Starting phenix.real_space_refine on Mon Aug 25 04:41:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwj_44976/08_2025/9bwj_44976.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwj_44976/08_2025/9bwj_44976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bwj_44976/08_2025/9bwj_44976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwj_44976/08_2025/9bwj_44976.map" model { file = "/net/cci-nas-00/data/ceres_data/9bwj_44976/08_2025/9bwj_44976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwj_44976/08_2025/9bwj_44976.cif" } resolution = 2.21 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13390 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 100 5.16 5 C 9630 2.51 5 N 2315 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14705 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 88 Unusual residues: {' ZN': 2, 'PX4': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PX4:plan-2': 7} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 88 Unusual residues: {' ZN': 2, 'PX4': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PX4:plan-2': 7} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, G, H, I, J Time building chain proxies: 2.63, per 1000 atoms: 0.18 Number of scatterers: 14705 At special positions: 0 Unit cell: (99.12, 99.96, 132.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 100 16.00 O 2650 8.00 N 2315 7.00 C 9630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 41 " distance=0.00 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 138 " distance=0.00 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 152 " distance=0.00 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 198 " distance=0.00 Simple disulfide: pdb=" SG CYS B 209 " - pdb=" SG CYS B 209 " distance=0.00 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 290 " distance=0.00 Simple disulfide: pdb=" SG CYS B 402 " - pdb=" SG CYS B 402 " distance=0.00 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 38 " " NAG G 1 " - " ASN B 38 " " NAG H 1 " - " ASN C 38 " " NAG I 1 " - " ASN D 38 " " NAG J 1 " - " ASN E 38 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 620.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 215 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 427 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 109 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 109 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 215 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 427 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 109 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 215 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 427 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 109 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 427 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 215 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 109 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 215 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 427 " 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 20 sheets defined 38.6% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.764A pdb=" N ALA A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.585A pdb=" N VAL A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 71 through 74 removed outlier: 3.764A pdb=" N ALA B 74 " --> pdb=" O PRO B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 240 removed outlier: 3.584A pdb=" N VAL B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.764A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.584A pdb=" N VAL C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'D' and resid 9 through 18 Processing helix chain 'D' and resid 71 through 74 removed outlier: 3.764A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.584A pdb=" N VAL D 240 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 244 Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'E' and resid 9 through 18 Processing helix chain 'E' and resid 71 through 74 removed outlier: 3.765A pdb=" N ALA E 74 " --> pdb=" O PRO E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 74' Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE E 93 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 227 through 240 removed outlier: 3.585A pdb=" N VAL E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU E 298 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Proline residue: E 404 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.236A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP A 57 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 51 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE A 63 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 45 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG A 65 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE A 43 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS A 67 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS A 41 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN A 69 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A 39 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE A 108 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ARG A 131 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP A 57 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 51 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE A 63 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 45 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG A 65 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE A 43 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS A 67 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS A 41 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN A 69 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A 39 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS A 215 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 192 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU A 217 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS A 190 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.237A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 57 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE B 51 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE B 63 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 45 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG B 65 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE B 43 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS B 67 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS B 41 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN B 69 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL B 39 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N PHE B 108 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ARG B 131 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 57 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE B 51 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE B 63 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 45 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG B 65 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE B 43 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS B 67 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS B 41 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN B 69 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL B 39 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS B 215 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU B 192 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU B 217 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS B 190 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.235A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP C 57 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE C 51 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE C 63 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE C 45 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG C 65 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE C 43 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS C 67 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS C 41 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN C 69 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL C 39 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 39 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N PHE C 108 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ARG C 131 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP C 57 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE C 51 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE C 63 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE C 45 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG C 65 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE C 43 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS C 67 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS C 41 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN C 69 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL C 39 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS C 215 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU C 192 " --> pdb=" O HIS C 215 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU C 217 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS C 190 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB4, first strand: chain 'D' and resid 82 through 84 removed outlier: 4.235A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP D 57 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE D 51 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE D 63 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE D 45 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG D 65 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE D 43 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS D 67 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS D 41 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN D 69 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL D 39 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE D 108 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ARG D 131 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP D 57 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE D 51 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE D 63 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE D 45 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG D 65 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE D 43 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS D 67 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS D 41 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN D 69 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL D 39 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS D 215 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU D 192 " --> pdb=" O HIS D 215 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLU D 217 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS D 190 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 84 removed outlier: 4.236A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP E 57 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 51 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE E 63 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE E 45 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG E 65 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE E 43 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS E 67 " --> pdb=" O CYS E 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS E 41 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN E 69 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL E 39 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL E 37 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU E 169 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL E 39 " --> pdb=" O GLU E 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE E 108 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ARG E 131 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP E 57 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 51 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE E 63 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE E 45 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG E 65 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE E 43 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS E 67 " --> pdb=" O CYS E 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS E 41 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN E 69 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL E 39 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS E 215 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU E 192 " --> pdb=" O HIS E 215 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLU E 217 " --> pdb=" O LYS E 190 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS E 190 " --> pdb=" O GLU E 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 200 through 201 737 hydrogen bonds defined for protein. 2160 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: 2.27 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4404 1.34 - 1.46: 3403 1.46 - 1.58: 6713 1.58 - 1.69: 325 1.69 - 1.81: 165 Bond restraints: 15010 Sorted by residual: bond pdb=" C9 PX4 D 509 " pdb=" O5 PX4 D 509 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C9 PX4 B 508 " pdb=" O5 PX4 B 508 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C9 PX4 E 507 " pdb=" O5 PX4 E 507 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C9 PX4 C 505 " pdb=" O5 PX4 C 505 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C9 PX4 D 504 " pdb=" O5 PX4 D 504 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.93e+01 ... (remaining 15005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 18927 1.75 - 3.50: 932 3.50 - 5.25: 279 5.25 - 7.00: 37 7.00 - 8.75: 50 Bond angle restraints: 20225 Sorted by residual: angle pdb=" CG ARG C 20 " pdb=" CD ARG C 20 " pdb=" NE ARG C 20 " ideal model delta sigma weight residual 112.00 120.75 -8.75 2.20e+00 2.07e-01 1.58e+01 angle pdb=" CG ARG A 20 " pdb=" CD ARG A 20 " pdb=" NE ARG A 20 " ideal model delta sigma weight residual 112.00 120.71 -8.71 2.20e+00 2.07e-01 1.57e+01 angle pdb=" CG ARG E 20 " pdb=" CD ARG E 20 " pdb=" NE ARG E 20 " ideal model delta sigma weight residual 112.00 120.71 -8.71 2.20e+00 2.07e-01 1.57e+01 angle pdb=" CG ARG D 20 " pdb=" CD ARG D 20 " pdb=" NE ARG D 20 " ideal model delta sigma weight residual 112.00 120.70 -8.70 2.20e+00 2.07e-01 1.57e+01 angle pdb=" CG ARG B 20 " pdb=" CD ARG B 20 " pdb=" NE ARG B 20 " ideal model delta sigma weight residual 112.00 120.70 -8.70 2.20e+00 2.07e-01 1.56e+01 ... (remaining 20220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8294 17.84 - 35.68: 618 35.68 - 53.51: 167 53.51 - 71.35: 40 71.35 - 89.19: 15 Dihedral angle restraints: 9134 sinusoidal: 3999 harmonic: 5135 Sorted by residual: dihedral pdb=" CA LEU E 142 " pdb=" C LEU E 142 " pdb=" N LYS E 143 " pdb=" CA LYS E 143 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LEU A 142 " pdb=" C LEU A 142 " pdb=" N LYS A 143 " pdb=" CA LYS A 143 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LEU D 142 " pdb=" C LEU D 142 " pdb=" N LYS D 143 " pdb=" CA LYS D 143 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 9131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1310 0.036 - 0.072: 592 0.072 - 0.108: 234 0.108 - 0.144: 104 0.144 - 0.180: 5 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 38 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 38 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 38 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 2242 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 250 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C PRO E 250 " 0.065 2.00e-02 2.50e+03 pdb=" O PRO E 250 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA E 251 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 250 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C PRO A 250 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO A 250 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA A 251 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 250 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C PRO D 250 " 0.064 2.00e-02 2.50e+03 pdb=" O PRO D 250 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA D 251 " -0.022 2.00e-02 2.50e+03 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 299 2.68 - 3.24: 13267 3.24 - 3.79: 22407 3.79 - 4.35: 32136 4.35 - 4.90: 52602 Nonbonded interactions: 120711 Sorted by model distance: nonbonded pdb=" OD1 ASP D 194 " pdb="ZN ZN D 502 " model vdw 2.131 2.230 nonbonded pdb=" OD1 ASP C 194 " pdb="ZN ZN C 502 " model vdw 2.131 2.230 nonbonded pdb=" OD1 ASP E 194 " pdb="ZN ZN E 502 " model vdw 2.131 2.230 nonbonded pdb=" OD1 ASP A 194 " pdb="ZN ZN A 501 " model vdw 2.131 2.230 nonbonded pdb=" OD1 ASP B 194 " pdb="ZN ZN B 502 " model vdw 2.131 2.230 ... (remaining 120706 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 506 or (resid 507 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C9 o \ r name O5 or name O6 )) or (resid 508 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C9 o \ r name O5 or name O6 )) or (resid 509 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C9 or name O5 or name O6 )))) selection = (chain 'B' and (resid 8 through 506 or (resid 507 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C9 o \ r name O5 or name O6 )) or (resid 508 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C9 o \ r name O5 or name O6 )) or (resid 509 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C9 or name O5 or name O6 )))) selection = (chain 'C' and (resid 8 through 506 or (resid 507 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C9 o \ r name O5 or name O6 )) or (resid 508 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C9 o \ r name O5 or name O6 )) or (resid 509 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C9 or name O5 or name O6 )))) selection = (chain 'D' and (resid 8 through 506 or (resid 507 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C9 o \ r name O5 or name O6 )) or (resid 508 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C9 o \ r name O5 or name O6 )) or (resid 509 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C9 or name O5 or name O6 )))) selection = (chain 'E' and (resid 8 through 502 or (resid 503 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C9 or name O5 or name O6 )) or (resid 504 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C9 or name O5 or name O6 )) \ or (resid 505 and (name C10 or name C11 or name C12 or name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C9 or name O5 or \ name O6 )) or (resid 506 and (name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C9 or name O5 or \ name O6 )) or resid 507 through 509)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.670 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 : 0.015 0.141 15035 Z= 0.739 Angle : 1.021 8.748 20262 Z= 0.518 Chirality : 0.049 0.180 2245 Planarity : 0.007 0.040 2505 Dihedral : 14.551 89.190 5780 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.51 % Allowed : 9.68 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.19), residues: 1710 helix: -1.20 (0.18), residues: 575 sheet: -0.53 (0.25), residues: 440 loop : -0.59 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 27 TYR 0.014 0.002 TYR D 301 PHE 0.022 0.002 PHE B 295 TRP 0.020 0.002 TRP E 415 HIS 0.014 0.002 HIS E 215 Details of bonding type rmsd covalent geometry : bond 0.01453 (15010) covalent geometry : angle 1.02138 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.14393 ( 657) hydrogen bonds : angle 6.71307 ( 2160) metal coordination : bond 0.01908 ( 15) link_BETA1-4 : bond 0.00199 ( 5) link_BETA1-4 : angle 1.27887 ( 15) link_NAG-ASN : bond 0.00095 ( 5) link_NAG-ASN : angle 0.39120 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.542 Fit side-chains REVERT: A 14 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8234 (mp) REVERT: B 78 TYR cc_start: 0.7192 (t80) cc_final: 0.6970 (t80) REVERT: C 78 TYR cc_start: 0.7155 (t80) cc_final: 0.6884 (t80) REVERT: D 18 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7481 (mtp) REVERT: D 78 TYR cc_start: 0.7145 (t80) cc_final: 0.6880 (t80) REVERT: E 78 TYR cc_start: 0.7137 (t80) cc_final: 0.6919 (t80) outliers start: 8 outliers final: 2 residues processed: 145 average time/residue: 0.5271 time to fit residues: 83.8452 Evaluate side-chains 133 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain E residue 14 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 171 GLN B 155 GLN B 171 GLN B 226 GLN C 155 GLN D 155 GLN D 171 GLN E 155 GLN E 171 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.073171 restraints weight = 20556.242| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.26 r_work: 0.2890 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15035 Z= 0.167 Angle : 0.579 5.439 20262 Z= 0.309 Chirality : 0.043 0.152 2245 Planarity : 0.004 0.031 2505 Dihedral : 7.880 52.315 2390 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.17 % Allowed : 8.15 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.20), residues: 1710 helix: 1.42 (0.20), residues: 590 sheet: 0.05 (0.27), residues: 415 loop : -0.37 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 422 TYR 0.019 0.002 TYR B 301 PHE 0.016 0.002 PHE E 48 TRP 0.013 0.001 TRP D 415 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00391 (15010) covalent geometry : angle 0.57824 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.05093 ( 657) hydrogen bonds : angle 4.83465 ( 2160) metal coordination : bond 0.00241 ( 15) link_BETA1-4 : bond 0.00147 ( 5) link_BETA1-4 : angle 1.01791 ( 15) link_NAG-ASN : bond 0.00180 ( 5) link_NAG-ASN : angle 0.62986 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.436 Fit side-chains REVERT: A 78 TYR cc_start: 0.7181 (t80) cc_final: 0.6887 (t80) REVERT: B 78 TYR cc_start: 0.7464 (t80) cc_final: 0.7264 (t80) REVERT: B 144 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7392 (m110) REVERT: C 78 TYR cc_start: 0.7434 (t80) cc_final: 0.7095 (t80) REVERT: C 422 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6481 (mtm180) REVERT: D 18 MET cc_start: 0.7712 (mtp) cc_final: 0.7245 (mtp) REVERT: D 78 TYR cc_start: 0.7396 (t80) cc_final: 0.7163 (t80) REVERT: D 422 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7901 (mtt-85) REVERT: E 422 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7824 (mmm160) outliers start: 34 outliers final: 18 residues processed: 159 average time/residue: 0.5316 time to fit residues: 93.3031 Evaluate side-chains 150 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 422 ARG Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 14 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 171 GLN C 226 GLN D 171 GLN D 226 GLN E 171 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.097200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073370 restraints weight = 20782.972| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.27 r_work: 0.2883 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15035 Z= 0.162 Angle : 0.540 5.430 20262 Z= 0.289 Chirality : 0.042 0.156 2245 Planarity : 0.004 0.031 2505 Dihedral : 7.297 50.168 2382 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.36 % Allowed : 9.04 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.20), residues: 1710 helix: 2.30 (0.20), residues: 575 sheet: 0.54 (0.26), residues: 435 loop : -0.12 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.022 0.001 TYR B 301 PHE 0.016 0.002 PHE E 48 TRP 0.010 0.001 TRP A 68 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00382 (15010) covalent geometry : angle 0.53912 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.04755 ( 657) hydrogen bonds : angle 4.58611 ( 2160) metal coordination : bond 0.00219 ( 15) link_BETA1-4 : bond 0.00241 ( 5) link_BETA1-4 : angle 1.11451 ( 15) link_NAG-ASN : bond 0.00146 ( 5) link_NAG-ASN : angle 0.70435 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.471 Fit side-chains REVERT: A 78 TYR cc_start: 0.7319 (t80) cc_final: 0.7023 (t80) REVERT: B 226 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8344 (mm110) REVERT: C 78 TYR cc_start: 0.7505 (t80) cc_final: 0.7195 (t80) REVERT: D 8 MET cc_start: 0.7486 (tpt) cc_final: 0.7251 (tpp) REVERT: D 18 MET cc_start: 0.7737 (mtp) cc_final: 0.7256 (mtp) REVERT: D 78 TYR cc_start: 0.7509 (t80) cc_final: 0.7252 (t80) REVERT: E 78 TYR cc_start: 0.7390 (t80) cc_final: 0.7177 (t80) outliers start: 37 outliers final: 21 residues processed: 159 average time/residue: 0.5398 time to fit residues: 94.6316 Evaluate side-chains 152 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 144 ASN B 171 GLN C 226 GLN D 171 GLN D 203 ASN D 226 GLN E 171 GLN E 203 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.074076 restraints weight = 20586.188| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.26 r_work: 0.2899 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15035 Z= 0.135 Angle : 0.515 5.361 20262 Z= 0.274 Chirality : 0.041 0.154 2245 Planarity : 0.004 0.032 2505 Dihedral : 6.879 48.390 2380 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.23 % Allowed : 10.51 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.20), residues: 1710 helix: 2.67 (0.20), residues: 575 sheet: 0.62 (0.26), residues: 435 loop : -0.02 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.022 0.001 TYR C 301 PHE 0.017 0.002 PHE C 295 TRP 0.010 0.001 TRP A 68 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00313 (15010) covalent geometry : angle 0.51410 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.04320 ( 657) hydrogen bonds : angle 4.42115 ( 2160) metal coordination : bond 0.00128 ( 15) link_BETA1-4 : bond 0.00216 ( 5) link_BETA1-4 : angle 1.16103 ( 15) link_NAG-ASN : bond 0.00065 ( 5) link_NAG-ASN : angle 0.61481 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.595 Fit side-chains REVERT: A 78 TYR cc_start: 0.7351 (t80) cc_final: 0.7041 (t80) REVERT: B 78 TYR cc_start: 0.7477 (t80) cc_final: 0.7268 (t80) REVERT: C 78 TYR cc_start: 0.7495 (t80) cc_final: 0.7239 (t80) REVERT: C 422 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.6471 (mtm180) REVERT: D 8 MET cc_start: 0.7548 (tpt) cc_final: 0.7215 (tpp) REVERT: D 18 MET cc_start: 0.7692 (mtp) cc_final: 0.7228 (mtp) REVERT: D 78 TYR cc_start: 0.7515 (t80) cc_final: 0.7284 (t80) REVERT: D 220 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8755 (mmm) REVERT: D 422 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8008 (mtt-85) REVERT: E 78 TYR cc_start: 0.7412 (t80) cc_final: 0.7096 (t80) REVERT: E 422 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7855 (mmm160) outliers start: 35 outliers final: 22 residues processed: 160 average time/residue: 0.5343 time to fit residues: 94.1184 Evaluate side-chains 157 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 422 ARG Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.0570 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN E 171 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.072839 restraints weight = 20668.727| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.28 r_work: 0.2879 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15035 Z= 0.173 Angle : 0.535 5.480 20262 Z= 0.285 Chirality : 0.042 0.156 2245 Planarity : 0.004 0.031 2505 Dihedral : 6.981 50.914 2380 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.29 % Allowed : 10.89 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.21), residues: 1710 helix: 2.75 (0.20), residues: 575 sheet: 0.67 (0.26), residues: 435 loop : -0.05 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.023 0.001 TYR B 301 PHE 0.016 0.002 PHE D 295 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00413 (15010) covalent geometry : angle 0.53434 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.04614 ( 657) hydrogen bonds : angle 4.47945 ( 2160) metal coordination : bond 0.00219 ( 15) link_BETA1-4 : bond 0.00144 ( 5) link_BETA1-4 : angle 1.19688 ( 15) link_NAG-ASN : bond 0.00186 ( 5) link_NAG-ASN : angle 0.75375 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.598 Fit side-chains REVERT: A 78 TYR cc_start: 0.7398 (t80) cc_final: 0.7094 (t80) REVERT: B 8 MET cc_start: 0.7309 (tpt) cc_final: 0.7021 (tpp) REVERT: B 78 TYR cc_start: 0.7520 (t80) cc_final: 0.7277 (t80) REVERT: B 422 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7977 (mtt-85) REVERT: C 78 TYR cc_start: 0.7491 (t80) cc_final: 0.7231 (t80) REVERT: C 422 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.6523 (mtm180) REVERT: D 8 MET cc_start: 0.7530 (tpt) cc_final: 0.7193 (tpp) REVERT: D 18 MET cc_start: 0.7711 (mtp) cc_final: 0.7288 (mtp) REVERT: D 78 TYR cc_start: 0.7543 (t80) cc_final: 0.7311 (t80) REVERT: D 220 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8760 (mmm) REVERT: E 78 TYR cc_start: 0.7448 (t80) cc_final: 0.7137 (t80) REVERT: E 422 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7884 (mmm160) outliers start: 36 outliers final: 22 residues processed: 159 average time/residue: 0.5476 time to fit residues: 95.9234 Evaluate side-chains 156 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 117 optimal weight: 0.0470 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN E 171 GLN E 203 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.073158 restraints weight = 20497.830| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.26 r_work: 0.2879 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15035 Z= 0.171 Angle : 0.538 5.627 20262 Z= 0.286 Chirality : 0.042 0.156 2245 Planarity : 0.004 0.032 2505 Dihedral : 7.005 53.293 2380 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.29 % Allowed : 11.40 % Favored : 86.31 % 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 aren not related in a simple way. whole: 1.65 (0.21), residues: 1710 helix: 2.82 (0.20), residues: 575 sheet: 0.69 (0.26), residues: 435 loop : -0.07 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.023 0.001 TYR B 301 PHE 0.018 0.002 PHE C 295 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00408 (15010) covalent geometry : angle 0.53671 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.04615 ( 657) hydrogen bonds : angle 4.47404 ( 2160) metal coordination : bond 0.00218 ( 15) link_BETA1-4 : bond 0.00170 ( 5) link_BETA1-4 : angle 1.21781 ( 15) link_NAG-ASN : bond 0.00170 ( 5) link_NAG-ASN : angle 0.73972 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.480 Fit side-chains REVERT: A 78 TYR cc_start: 0.7402 (t80) cc_final: 0.7084 (t80) REVERT: B 78 TYR cc_start: 0.7535 (t80) cc_final: 0.7297 (t80) REVERT: B 421 LEU cc_start: 0.8493 (tt) cc_final: 0.8184 (mp) REVERT: B 422 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8053 (mtt-85) REVERT: C 8 MET cc_start: 0.7289 (tpt) cc_final: 0.6975 (tpp) REVERT: C 78 TYR cc_start: 0.7500 (t80) cc_final: 0.7218 (t80) REVERT: C 422 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.6543 (mtm180) REVERT: D 8 MET cc_start: 0.7517 (tpt) cc_final: 0.7094 (tpp) REVERT: D 18 MET cc_start: 0.7707 (mtp) cc_final: 0.7303 (mtp) REVERT: D 78 TYR cc_start: 0.7546 (t80) cc_final: 0.7304 (t80) REVERT: D 220 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8770 (mmm) REVERT: E 78 TYR cc_start: 0.7449 (t80) cc_final: 0.7185 (t80) REVERT: E 422 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7905 (mmm160) outliers start: 36 outliers final: 24 residues processed: 157 average time/residue: 0.5487 time to fit residues: 94.8736 Evaluate side-chains 158 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 90 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN E 171 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074822 restraints weight = 20507.256| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.28 r_work: 0.2915 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15035 Z= 0.109 Angle : 0.501 5.356 20262 Z= 0.264 Chirality : 0.040 0.154 2245 Planarity : 0.003 0.032 2505 Dihedral : 6.567 52.769 2380 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.97 % Allowed : 11.97 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.21), residues: 1710 helix: 3.00 (0.20), residues: 575 sheet: 0.80 (0.26), residues: 435 loop : 0.03 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.021 0.001 TYR C 301 PHE 0.019 0.001 PHE D 295 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00244 (15010) covalent geometry : angle 0.50003 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.03980 ( 657) hydrogen bonds : angle 4.27212 ( 2160) metal coordination : bond 0.00081 ( 15) link_BETA1-4 : bond 0.00222 ( 5) link_BETA1-4 : angle 1.21852 ( 15) link_NAG-ASN : bond 0.00061 ( 5) link_NAG-ASN : angle 0.49167 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.556 Fit side-chains REVERT: A 78 TYR cc_start: 0.7431 (t80) cc_final: 0.7119 (t80) REVERT: B 8 MET cc_start: 0.7281 (tpt) cc_final: 0.7013 (tpp) REVERT: B 78 TYR cc_start: 0.7528 (t80) cc_final: 0.7281 (t80) REVERT: B 421 LEU cc_start: 0.8509 (tt) cc_final: 0.8209 (mp) REVERT: B 422 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8070 (mtt-85) REVERT: C 78 TYR cc_start: 0.7467 (t80) cc_final: 0.7194 (t80) REVERT: C 421 LEU cc_start: 0.8682 (tt) cc_final: 0.8290 (mp) REVERT: C 422 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6481 (mtm180) REVERT: D 8 MET cc_start: 0.7551 (tpt) cc_final: 0.7126 (tpp) REVERT: D 18 MET cc_start: 0.7658 (mtp) cc_final: 0.7255 (mtp) REVERT: D 220 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8714 (mmm) REVERT: E 78 TYR cc_start: 0.7463 (t80) cc_final: 0.7114 (t80) REVERT: E 422 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7907 (mmm160) outliers start: 31 outliers final: 20 residues processed: 160 average time/residue: 0.5257 time to fit residues: 92.7822 Evaluate side-chains 157 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 120 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073999 restraints weight = 20487.761| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.26 r_work: 0.2896 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15035 Z= 0.142 Angle : 0.525 6.713 20262 Z= 0.277 Chirality : 0.041 0.154 2245 Planarity : 0.003 0.032 2505 Dihedral : 6.593 54.156 2380 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.97 % Allowed : 12.55 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.21), residues: 1710 helix: 2.98 (0.20), residues: 575 sheet: 0.80 (0.26), residues: 435 loop : 0.00 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 20 TYR 0.022 0.001 TYR C 301 PHE 0.019 0.002 PHE C 295 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.000 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00336 (15010) covalent geometry : angle 0.52365 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.04271 ( 657) hydrogen bonds : angle 4.31614 ( 2160) metal coordination : bond 0.00165 ( 15) link_BETA1-4 : bond 0.00189 ( 5) link_BETA1-4 : angle 1.23083 ( 15) link_NAG-ASN : bond 0.00080 ( 5) link_NAG-ASN : angle 0.63322 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.381 Fit side-chains REVERT: A 78 TYR cc_start: 0.7449 (t80) cc_final: 0.7187 (t80) REVERT: B 8 MET cc_start: 0.7247 (tpt) cc_final: 0.6965 (tpp) REVERT: B 78 TYR cc_start: 0.7539 (t80) cc_final: 0.7300 (t80) REVERT: B 421 LEU cc_start: 0.8517 (tt) cc_final: 0.8215 (mp) REVERT: B 422 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8081 (mtt-85) REVERT: C 8 MET cc_start: 0.7279 (tpt) cc_final: 0.6986 (tpp) REVERT: C 78 TYR cc_start: 0.7487 (t80) cc_final: 0.7201 (t80) REVERT: C 421 LEU cc_start: 0.8688 (tt) cc_final: 0.8300 (mp) REVERT: C 422 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.6501 (mtm180) REVERT: D 8 MET cc_start: 0.7461 (tpt) cc_final: 0.7204 (tpp) REVERT: D 18 MET cc_start: 0.7648 (mtp) cc_final: 0.7257 (mtp) REVERT: D 78 TYR cc_start: 0.7378 (t80) cc_final: 0.7126 (t80) REVERT: D 220 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8733 (mmm) REVERT: E 78 TYR cc_start: 0.7490 (t80) cc_final: 0.7198 (t80) REVERT: E 422 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7899 (mmm160) outliers start: 31 outliers final: 22 residues processed: 156 average time/residue: 0.5708 time to fit residues: 97.9479 Evaluate side-chains 160 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 72 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN E 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.074527 restraints weight = 20629.316| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.26 r_work: 0.2909 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15035 Z= 0.124 Angle : 0.522 7.042 20262 Z= 0.274 Chirality : 0.041 0.153 2245 Planarity : 0.003 0.032 2505 Dihedral : 6.445 54.549 2380 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.91 % Allowed : 12.74 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.21), residues: 1710 helix: 3.08 (0.20), residues: 570 sheet: 0.83 (0.26), residues: 435 loop : -0.00 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.022 0.001 TYR C 301 PHE 0.019 0.001 PHE C 295 TRP 0.009 0.001 TRP A 68 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00290 (15010) covalent geometry : angle 0.52097 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.04101 ( 657) hydrogen bonds : angle 4.26038 ( 2160) metal coordination : bond 0.00127 ( 15) link_BETA1-4 : bond 0.00199 ( 5) link_BETA1-4 : angle 1.21907 ( 15) link_NAG-ASN : bond 0.00028 ( 5) link_NAG-ASN : angle 0.55004 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.379 Fit side-chains REVERT: A 78 TYR cc_start: 0.7450 (t80) cc_final: 0.7178 (t80) REVERT: A 421 LEU cc_start: 0.8598 (tt) cc_final: 0.8226 (mp) REVERT: B 8 MET cc_start: 0.7226 (tpt) cc_final: 0.6909 (tpp) REVERT: B 78 TYR cc_start: 0.7535 (t80) cc_final: 0.7299 (t80) REVERT: B 421 LEU cc_start: 0.8519 (tt) cc_final: 0.8236 (mp) REVERT: B 422 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8070 (mtt-85) REVERT: C 8 MET cc_start: 0.7316 (tpt) cc_final: 0.7009 (tpp) REVERT: C 78 TYR cc_start: 0.7490 (t80) cc_final: 0.7187 (t80) REVERT: C 421 LEU cc_start: 0.8688 (tt) cc_final: 0.8310 (mp) REVERT: C 422 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.6535 (mtm180) REVERT: D 8 MET cc_start: 0.7512 (tpt) cc_final: 0.7231 (tpp) REVERT: D 18 MET cc_start: 0.7677 (mtp) cc_final: 0.7272 (mtp) REVERT: D 78 TYR cc_start: 0.7384 (t80) cc_final: 0.7174 (t80) REVERT: D 220 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8724 (mmm) REVERT: E 78 TYR cc_start: 0.7446 (t80) cc_final: 0.7160 (t80) REVERT: E 422 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7922 (mmm160) outliers start: 30 outliers final: 22 residues processed: 157 average time/residue: 0.5640 time to fit residues: 97.3274 Evaluate side-chains 160 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.073691 restraints weight = 20636.026| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.27 r_work: 0.2891 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15035 Z= 0.152 Angle : 0.551 8.067 20262 Z= 0.290 Chirality : 0.042 0.153 2245 Planarity : 0.004 0.049 2505 Dihedral : 6.571 56.602 2380 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.78 % Allowed : 12.87 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.21), residues: 1710 helix: 2.99 (0.20), residues: 575 sheet: 0.79 (0.26), residues: 435 loop : 0.01 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 20 TYR 0.023 0.001 TYR C 301 PHE 0.018 0.002 PHE C 295 TRP 0.008 0.001 TRP A 68 HIS 0.002 0.000 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00362 (15010) covalent geometry : angle 0.55047 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.04409 ( 657) hydrogen bonds : angle 4.34920 ( 2160) metal coordination : bond 0.00180 ( 15) link_BETA1-4 : bond 0.00159 ( 5) link_BETA1-4 : angle 1.23662 ( 15) link_NAG-ASN : bond 0.00109 ( 5) link_NAG-ASN : angle 0.66543 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.568 Fit side-chains REVERT: A 78 TYR cc_start: 0.7467 (t80) cc_final: 0.7181 (t80) REVERT: A 421 LEU cc_start: 0.8565 (tt) cc_final: 0.8201 (mp) REVERT: B 8 MET cc_start: 0.7202 (tpt) cc_final: 0.6870 (tpp) REVERT: B 78 TYR cc_start: 0.7550 (t80) cc_final: 0.7310 (t80) REVERT: B 421 LEU cc_start: 0.8514 (tt) cc_final: 0.8225 (mp) REVERT: B 422 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8103 (mtt-85) REVERT: C 8 MET cc_start: 0.7288 (tpt) cc_final: 0.6916 (tpp) REVERT: C 78 TYR cc_start: 0.7497 (t80) cc_final: 0.7192 (t80) REVERT: C 421 LEU cc_start: 0.8686 (tt) cc_final: 0.8320 (mp) REVERT: C 422 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.6561 (mtm180) REVERT: D 8 MET cc_start: 0.7477 (tpt) cc_final: 0.7185 (tpp) REVERT: D 18 MET cc_start: 0.7663 (mtp) cc_final: 0.7244 (mtp) REVERT: D 78 TYR cc_start: 0.7417 (t80) cc_final: 0.7207 (t80) REVERT: E 78 TYR cc_start: 0.7435 (t80) cc_final: 0.7087 (t80) REVERT: E 422 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7919 (mmm160) outliers start: 28 outliers final: 24 residues processed: 155 average time/residue: 0.5740 time to fit residues: 97.6467 Evaluate side-chains 160 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 153 optimal weight: 0.2980 chunk 157 optimal weight: 5.9990 chunk 32 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 77 optimal weight: 7.9990 chunk 104 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.100358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077128 restraints weight = 20501.532| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.26 r_work: 0.2964 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15035 Z= 0.094 Angle : 0.509 8.616 20262 Z= 0.264 Chirality : 0.040 0.152 2245 Planarity : 0.003 0.036 2505 Dihedral : 5.903 54.416 2380 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.15 % Allowed : 13.69 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.21), residues: 1710 helix: 3.22 (0.20), residues: 570 sheet: 0.94 (0.26), residues: 435 loop : 0.09 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 20 TYR 0.018 0.001 TYR C 301 PHE 0.022 0.001 PHE C 121 TRP 0.011 0.001 TRP D 68 HIS 0.002 0.000 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00208 (15010) covalent geometry : angle 0.50862 (20225) SS BOND : angle 0.00000 ( 7) hydrogen bonds : bond 0.03472 ( 657) hydrogen bonds : angle 4.06444 ( 2160) metal coordination : bond 0.00022 ( 15) link_BETA1-4 : bond 0.00279 ( 5) link_BETA1-4 : angle 1.18823 ( 15) link_NAG-ASN : bond 0.00208 ( 5) link_NAG-ASN : angle 0.31955 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6120.19 seconds wall clock time: 104 minutes 27.53 seconds (6267.53 seconds total)