=0.47 ... (14 atoms not shown) pdb=" CD2BLEU A 313 " occ=0.53 residue: pdb=" N ALEU B 313 " occ=0.49 ... (14 atoms not shown) pdb=" CD2BLEU B 313 " occ=0.51 residue: pdb=" N ALEU C 313 " occ=0.54 ... (14 atoms not shown) pdb=" CD2BLEU C 313 " occ=0.46 residue: pdb=" N ALEU D 313 " occ=0.46 ... (14 atoms not shown) pdb=" CD2BLEU D 313 " occ=0.54 residue: pdb=" N ALEU E 313 " occ=0.52 ... (14 atoms not shown) pdb=" CD2BLEU E 313 " occ=0.48 Time building chain proxies: 5.92, per 1000 atoms: 0.42 Number of scatterers: 14060 At special positions: 0 Unit cell: (98.8, 98.04, 120.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 40 15.00 O 2595 8.00 N 2055 7.00 C 9350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 36.5% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 202 through 213 removed outlier: 3.503A pdb=" N SER A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.558A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 242 Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.534A pdb=" N ALA A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 314 removed outlier: 3.830A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 146 through 149 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 202 through 213 removed outlier: 3.504A pdb=" N SER B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 218 removed outlier: 3.557A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 242 Processing helix chain 'B' and resid 253 through 282 removed outlier: 3.535A pdb=" N ALA B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 314 removed outlier: 3.831A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.504A pdb=" N SER C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 218 removed outlier: 3.556A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 242 Processing helix chain 'C' and resid 253 through 282 removed outlier: 3.534A pdb=" N ALA C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 314 removed outlier: 3.830A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 194 through 198 Processing helix chain 'D' and resid 202 through 213 removed outlier: 3.504A pdb=" N SER D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 218 removed outlier: 3.557A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 242 Processing helix chain 'D' and resid 253 through 282 removed outlier: 3.534A pdb=" N ALA D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 314 removed outlier: 3.831A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 146 through 149 Processing helix chain 'E' and resid 194 through 198 Processing helix chain 'E' and resid 202 through 213 removed outlier: 3.504A pdb=" N SER E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 218 removed outlier: 3.557A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 242 Processing helix chain 'E' and resid 253 through 282 removed outlier: 3.535A pdb=" N ALA E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 314 removed outlier: 3.831A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 95 removed outlier: 5.920A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER A 95 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N THR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 102 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 41 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 37 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR A 36 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER A 29 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 4.007A pdb=" N LEU A 130 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 184 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 95 removed outlier: 5.921A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 95 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR B 102 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 41 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 37 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR B 36 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N SER B 29 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78 removed outlier: 4.006A pdb=" N LEU B 130 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 184 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 88 through 95 removed outlier: 5.920A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER C 95 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 102 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 41 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 37 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR C 36 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER C 29 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78 removed outlier: 4.007A pdb=" N LEU C 130 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 184 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 88 through 95 removed outlier: 5.921A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER D 95 " --> pdb=" O THR D 99 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 102 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 41 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE D 37 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR D 36 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N SER D 29 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 76 through 78 removed outlier: 4.007A pdb=" N LEU D 130 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 184 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 88 through 95 removed outlier: 5.921A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER E 95 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 102 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 41 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE E 37 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR E 36 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER E 29 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 78 removed outlier: 4.007A pdb=" N LEU E 130 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 184 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1505 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: 2.12 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2200 1.32 - 1.44: 3770 1.44 - 1.56: 8280 1.56 - 1.69: 80 1.69 - 1.81: 35 Bond restraints: 14365 Sorted by residual: bond pdb=" CB GLN C 124 " pdb=" CG GLN C 124 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.80e-01 bond pdb=" CB GLN D 124 " pdb=" CG GLN D 124 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.78e-01 bond pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.77e-01 bond pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.74e-01 bond pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.55e-01 ... (remaining 14360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 18691 1.21 - 2.42: 496 2.42 - 3.63: 112 3.63 - 4.84: 36 4.84 - 6.05: 20 Bond angle restraints: 19355 Sorted by residual: angle pdb=" CB GLN C 124 " pdb=" CG GLN C 124 " pdb=" CD GLN C 124 " ideal model delta sigma weight residual 112.60 116.52 -3.92 1.70e+00 3.46e-01 5.32e+00 angle pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " pdb=" CD GLN A 124 " ideal model delta sigma weight residual 112.60 116.49 -3.89 1.70e+00 3.46e-01 5.23e+00 angle pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " pdb=" CD GLN B 124 " ideal model delta sigma weight residual 112.60 116.48 -3.88 1.70e+00 3.46e-01 5.21e+00 angle pdb=" CB GLN D 124 " pdb=" CG GLN D 124 " pdb=" CD GLN D 124 " ideal model delta sigma weight residual 112.60 116.48 -3.88 1.70e+00 3.46e-01 5.20e+00 angle pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " pdb=" CD GLN E 124 " ideal model delta sigma weight residual 112.60 116.47 -3.87 1.70e+00 3.46e-01 5.18e+00 ... (remaining 19350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.84: 8309 32.84 - 65.68: 386 65.68 - 98.53: 90 98.53 - 131.37: 40 131.37 - 164.21: 45 Dihedral angle restraints: 8870 sinusoidal: 4170 harmonic: 4700 Sorted by residual: dihedral pdb=" C4 PEE B 402 " pdb=" O4P PEE B 402 " pdb=" P PEE B 402 " pdb=" O1P PEE B 402 " ideal model delta sinusoidal sigma weight residual 57.28 -106.93 164.21 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4 PEE E 402 " pdb=" O4P PEE E 402 " pdb=" P PEE E 402 " pdb=" O1P PEE E 402 " ideal model delta sinusoidal sigma weight residual 57.28 -106.92 164.20 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4 PEE C 402 " pdb=" O4P PEE C 402 " pdb=" P PEE C 402 " pdb=" O1P PEE C 402 " ideal model delta sinusoidal sigma weight residual 57.28 -106.92 164.20 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 8867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1191 0.026 - 0.052: 523 0.052 - 0.078: 278 0.078 - 0.105: 99 0.105 - 0.131: 34 Chirality restraints: 2125 Sorted by residual: chirality pdb=" CA ILE A 92 " pdb=" N ILE A 92 " pdb=" C ILE A 92 " pdb=" CB ILE A 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE B 92 " pdb=" N ILE B 92 " pdb=" C ILE B 92 " pdb=" CB ILE B 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE C 92 " pdb=" N ILE C 92 " pdb=" C ILE C 92 " pdb=" CB ILE C 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 2122 not shown) Planarity restraints: 2315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 95 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO D 96 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 96 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 96 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 95 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO E 96 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 95 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO C 96 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 96 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 96 " 0.024 5.00e-02 4.00e+02 ... (remaining 2312 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 406 2.71 - 3.26: 13111 3.26 - 3.80: 20557 3.80 - 4.35: 25649 4.35 - 4.90: 44445 Nonbonded interactions: 104168 Sorted by model distance: nonbonded pdb=" O LEU B 227 " pdb=" OG1 THR B 231 " model vdw 2.160 3.040 nonbonded pdb=" O LEU C 227 " pdb=" OG1 THR C 231 " model vdw 2.160 3.040 nonbonded pdb=" O LEU A 227 " pdb=" OG1 THR A 231 " model vdw 2.160 3.040 nonbonded pdb=" O LEU E 227 " pdb=" OG1 THR E 231 " model vdw 2.160 3.040 nonbonded pdb=" O LEU D 227 " pdb=" OG1 THR D 231 " model vdw 2.160 3.040 ... (remaining 104163 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 312 or resid 314 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or nam \ e P )) or resid 402 or (resid 403 and (name C1 or name C10 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O1P or name O2 or name O2P or name O3 o \ r name O3P or name O4 or name O4P or name O5 or name P )) or (resid 404 and (nam \ e C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name O1P or na \ me O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or na \ me P )) or (resid 405 and (name C1 or name C10 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C2 or name C3 or name C30 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name O1P or name O2 or n \ ame O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or \ (resid 406 and (name C1 or name C10 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or n \ ame C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 o \ r name C36 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 \ or name O4P or name O5 or name P )) or (resid 407 and (name N or name C1 or name \ C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 o \ r name C35 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3 o \ r name O3P or name O4 or name O4P or name O5 or name P )) or (resid 408 and (nam \ e N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or \ name C21 or name C22 or name C23 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O \ 1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name \ O5 or name P )))) selection = (chain 'B' and (resid 5 through 312 or resid 314 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or nam \ e P )) or (resid 402 and (name N or name C1 or name C10 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C4 or name C40 or name C41 or name C42 or name C5 or name O1P or name O2 o \ r name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) \ or resid 403 or (resid 404 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or na \ me C41 or name C42 or name O1P or name O2 or name O2P or name O3 or name O3P or \ name O4 or name O4P or name O5 or name P )) or (resid 405 and (name C1 or name C \ 10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or \ name O4P or name O5 or name P )) or (resid 406 and (name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 407 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C4 or name C5 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )) or (resid 408 and (name N or name C1 or name C10 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name \ O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'C' and (resid 5 through 312 or resid 314 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or nam \ e P )) or (resid 402 and (name N or name C1 or name C10 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C4 or name C40 or name C41 or name C42 or name C5 or name O1P or name O2 o \ r name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) \ or resid 403 or (resid 404 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or na \ me C41 or name C42 or name O1P or name O2 or name O2P or name O3 or name O3P or \ name O4 or name O4P or name O5 or name P )) or (resid 405 and (name C1 or name C \ 10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or \ name O4P or name O5 or name P )) or (resid 406 and (name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 407 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C4 or name C5 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )) or (resid 408 and (name N or name C1 or name C10 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name \ O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'D' and (resid 5 through 312 or resid 314 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or nam \ e P )) or (resid 402 and (name N or name C1 or name C10 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C4 or name C40 or name C41 or name C42 or name C5 or name O1P or name O2 o \ r name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) \ or resid 403 or (resid 404 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or na \ me C41 or name C42 or name O1P or name O2 or name O2P or name O3 or name O3P or \ name O4 or name O4P or name O5 or name P )) or (resid 405 and (name C1 or name C \ 10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or \ name O4P or name O5 or name P )) or (resid 406 and (name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 407 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C4 or name C5 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )) or (resid 408 and (name N or name C1 or name C10 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name \ O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'E' and (resid 5 through 312 or resid 314 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or nam \ e P )) or (resid 402 and (name N or name C1 or name C10 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C4 or name C40 or name C41 or name C42 or name C5 or name O1P or name O2 o \ r name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) \ or resid 403 or (resid 404 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or na \ me C41 or name C42 or name O1P or name O2 or name O2P or name O3 or name O3P or \ name O4 or name O4P or name O5 or name P )) or (resid 405 and (name C1 or name C \ 10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or \ name O4P or name O5 or name P )) or (resid 406 and (name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 407 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C4 or name C5 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )) or (resid 408 and (name N or name C1 or name C10 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name \ O3P or name O4 or name O4P or name O5 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.790 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14365 Z= 0.110 Angle : 0.533 6.046 19355 Z= 0.271 Chirality : 0.040 0.131 2125 Planarity : 0.004 0.044 2315 Dihedral : 24.493 164.209 5810 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.28 % Allowed : 25.48 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1565 helix: 3.05 (0.22), residues: 495 sheet: -1.47 (0.26), residues: 350 loop : -1.78 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 105 TYR 0.022 0.001 TYR D 102 PHE 0.008 0.001 PHE E 314 TRP 0.005 0.001 TRP D 47 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00246 (14365) covalent geometry : angle 0.53266 (19355) hydrogen bonds : bond 0.18677 ( 525) hydrogen bonds : angle 5.02852 ( 1505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6373 (pt0) REVERT: B 104 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6356 (pt0) REVERT: C 104 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6181 (pp20) REVERT: D 104 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6373 (pt0) REVERT: E 104 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6410 (pt0) outliers start: 27 outliers final: 16 residues processed: 140 average time/residue: 0.6635 time to fit residues: 101.2671 Evaluate side-chains 132 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.212148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111289 restraints weight = 46919.739| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.35 r_work: 0.2821 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14365 Z= 0.159 Angle : 0.598 7.938 19355 Z= 0.297 Chirality : 0.044 0.161 2125 Planarity : 0.004 0.042 2315 Dihedral : 26.563 165.569 2913 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.20 % Allowed : 22.85 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1565 helix: 2.50 (0.22), residues: 525 sheet: -1.41 (0.30), residues: 260 loop : -1.84 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 105 TYR 0.009 0.001 TYR A 254 PHE 0.010 0.001 PHE C 195 TRP 0.008 0.001 TRP B 160 HIS 0.003 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00394 (14365) covalent geometry : angle 0.59784 (19355) hydrogen bonds : bond 0.07012 ( 525) hydrogen bonds : angle 4.04998 ( 1505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7788 (mp) REVERT: D 231 THR cc_start: 0.9165 (m) cc_final: 0.8954 (p) outliers start: 40 outliers final: 16 residues processed: 157 average time/residue: 0.7254 time to fit residues: 123.3385 Evaluate side-chains 142 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 212 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 7 optimal weight: 0.0370 chunk 97 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.212129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113379 restraints weight = 50051.575| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 6.10 r_work: 0.2820 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14365 Z= 0.126 Angle : 0.569 7.884 19355 Z= 0.280 Chirality : 0.042 0.156 2125 Planarity : 0.004 0.042 2315 Dihedral : 25.617 169.098 2886 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.99 % Allowed : 22.92 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1565 helix: 2.69 (0.22), residues: 525 sheet: -1.50 (0.30), residues: 250 loop : -1.83 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 109 TYR 0.007 0.001 TYR B 254 PHE 0.006 0.001 PHE D 165 TRP 0.006 0.001 TRP D 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00301 (14365) covalent geometry : angle 0.56941 (19355) hydrogen bonds : bond 0.06112 ( 525) hydrogen bonds : angle 3.79913 ( 1505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 THR cc_start: 0.9094 (m) cc_final: 0.8818 (p) REVERT: B 231 THR cc_start: 0.9090 (m) cc_final: 0.8861 (p) REVERT: B 272 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8208 (tm-30) REVERT: C 147 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: C 189 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6981 (mtp-110) REVERT: C 231 THR cc_start: 0.9048 (m) cc_final: 0.8814 (p) REVERT: D 231 THR cc_start: 0.9151 (m) cc_final: 0.8891 (p) REVERT: D 307 ASN cc_start: 0.8689 (m-40) cc_final: 0.8483 (m-40) REVERT: E 231 THR cc_start: 0.9087 (m) cc_final: 0.8834 (p) outliers start: 37 outliers final: 11 residues processed: 164 average time/residue: 0.6952 time to fit residues: 123.1992 Evaluate side-chains 134 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 168 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 141 optimal weight: 0.0000 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 132 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.210920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113787 restraints weight = 42659.083| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 5.37 r_work: 0.2843 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14365 Z= 0.131 Angle : 0.583 8.061 19355 Z= 0.287 Chirality : 0.043 0.165 2125 Planarity : 0.005 0.051 2315 Dihedral : 25.265 170.083 2878 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.27 % Allowed : 21.99 % Favored : 74.73 % 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 are not related in a simple way. whole: -0.19 (0.22), residues: 1565 helix: 2.73 (0.22), residues: 525 sheet: -1.31 (0.29), residues: 265 loop : -1.82 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 109 TYR 0.008 0.001 TYR B 251 PHE 0.008 0.001 PHE A 165 TRP 0.006 0.001 TRP D 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00316 (14365) covalent geometry : angle 0.58258 (19355) hydrogen bonds : bond 0.06352 ( 525) hydrogen bonds : angle 3.73183 ( 1505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 THR cc_start: 0.9185 (m) cc_final: 0.8910 (p) REVERT: B 272 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8291 (tm-30) REVERT: C 109 ARG cc_start: 0.7280 (mmm-85) cc_final: 0.6714 (mtp85) REVERT: C 148 LYS cc_start: 0.8188 (mmtp) cc_final: 0.7955 (mmtp) REVERT: C 305 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7871 (mp) REVERT: D 109 ARG cc_start: 0.7385 (mtp-110) cc_final: 0.6805 (mtm180) REVERT: D 231 THR cc_start: 0.9181 (m) cc_final: 0.8932 (p) REVERT: D 307 ASN cc_start: 0.8856 (m-40) cc_final: 0.8653 (m-40) REVERT: E 109 ARG cc_start: 0.7277 (mtp-110) cc_final: 0.6745 (mtm180) REVERT: E 231 THR cc_start: 0.9189 (m) cc_final: 0.8924 (p) outliers start: 41 outliers final: 13 residues processed: 159 average time/residue: 0.7033 time to fit residues: 120.8144 Evaluate side-chains 130 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 168 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 42 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 129 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.211629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111793 restraints weight = 42941.692| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 5.17 r_work: 0.2864 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14365 Z= 0.122 Angle : 0.575 7.998 19355 Z= 0.283 Chirality : 0.042 0.161 2125 Planarity : 0.004 0.044 2315 Dihedral : 24.724 172.150 2875 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.92 % Allowed : 23.20 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.22), residues: 1565 helix: 2.83 (0.22), residues: 525 sheet: -1.12 (0.27), residues: 340 loop : -1.81 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 109 TYR 0.009 0.001 TYR A 251 PHE 0.007 0.001 PHE D 165 TRP 0.006 0.001 TRP E 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00292 (14365) covalent geometry : angle 0.57528 (19355) hydrogen bonds : bond 0.05861 ( 525) hydrogen bonds : angle 3.64639 ( 1505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7949 (mp0) cc_final: 0.7728 (mp0) REVERT: A 163 GLU cc_start: 0.7925 (pt0) cc_final: 0.7625 (pt0) REVERT: A 272 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8225 (tm-30) REVERT: B 231 THR cc_start: 0.9156 (m) cc_final: 0.8857 (p) REVERT: C 104 GLU cc_start: 0.6232 (pm20) cc_final: 0.5948 (pt0) REVERT: C 109 ARG cc_start: 0.7187 (mmm-85) cc_final: 0.6930 (mmm160) REVERT: C 148 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7937 (mmtp) REVERT: C 305 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7862 (mp) REVERT: D 35 GLU cc_start: 0.7996 (mp0) cc_final: 0.7759 (mp0) REVERT: D 231 THR cc_start: 0.9180 (m) cc_final: 0.8914 (p) REVERT: D 272 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8341 (tm-30) REVERT: D 307 ASN cc_start: 0.8853 (m-40) cc_final: 0.8632 (m-40) REVERT: E 109 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.6691 (mtm180) REVERT: E 163 GLU cc_start: 0.7993 (pt0) cc_final: 0.7747 (pt0) REVERT: E 231 THR cc_start: 0.9187 (m) cc_final: 0.8906 (p) REVERT: E 272 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8233 (tm-30) outliers start: 36 outliers final: 14 residues processed: 169 average time/residue: 0.7320 time to fit residues: 133.2006 Evaluate side-chains 137 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 168 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.211561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115925 restraints weight = 41512.301| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 5.68 r_work: 0.2815 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14365 Z= 0.138 Angle : 0.596 8.097 19355 Z= 0.293 Chirality : 0.043 0.172 2125 Planarity : 0.005 0.057 2315 Dihedral : 24.428 176.166 2875 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.49 % Allowed : 23.99 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1565 helix: 2.82 (0.22), residues: 525 sheet: -1.13 (0.27), residues: 345 loop : -1.74 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 109 TYR 0.009 0.001 TYR B 251 PHE 0.010 0.001 PHE A 165 TRP 0.006 0.001 TRP B 160 HIS 0.002 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00336 (14365) covalent geometry : angle 0.59616 (19355) hydrogen bonds : bond 0.06532 ( 525) hydrogen bonds : angle 3.66334 ( 1505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 THR cc_start: 0.9150 (m) cc_final: 0.8840 (p) REVERT: C 109 ARG cc_start: 0.7188 (mmm-85) cc_final: 0.6936 (mmm160) REVERT: C 305 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7821 (mp) REVERT: D 231 THR cc_start: 0.9161 (m) cc_final: 0.8879 (p) REVERT: D 307 ASN cc_start: 0.8853 (m-40) cc_final: 0.8635 (m-40) REVERT: E 231 THR cc_start: 0.9133 (m) cc_final: 0.8833 (p) outliers start: 30 outliers final: 12 residues processed: 149 average time/residue: 0.6983 time to fit residues: 112.4997 Evaluate side-chains 131 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 168 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 124 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 24 optimal weight: 0.0050 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.213273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115382 restraints weight = 46483.004| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.43 r_work: 0.2851 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14365 Z= 0.110 Angle : 0.564 8.223 19355 Z= 0.275 Chirality : 0.042 0.160 2125 Planarity : 0.005 0.060 2315 Dihedral : 23.893 179.644 2875 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.28 % Allowed : 24.20 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.22), residues: 1565 helix: 3.01 (0.21), residues: 525 sheet: -1.14 (0.27), residues: 345 loop : -1.70 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 109 TYR 0.013 0.001 TYR A 251 PHE 0.010 0.001 PHE B 165 TRP 0.006 0.001 TRP E 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00254 (14365) covalent geometry : angle 0.56411 (19355) hydrogen bonds : bond 0.05239 ( 525) hydrogen bonds : angle 3.51858 ( 1505) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 THR cc_start: 0.9129 (m) cc_final: 0.8824 (p) REVERT: C 104 GLU cc_start: 0.6234 (pm20) cc_final: 0.5978 (pt0) REVERT: C 109 ARG cc_start: 0.7163 (mmm-85) cc_final: 0.6448 (ttt90) REVERT: C 305 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7770 (mp) REVERT: D 109 ARG cc_start: 0.7266 (mtp-110) cc_final: 0.6640 (mtm180) REVERT: D 231 THR cc_start: 0.9139 (m) cc_final: 0.8858 (p) REVERT: D 307 ASN cc_start: 0.8800 (m-40) cc_final: 0.8595 (m-40) REVERT: E 109 ARG cc_start: 0.7220 (mtp-110) cc_final: 0.6595 (mtm180) REVERT: E 231 THR cc_start: 0.9130 (m) cc_final: 0.8825 (p) outliers start: 27 outliers final: 12 residues processed: 143 average time/residue: 0.7228 time to fit residues: 111.2844 Evaluate side-chains 133 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 168 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.207408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106740 restraints weight = 41696.423| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.38 r_work: 0.2763 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14365 Z= 0.224 Angle : 0.653 8.179 19355 Z= 0.320 Chirality : 0.046 0.201 2125 Planarity : 0.005 0.056 2315 Dihedral : 24.115 179.850 2875 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.42 % Allowed : 24.27 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.22), residues: 1565 helix: 2.69 (0.22), residues: 525 sheet: -1.25 (0.28), residues: 315 loop : -1.73 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 109 TYR 0.008 0.001 TYR A 23 PHE 0.017 0.001 PHE D 165 TRP 0.007 0.002 TRP B 160 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00572 (14365) covalent geometry : angle 0.65309 (19355) hydrogen bonds : bond 0.08659 ( 525) hydrogen bonds : angle 3.83531 ( 1505) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.7286 (p0) cc_final: 0.7080 (p0) REVERT: B 280 LYS cc_start: 0.7489 (ttpp) cc_final: 0.7287 (ttmm) REVERT: C 109 ARG cc_start: 0.7148 (mmm-85) cc_final: 0.6674 (tpp80) REVERT: C 189 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6961 (mtp180) REVERT: C 305 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7622 (mp) REVERT: D 35 GLU cc_start: 0.8063 (mp0) cc_final: 0.7743 (mp0) REVERT: D 109 ARG cc_start: 0.7250 (mtp-110) cc_final: 0.6636 (mtm180) REVERT: E 109 ARG cc_start: 0.7169 (mtp-110) cc_final: 0.6523 (mtm180) REVERT: E 280 LYS cc_start: 0.7449 (ttpp) cc_final: 0.7228 (ttmm) outliers start: 29 outliers final: 12 residues processed: 137 average time/residue: 0.7933 time to fit residues: 117.1082 Evaluate side-chains 127 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 128 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.212374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114727 restraints weight = 38921.857| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.60 r_work: 0.2880 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14365 Z= 0.115 Angle : 0.587 8.317 19355 Z= 0.285 Chirality : 0.043 0.162 2125 Planarity : 0.005 0.056 2315 Dihedral : 23.162 175.460 2875 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.85 % Allowed : 24.98 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1565 helix: 3.04 (0.21), residues: 525 sheet: -1.13 (0.26), residues: 345 loop : -1.67 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 109 TYR 0.015 0.001 TYR C 251 PHE 0.009 0.001 PHE B 165 TRP 0.007 0.001 TRP E 160 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00267 (14365) covalent geometry : angle 0.58657 (19355) hydrogen bonds : bond 0.05370 ( 525) hydrogen bonds : angle 3.52205 ( 1505) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.6952 (p0) cc_final: 0.6749 (p0) REVERT: A 231 THR cc_start: 0.9075 (m) cc_final: 0.8856 (p) REVERT: C 35 GLU cc_start: 0.8066 (mp0) cc_final: 0.7820 (mp0) REVERT: C 109 ARG cc_start: 0.7147 (mmm-85) cc_final: 0.6818 (tpp80) REVERT: C 305 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7594 (mp) REVERT: D 35 GLU cc_start: 0.8010 (mp0) cc_final: 0.7728 (mp0) REVERT: D 109 ARG cc_start: 0.7262 (mtp-110) cc_final: 0.6655 (mtm180) REVERT: D 307 ASN cc_start: 0.8702 (m-40) cc_final: 0.8494 (m-40) REVERT: E 109 ARG cc_start: 0.7182 (mtp-110) cc_final: 0.6589 (mtm180) REVERT: E 231 THR cc_start: 0.9068 (m) cc_final: 0.8734 (p) outliers start: 21 outliers final: 10 residues processed: 139 average time/residue: 0.7366 time to fit residues: 110.6583 Evaluate side-chains 130 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain E residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 131 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.212738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115717 restraints weight = 42968.363| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 5.63 r_work: 0.2850 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14365 Z= 0.117 Angle : 0.590 8.243 19355 Z= 0.285 Chirality : 0.043 0.177 2125 Planarity : 0.005 0.058 2315 Dihedral : 22.470 175.203 2875 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.57 % Allowed : 25.27 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.22), residues: 1565 helix: 3.12 (0.21), residues: 525 sheet: -1.24 (0.28), residues: 315 loop : -1.67 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 109 TYR 0.015 0.001 TYR B 251 PHE 0.015 0.001 PHE E 165 TRP 0.006 0.001 TRP E 160 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00275 (14365) covalent geometry : angle 0.59014 (19355) hydrogen bonds : bond 0.05527 ( 525) hydrogen bonds : angle 3.47474 ( 1505) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.7147 (p0) cc_final: 0.6924 (p0) REVERT: B 109 ARG cc_start: 0.7225 (mtp-110) cc_final: 0.6957 (mtp-110) REVERT: C 35 GLU cc_start: 0.8043 (mp0) cc_final: 0.7801 (mp0) REVERT: C 109 ARG cc_start: 0.7140 (mmm-85) cc_final: 0.6796 (tpp80) REVERT: C 305 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7794 (mp) REVERT: D 35 GLU cc_start: 0.7977 (mp0) cc_final: 0.7716 (mp0) REVERT: D 109 ARG cc_start: 0.7295 (mtp-110) cc_final: 0.6708 (mtm180) REVERT: E 109 ARG cc_start: 0.7229 (mtp-110) cc_final: 0.6637 (mtm180) REVERT: E 231 THR cc_start: 0.9147 (m) cc_final: 0.8847 (p) outliers start: 17 outliers final: 10 residues processed: 137 average time/residue: 0.6697 time to fit residues: 98.9261 Evaluate side-chains 130 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain E residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 142 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 148 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.211522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113503 restraints weight = 43750.416| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 5.05 r_work: 0.2832 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14365 Z= 0.132 Angle : 0.602 8.368 19355 Z= 0.291 Chirality : 0.044 0.181 2125 Planarity : 0.005 0.059 2315 Dihedral : 22.259 175.881 2875 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.49 % Allowed : 25.34 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1565 helix: 3.04 (0.21), residues: 525 sheet: -1.07 (0.26), residues: 345 loop : -1.66 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 109 TYR 0.010 0.001 TYR C 251 PHE 0.010 0.001 PHE E 165 TRP 0.006 0.001 TRP E 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00319 (14365) covalent geometry : angle 0.60162 (19355) hydrogen bonds : bond 0.06288 ( 525) hydrogen bonds : angle 3.55154 ( 1505) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5603.89 seconds wall clock time: 95 minutes 50.56 seconds (5750.56 seconds total)