Starting phenix.real_space_refine on Sat May 24 09:55:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwj_44976/05_2025/9bwj_44976.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwj_44976/05_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_44976/05_2025/9bwj_44976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwj_44976/05_2025/9bwj_44976.map" model { file = "/net/cci-nas-00/data/ceres_data/9bwj_44976/05_2025/9bwj_44976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwj_44976/05_2025/9bwj_44976.cif" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.44, per 1000 atoms: 0.51 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: 3.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.53 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: 4.35 Time building geometry restraints manager: 4.11 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: 0.08 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 427 or resid 501 through 506 or (resid 507 and ( \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C9 or name O5 or name O6 )) or (resid 508 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C9 or name O5 or name O6 )) or (resid 509 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C9 or name O5 o \ r name O6 )))) selection = (chain 'B' and (resid 8 through 427 or resid 501 through 506 or (resid 507 and ( \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C9 or name O5 or name O6 )) or (resid 508 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C9 or name O5 or name O6 )) or (resid 509 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C9 or name O5 o \ r name O6 )))) selection = (chain 'C' and (resid 8 through 427 or resid 501 through 506 or (resid 507 and ( \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C9 or name O5 or name O6 )) or (resid 508 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C9 or name O5 or name O6 )) or (resid 509 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C9 or name O5 o \ r name O6 )))) selection = (chain 'D' and (resid 8 through 427 or resid 501 through 506 or (resid 507 and ( \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C9 or name O5 or name O6 )) or (resid 508 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C9 or name O5 or name O6 )) or (resid 509 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C9 or name O5 o \ r name O6 )))) selection = (chain 'E' and (resid 8 through 427 or resid 501 through 502 or (resid 503 and ( \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C9 or name O5 or name O6 )) or (resid 504 and ( \ name C10 or name C11 or name 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 name 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 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 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.800 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP E 415 HIS 0.014 0.002 HIS E 215 PHE 0.022 0.002 PHE B 295 TYR 0.014 0.002 TYR D 301 ARG 0.013 0.002 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 5) link_NAG-ASN : angle 0.39120 ( 15) link_BETA1-4 : bond 0.00199 ( 5) link_BETA1-4 : angle 1.27887 ( 15) hydrogen bonds : bond 0.14393 ( 657) hydrogen bonds : angle 6.71307 ( 2160) metal coordination : bond 0.01908 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.01453 (15010) covalent geometry : angle 1.02138 (20225) *********************** 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 : 1.647 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: 1.3160 time to fit residues: 210.6113 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 : 1.626 ------------------------------------------------------------------------------- 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 143 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 133 optimal weight: 0.3980 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 chunk 99 optimal weight: 0.0370 chunk 154 optimal weight: 4.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.097596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.073711 restraints weight = 20583.562| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.26 r_work: 0.2901 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15035 Z= 0.148 Angle : 0.569 5.377 20262 Z= 0.303 Chirality : 0.042 0.152 2245 Planarity : 0.004 0.031 2505 Dihedral : 7.752 51.705 2390 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.10 % Allowed : 8.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1710 helix: 1.37 (0.20), residues: 590 sheet: 0.06 (0.27), residues: 415 loop : -0.35 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 415 HIS 0.006 0.001 HIS A 215 PHE 0.016 0.002 PHE C 295 TYR 0.019 0.002 TYR C 301 ARG 0.002 0.000 ARG B 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 5) link_NAG-ASN : angle 0.60374 ( 15) link_BETA1-4 : bond 0.00170 ( 5) link_BETA1-4 : angle 1.00033 ( 15) hydrogen bonds : bond 0.05031 ( 657) hydrogen bonds : angle 4.82426 ( 2160) metal coordination : bond 0.00192 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00339 (15010) covalent geometry : angle 0.56896 (20225) *********************** 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 170 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.575 Fit side-chains REVERT: A 78 TYR cc_start: 0.7151 (t80) cc_final: 0.6853 (t80) REVERT: B 78 TYR cc_start: 0.7444 (t80) cc_final: 0.7167 (t80) REVERT: B 144 ASN cc_start: 0.7540 (OUTLIER) cc_final: 0.7327 (m110) REVERT: C 78 TYR cc_start: 0.7419 (t80) cc_final: 0.7066 (t80) REVERT: D 18 MET cc_start: 0.7694 (mtp) cc_final: 0.7229 (mtp) REVERT: D 78 TYR cc_start: 0.7385 (t80) cc_final: 0.7145 (t80) REVERT: E 422 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7766 (mmm160) outliers start: 33 outliers final: 16 residues processed: 157 average time/residue: 1.2727 time to fit residues: 220.2691 Evaluate side-chains 147 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 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 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 E residue 14 LEU Chi-restraints excluded: chain E residue 111 VAL 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 166 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.096233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072253 restraints weight = 20450.673| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.26 r_work: 0.2865 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15035 Z= 0.198 Angle : 0.567 5.585 20262 Z= 0.304 Chirality : 0.043 0.155 2245 Planarity : 0.004 0.030 2505 Dihedral : 7.530 50.802 2382 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.29 % Allowed : 9.24 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1710 helix: 2.19 (0.20), residues: 575 sheet: 0.50 (0.28), residues: 385 loop : -0.30 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 68 HIS 0.003 0.001 HIS A 215 PHE 0.017 0.002 PHE E 48 TYR 0.022 0.002 TYR B 301 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 5) link_NAG-ASN : angle 0.83736 ( 15) link_BETA1-4 : bond 0.00234 ( 5) link_BETA1-4 : angle 1.13936 ( 15) hydrogen bonds : bond 0.05136 ( 657) hydrogen bonds : angle 4.69615 ( 2160) metal coordination : bond 0.00269 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00472 (15010) covalent geometry : angle 0.56624 (20225) *********************** 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 169 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.819 Fit side-chains REVERT: A 8 MET cc_start: 0.7501 (tpt) cc_final: 0.7284 (tpp) REVERT: A 78 TYR cc_start: 0.7322 (t80) cc_final: 0.7031 (t80) REVERT: B 78 TYR cc_start: 0.7513 (t80) cc_final: 0.7305 (t80) REVERT: B 226 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8327 (mm110) REVERT: C 78 TYR cc_start: 0.7484 (t80) cc_final: 0.7183 (t80) REVERT: D 8 MET cc_start: 0.7408 (tpt) cc_final: 0.7198 (tpp) REVERT: D 18 MET cc_start: 0.7769 (mtp) cc_final: 0.7327 (mtp) REVERT: D 78 TYR cc_start: 0.7497 (t80) cc_final: 0.7284 (t80) outliers start: 36 outliers final: 24 residues processed: 157 average time/residue: 1.2653 time to fit residues: 219.1293 Evaluate side-chains 155 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET 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 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 220 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 20 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN C 226 GLN D 171 GLN D 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073047 restraints weight = 20461.447| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.27 r_work: 0.2875 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15035 Z= 0.172 Angle : 0.545 6.054 20262 Z= 0.290 Chirality : 0.043 0.156 2245 Planarity : 0.004 0.032 2505 Dihedral : 7.293 52.319 2380 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.42 % Allowed : 10.06 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1710 helix: 2.55 (0.20), residues: 575 sheet: 0.57 (0.26), residues: 435 loop : -0.13 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.002 0.001 HIS D 109 PHE 0.016 0.002 PHE D 295 TYR 0.022 0.001 TYR B 301 ARG 0.007 0.000 ARG C 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 5) link_NAG-ASN : angle 0.74498 ( 15) link_BETA1-4 : bond 0.00154 ( 5) link_BETA1-4 : angle 1.17936 ( 15) hydrogen bonds : bond 0.04724 ( 657) hydrogen bonds : angle 4.55417 ( 2160) metal coordination : bond 0.00211 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00409 (15010) covalent geometry : angle 0.54433 (20225) *********************** 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 174 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.718 Fit side-chains REVERT: A 8 MET cc_start: 0.7474 (tpt) cc_final: 0.7256 (tpp) REVERT: A 78 TYR cc_start: 0.7339 (t80) cc_final: 0.7031 (t80) REVERT: B 144 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7202 (m110) REVERT: B 421 LEU cc_start: 0.8445 (tt) cc_final: 0.8208 (mp) REVERT: B 422 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7970 (mtt-85) REVERT: C 78 TYR cc_start: 0.7491 (t80) cc_final: 0.7244 (t80) REVERT: D 8 MET cc_start: 0.7558 (tpt) cc_final: 0.7200 (tpp) REVERT: D 18 MET cc_start: 0.7755 (mtp) cc_final: 0.7296 (mtp) REVERT: D 78 TYR cc_start: 0.7559 (t80) cc_final: 0.7320 (t80) REVERT: E 417 ILE cc_start: 0.8739 (mm) cc_final: 0.8385 (mm) REVERT: E 422 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7892 (mmm160) outliers start: 38 outliers final: 24 residues processed: 158 average time/residue: 1.2241 time to fit residues: 213.9003 Evaluate side-chains 157 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 A residue 416 VAL 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 220 MET 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 145 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 47 optimal weight: 0.0000 chunk 70 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 203 ASN D 226 GLN E 171 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.076207 restraints weight = 20747.984| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.27 r_work: 0.2945 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15035 Z= 0.097 Angle : 0.487 5.099 20262 Z= 0.256 Chirality : 0.040 0.158 2245 Planarity : 0.003 0.032 2505 Dihedral : 6.399 49.912 2380 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.59 % Allowed : 11.66 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.21), residues: 1710 helix: 2.98 (0.20), residues: 570 sheet: 0.75 (0.26), residues: 435 loop : 0.02 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.003 0.001 HIS C 215 PHE 0.019 0.001 PHE C 295 TYR 0.020 0.001 TYR C 301 ARG 0.009 0.000 ARG C 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 5) link_NAG-ASN : angle 0.43229 ( 15) link_BETA1-4 : bond 0.00291 ( 5) link_BETA1-4 : angle 1.18064 ( 15) hydrogen bonds : bond 0.03642 ( 657) hydrogen bonds : angle 4.18177 ( 2160) metal coordination : bond 0.00074 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00212 (15010) covalent geometry : angle 0.48653 (20225) *********************** 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 164 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.755 Fit side-chains REVERT: A 8 MET cc_start: 0.7433 (tpt) cc_final: 0.7218 (tpp) REVERT: A 78 TYR cc_start: 0.7372 (t80) cc_final: 0.7054 (t80) REVERT: A 421 LEU cc_start: 0.8593 (tt) cc_final: 0.8195 (mp) REVERT: B 8 MET cc_start: 0.7323 (tpt) cc_final: 0.7040 (tpp) REVERT: B 78 TYR cc_start: 0.7458 (t80) cc_final: 0.7175 (t80) REVERT: C 78 TYR cc_start: 0.7445 (t80) cc_final: 0.7223 (t80) REVERT: D 8 MET cc_start: 0.7477 (tpt) cc_final: 0.7106 (tpp) REVERT: D 18 MET cc_start: 0.7634 (mtp) cc_final: 0.7263 (mtp) REVERT: D 78 TYR cc_start: 0.7511 (t80) cc_final: 0.7290 (t80) REVERT: D 220 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8689 (mmm) REVERT: E 8 MET cc_start: 0.7558 (tpt) cc_final: 0.7329 (tpp) REVERT: E 78 TYR cc_start: 0.7386 (t80) cc_final: 0.7110 (t80) REVERT: E 417 ILE cc_start: 0.8734 (mm) cc_final: 0.8357 (mm) REVERT: E 421 LEU cc_start: 0.8660 (tt) cc_final: 0.8168 (mp) outliers start: 25 outliers final: 11 residues processed: 156 average time/residue: 1.1721 time to fit residues: 203.0681 Evaluate side-chains 145 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 103 GLU 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 144 ASN Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 117 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.0870 chunk 153 optimal weight: 0.0170 chunk 122 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.100687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077382 restraints weight = 20849.484| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.28 r_work: 0.2971 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15035 Z= 0.089 Angle : 0.471 5.059 20262 Z= 0.247 Chirality : 0.040 0.147 2245 Planarity : 0.003 0.035 2505 Dihedral : 5.817 45.860 2380 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.66 % Allowed : 12.10 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1710 helix: 3.19 (0.20), residues: 565 sheet: 0.89 (0.26), residues: 435 loop : 0.07 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.002 0.001 HIS E 215 PHE 0.019 0.001 PHE C 295 TYR 0.019 0.001 TYR D 301 ARG 0.007 0.000 ARG C 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 5) link_NAG-ASN : angle 0.40272 ( 15) link_BETA1-4 : bond 0.00231 ( 5) link_BETA1-4 : angle 1.18025 ( 15) hydrogen bonds : bond 0.03386 ( 657) hydrogen bonds : angle 3.99150 ( 2160) metal coordination : bond 0.00054 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00193 (15010) covalent geometry : angle 0.47023 (20225) *********************** 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 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.938 Fit side-chains REVERT: A 8 MET cc_start: 0.7489 (tpt) cc_final: 0.7248 (tpp) REVERT: A 78 TYR cc_start: 0.7408 (t80) cc_final: 0.7093 (t80) REVERT: A 171 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7934 (mm-40) REVERT: A 421 LEU cc_start: 0.8587 (tt) cc_final: 0.8204 (mp) REVERT: B 8 MET cc_start: 0.7312 (tpt) cc_final: 0.6984 (tpp) REVERT: B 78 TYR cc_start: 0.7470 (t80) cc_final: 0.7180 (t80) REVERT: C 78 TYR cc_start: 0.7456 (t80) cc_final: 0.7240 (t80) REVERT: D 8 MET cc_start: 0.7521 (tpt) cc_final: 0.7075 (tpp) REVERT: D 18 MET cc_start: 0.7575 (mtp) cc_final: 0.7184 (mtp) REVERT: D 78 TYR cc_start: 0.7496 (t80) cc_final: 0.7284 (t80) REVERT: D 220 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8600 (mmm) REVERT: E 8 MET cc_start: 0.7559 (tpt) cc_final: 0.7357 (tpp) REVERT: E 78 TYR cc_start: 0.7382 (t80) cc_final: 0.7117 (t80) REVERT: E 417 ILE cc_start: 0.8723 (mm) cc_final: 0.8426 (mm) REVERT: E 421 LEU cc_start: 0.8669 (tt) cc_final: 0.8193 (mp) REVERT: E 422 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7825 (mmm160) outliers start: 26 outliers final: 15 residues processed: 166 average time/residue: 1.2523 time to fit residues: 229.4899 Evaluate side-chains 161 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL 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 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 47 optimal weight: 0.0070 chunk 144 optimal weight: 0.0020 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.099785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.076380 restraints weight = 20800.219| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.27 r_work: 0.2955 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15035 Z= 0.099 Angle : 0.485 5.349 20262 Z= 0.254 Chirality : 0.040 0.154 2245 Planarity : 0.003 0.030 2505 Dihedral : 5.742 44.620 2380 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.21), residues: 1710 helix: 3.23 (0.20), residues: 565 sheet: 0.92 (0.26), residues: 435 loop : 0.09 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 68 HIS 0.002 0.000 HIS E 215 PHE 0.017 0.001 PHE C 295 TYR 0.021 0.001 TYR D 301 ARG 0.006 0.000 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 5) link_NAG-ASN : angle 0.47954 ( 15) link_BETA1-4 : bond 0.00243 ( 5) link_BETA1-4 : angle 1.17394 ( 15) hydrogen bonds : bond 0.03535 ( 657) hydrogen bonds : angle 4.01148 ( 2160) metal coordination : bond 0.00078 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00224 (15010) covalent geometry : angle 0.48387 (20225) *********************** 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 170 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.580 Fit side-chains REVERT: A 8 MET cc_start: 0.7534 (tpt) cc_final: 0.7302 (tpp) REVERT: A 78 TYR cc_start: 0.7435 (t80) cc_final: 0.7147 (t80) REVERT: A 421 LEU cc_start: 0.8596 (tt) cc_final: 0.8221 (mp) REVERT: B 8 MET cc_start: 0.7268 (tpt) cc_final: 0.6973 (tpp) REVERT: B 78 TYR cc_start: 0.7507 (t80) cc_final: 0.7238 (t80) REVERT: B 422 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7983 (mtt-85) REVERT: C 8 MET cc_start: 0.7301 (tpt) cc_final: 0.7036 (tpp) REVERT: C 78 TYR cc_start: 0.7462 (t80) cc_final: 0.7237 (t80) REVERT: D 8 MET cc_start: 0.7536 (tpt) cc_final: 0.7088 (tpp) REVERT: D 18 MET cc_start: 0.7600 (mtp) cc_final: 0.7233 (mtp) REVERT: D 220 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8634 (mmm) REVERT: E 8 MET cc_start: 0.7600 (tpt) cc_final: 0.7386 (tpp) REVERT: E 78 TYR cc_start: 0.7409 (t80) cc_final: 0.7133 (t80) REVERT: E 417 ILE cc_start: 0.8788 (mm) cc_final: 0.8484 (mm) REVERT: E 421 LEU cc_start: 0.8690 (tt) cc_final: 0.8228 (mp) REVERT: E 422 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7886 (mmm160) outliers start: 28 outliers final: 17 residues processed: 159 average time/residue: 1.2269 time to fit residues: 215.4899 Evaluate side-chains 160 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL 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 D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL 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 387 VAL 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 136 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 50 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 168 optimal weight: 0.4980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 177 GLN B 226 GLN C 226 GLN D 226 GLN E 203 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.098088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.074392 restraints weight = 20588.069| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.27 r_work: 0.2909 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1708 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= 0.138 Angle : 0.526 6.374 20262 Z= 0.277 Chirality : 0.041 0.151 2245 Planarity : 0.003 0.029 2505 Dihedral : 6.076 46.411 2380 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.85 % Allowed : 13.25 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.21), residues: 1710 helix: 3.02 (0.20), residues: 585 sheet: 0.88 (0.26), residues: 435 loop : 0.25 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 68 HIS 0.001 0.000 HIS D 109 PHE 0.016 0.001 PHE C 295 TYR 0.024 0.001 TYR D 301 ARG 0.006 0.000 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 5) link_NAG-ASN : angle 0.66561 ( 15) link_BETA1-4 : bond 0.00204 ( 5) link_BETA1-4 : angle 1.21311 ( 15) hydrogen bonds : bond 0.04171 ( 657) hydrogen bonds : angle 4.23082 ( 2160) metal coordination : bond 0.00162 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00327 (15010) covalent geometry : angle 0.52531 (20225) *********************** 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 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.553 Fit side-chains REVERT: A 8 MET cc_start: 0.7358 (tpt) cc_final: 0.7145 (tpp) REVERT: A 78 TYR cc_start: 0.7452 (t80) cc_final: 0.7208 (t80) REVERT: A 421 LEU cc_start: 0.8523 (tt) cc_final: 0.8165 (mp) REVERT: B 8 MET cc_start: 0.7291 (tpt) cc_final: 0.6982 (tpp) REVERT: B 78 TYR cc_start: 0.7517 (t80) cc_final: 0.7300 (t80) REVERT: B 422 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8022 (mtt-85) REVERT: C 8 MET cc_start: 0.7264 (tpt) cc_final: 0.6929 (tpp) REVERT: C 78 TYR cc_start: 0.7481 (t80) cc_final: 0.7245 (t80) REVERT: D 8 MET cc_start: 0.7504 (tpt) cc_final: 0.7223 (tpp) REVERT: D 18 MET cc_start: 0.7617 (mtp) cc_final: 0.7257 (mtp) REVERT: D 78 TYR cc_start: 0.7359 (t80) cc_final: 0.7126 (t80) REVERT: D 220 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8697 (mmm) REVERT: E 8 MET cc_start: 0.7573 (tpt) cc_final: 0.7329 (tpp) REVERT: E 78 TYR cc_start: 0.7432 (t80) cc_final: 0.7174 (t80) REVERT: E 417 ILE cc_start: 0.8843 (mm) cc_final: 0.8613 (mm) REVERT: E 421 LEU cc_start: 0.8666 (tt) cc_final: 0.8203 (mp) REVERT: E 422 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7891 (mmm160) outliers start: 29 outliers final: 21 residues processed: 157 average time/residue: 1.2576 time to fit residues: 218.2496 Evaluate side-chains 159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU 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 D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL 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 387 VAL 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 109 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 0.0170 chunk 69 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 177 GLN B 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.098375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.074739 restraints weight = 20613.471| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.27 r_work: 0.2916 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1728 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= 0.127 Angle : 0.523 7.890 20262 Z= 0.274 Chirality : 0.041 0.153 2245 Planarity : 0.003 0.029 2505 Dihedral : 6.051 46.687 2380 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.72 % Allowed : 13.57 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.21), residues: 1710 helix: 3.05 (0.20), residues: 585 sheet: 0.88 (0.26), residues: 435 loop : 0.24 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 68 HIS 0.001 0.000 HIS D 109 PHE 0.018 0.001 PHE C 295 TYR 0.022 0.001 TYR C 301 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00027 ( 5) link_NAG-ASN : angle 0.56288 ( 15) link_BETA1-4 : bond 0.00226 ( 5) link_BETA1-4 : angle 1.20338 ( 15) hydrogen bonds : bond 0.04066 ( 657) hydrogen bonds : angle 4.21015 ( 2160) metal coordination : bond 0.00133 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00299 (15010) covalent geometry : angle 0.52269 (20225) *********************** 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 162 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.819 Fit side-chains REVERT: A 8 MET cc_start: 0.7351 (tpt) cc_final: 0.7133 (tpp) REVERT: A 78 TYR cc_start: 0.7458 (t80) cc_final: 0.7207 (t80) REVERT: A 421 LEU cc_start: 0.8511 (tt) cc_final: 0.8162 (mp) REVERT: B 8 MET cc_start: 0.7257 (tpt) cc_final: 0.6940 (tpp) REVERT: B 78 TYR cc_start: 0.7524 (t80) cc_final: 0.7280 (t80) REVERT: B 422 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8057 (mtt-85) REVERT: C 8 MET cc_start: 0.7279 (tpt) cc_final: 0.6906 (tpp) REVERT: C 78 TYR cc_start: 0.7480 (t80) cc_final: 0.7232 (t80) REVERT: D 8 MET cc_start: 0.7438 (tpt) cc_final: 0.7097 (tpp) REVERT: D 18 MET cc_start: 0.7599 (mtp) cc_final: 0.7249 (mtp) REVERT: D 78 TYR cc_start: 0.7359 (t80) cc_final: 0.7103 (t80) REVERT: D 220 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8700 (mmm) REVERT: E 8 MET cc_start: 0.7551 (tpt) cc_final: 0.7312 (tpp) REVERT: E 78 TYR cc_start: 0.7416 (t80) cc_final: 0.7185 (t80) REVERT: E 417 ILE cc_start: 0.8843 (mm) cc_final: 0.8612 (mm) REVERT: E 421 LEU cc_start: 0.8662 (tt) cc_final: 0.8208 (mp) REVERT: E 422 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7900 (mmm160) outliers start: 27 outliers final: 19 residues processed: 154 average time/residue: 1.2939 time to fit residues: 219.4755 Evaluate side-chains 158 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL 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 387 VAL 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 78 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 226 GLN C 226 GLN D 226 GLN E 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.074524 restraints weight = 20757.472| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.30 r_work: 0.2909 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15035 Z= 0.131 Angle : 0.538 8.750 20262 Z= 0.281 Chirality : 0.041 0.153 2245 Planarity : 0.003 0.029 2505 Dihedral : 6.076 47.100 2380 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.59 % Allowed : 13.63 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.21), residues: 1710 helix: 3.02 (0.20), residues: 585 sheet: 0.87 (0.26), residues: 435 loop : 0.24 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 68 HIS 0.001 0.000 HIS D 109 PHE 0.018 0.001 PHE A 295 TYR 0.023 0.001 TYR C 301 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00036 ( 5) link_NAG-ASN : angle 0.58029 ( 15) link_BETA1-4 : bond 0.00210 ( 5) link_BETA1-4 : angle 1.21467 ( 15) hydrogen bonds : bond 0.04127 ( 657) hydrogen bonds : angle 4.22447 ( 2160) metal coordination : bond 0.00143 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00309 (15010) covalent geometry : angle 0.53766 (20225) ********************** 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 160 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.627 Fit side-chains REVERT: A 8 MET cc_start: 0.7379 (tpt) cc_final: 0.7161 (tpp) REVERT: A 78 TYR cc_start: 0.7451 (t80) cc_final: 0.7197 (t80) REVERT: A 421 LEU cc_start: 0.8513 (tt) cc_final: 0.8184 (mp) REVERT: B 8 MET cc_start: 0.7265 (tpt) cc_final: 0.6943 (tpp) REVERT: B 78 TYR cc_start: 0.7533 (t80) cc_final: 0.7288 (t80) REVERT: B 422 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8081 (mtt-85) REVERT: C 8 MET cc_start: 0.7288 (tpt) cc_final: 0.6906 (tpp) REVERT: C 78 TYR cc_start: 0.7484 (t80) cc_final: 0.7242 (t80) REVERT: D 8 MET cc_start: 0.7447 (tpt) cc_final: 0.7109 (tpp) REVERT: D 18 MET cc_start: 0.7651 (mtp) cc_final: 0.7250 (mtp) REVERT: D 78 TYR cc_start: 0.7397 (t80) cc_final: 0.7187 (t80) REVERT: D 220 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8701 (mmm) REVERT: E 8 MET cc_start: 0.7571 (tpt) cc_final: 0.7333 (tpp) REVERT: E 78 TYR cc_start: 0.7425 (t80) cc_final: 0.7199 (t80) REVERT: E 417 ILE cc_start: 0.8856 (mm) cc_final: 0.8615 (mm) REVERT: E 421 LEU cc_start: 0.8663 (tt) cc_final: 0.8216 (mp) REVERT: E 422 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7917 (mmm160) outliers start: 25 outliers final: 22 residues processed: 152 average time/residue: 1.2240 time to fit residues: 205.5997 Evaluate side-chains 159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL 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 387 VAL 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 246 MET 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 34 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075608 restraints weight = 20754.738| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.27 r_work: 0.2934 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15035 Z= 0.109 Angle : 0.524 8.447 20262 Z= 0.272 Chirality : 0.041 0.152 2245 Planarity : 0.003 0.041 2505 Dihedral : 5.845 45.771 2380 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.72 % Allowed : 13.44 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.21), residues: 1710 helix: 3.15 (0.20), residues: 580 sheet: 0.91 (0.26), residues: 435 loop : 0.26 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.001 0.000 HIS A 109 PHE 0.019 0.001 PHE A 295 TYR 0.021 0.001 TYR D 301 ARG 0.013 0.000 ARG C 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 5) link_NAG-ASN : angle 0.45785 ( 15) link_BETA1-4 : bond 0.00263 ( 5) link_BETA1-4 : angle 1.20218 ( 15) hydrogen bonds : bond 0.03792 ( 657) hydrogen bonds : angle 4.12107 ( 2160) metal coordination : bond 0.00081 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00252 (15010) covalent geometry : angle 0.52312 (20225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12472.23 seconds wall clock time: 214 minutes 36.93 seconds (12876.93 seconds total)