Starting phenix.real_space_refine on Sat Jun 21 23:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwj_44976/06_2025/9bwj_44976.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwj_44976/06_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_44976/06_2025/9bwj_44976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwj_44976/06_2025/9bwj_44976.map" model { file = "/net/cci-nas-00/data/ceres_data/9bwj_44976/06_2025/9bwj_44976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwj_44976/06_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-5710/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: 7.80, per 1000 atoms: 0.53 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: 3.71 Conformation dependent library (CDL) restraints added in 1.6 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: 1.67 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: 4.68 Time building geometry restraints manager: 4.36 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: 1.850 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.630 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.030 ------------------------------------------------------------------------------- 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 : 1.581 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: 1.2930 time to fit residues: 206.5939 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 : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain E residue 14 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 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 = 0.097549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.073713 restraints weight = 20578.946| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.25 r_work: 0.2902 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 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 : 1.523 Fit side-chains REVERT: A 78 TYR cc_start: 0.7155 (t80) cc_final: 0.6860 (t80) REVERT: B 78 TYR cc_start: 0.7448 (t80) cc_final: 0.7171 (t80) REVERT: B 144 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7327 (m110) REVERT: C 78 TYR cc_start: 0.7426 (t80) cc_final: 0.7075 (t80) REVERT: D 18 MET cc_start: 0.7709 (mtp) cc_final: 0.7246 (mtp) REVERT: D 78 TYR cc_start: 0.7389 (t80) cc_final: 0.7151 (t80) REVERT: E 422 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7772 (mmm160) outliers start: 33 outliers final: 16 residues processed: 157 average time/residue: 1.2537 time to fit residues: 217.0103 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 : 1.513 ------------------------------------------------------------------------------- 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: 1.9990 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: 5.9990 chunk 65 optimal weight: 2.9990 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 = 0.3473 r_free = 0.3473 target = 0.096386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072333 restraints weight = 20470.121| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.27 r_work: 0.2867 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15035 Z= 0.195 Angle : 0.564 5.568 20262 Z= 0.302 Chirality : 0.043 0.156 2245 Planarity : 0.004 0.030 2505 Dihedral : 7.515 50.837 2382 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.29 % Allowed : 9.30 % Favored : 88.41 % 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: 1.05 (0.20), residues: 1710 helix: 2.15 (0.20), residues: 575 sheet: 0.49 (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 0.81270 ( 15) link_BETA1-4 : bond 0.00151 ( 5) link_BETA1-4 : angle 1.10326 ( 15) hydrogen bonds : bond 0.05119 ( 657) hydrogen bonds : angle 4.70311 ( 2160) metal coordination : bond 0.00257 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00463 (15010) covalent geometry : angle 0.56297 (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 : 1.557 Fit side-chains REVERT: A 8 MET cc_start: 0.7503 (tpt) cc_final: 0.7294 (tpp) REVERT: A 78 TYR cc_start: 0.7290 (t80) cc_final: 0.7004 (t80) REVERT: B 78 TYR cc_start: 0.7505 (t80) cc_final: 0.7296 (t80) REVERT: B 226 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8329 (mm110) REVERT: C 78 TYR cc_start: 0.7479 (t80) cc_final: 0.7172 (t80) REVERT: C 422 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6497 (mtm180) REVERT: D 18 MET cc_start: 0.7763 (mtp) cc_final: 0.7321 (mtp) REVERT: D 78 TYR cc_start: 0.7488 (t80) cc_final: 0.7276 (t80) REVERT: E 78 TYR cc_start: 0.7382 (t80) cc_final: 0.7172 (t80) outliers start: 36 outliers final: 24 residues processed: 157 average time/residue: 1.2752 time to fit residues: 220.4580 Evaluate side-chains 154 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 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: 0.9990 chunk 3 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.096535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.072800 restraints weight = 20407.894| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.25 r_work: 0.2870 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15035 Z= 0.185 Angle : 0.553 6.352 20262 Z= 0.294 Chirality : 0.043 0.156 2245 Planarity : 0.004 0.036 2505 Dihedral : 7.374 53.001 2380 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.42 % Allowed : 10.19 % Favored : 87.39 % 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: 1.38 (0.20), residues: 1710 helix: 2.51 (0.20), residues: 575 sheet: 0.55 (0.26), residues: 435 loop : -0.16 (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 0.023 0.001 TYR B 301 ARG 0.006 0.000 ARG C 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 5) link_NAG-ASN : angle 0.78571 ( 15) link_BETA1-4 : bond 0.00196 ( 5) link_BETA1-4 : angle 1.19422 ( 15) hydrogen bonds : bond 0.04841 ( 657) hydrogen bonds : angle 4.58745 ( 2160) metal coordination : bond 0.00215 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00442 (15010) covalent geometry : angle 0.55204 (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 172 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 1.941 Fit side-chains REVERT: A 8 MET cc_start: 0.7468 (tpt) cc_final: 0.7230 (tpp) REVERT: A 78 TYR cc_start: 0.7363 (t80) cc_final: 0.7050 (t80) REVERT: B 78 TYR cc_start: 0.7533 (t80) cc_final: 0.7331 (t80) REVERT: B 421 LEU cc_start: 0.8440 (tt) cc_final: 0.8190 (mp) REVERT: C 78 TYR cc_start: 0.7475 (t80) cc_final: 0.7231 (t80) REVERT: C 422 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.6539 (mtm180) REVERT: D 18 MET cc_start: 0.7770 (mtp) cc_final: 0.7299 (mtp) REVERT: D 78 TYR cc_start: 0.7571 (t80) cc_final: 0.7333 (t80) REVERT: E 78 TYR cc_start: 0.7435 (t80) cc_final: 0.7225 (t80) REVERT: E 422 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7880 (mmm160) outliers start: 38 outliers final: 24 residues processed: 156 average time/residue: 1.6573 time to fit residues: 283.9077 Evaluate side-chains 156 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 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 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain 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: 3.9990 chunk 135 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.097899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.074168 restraints weight = 20652.117| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.28 r_work: 0.2902 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15035 Z= 0.124 Angle : 0.511 5.272 20262 Z= 0.271 Chirality : 0.041 0.155 2245 Planarity : 0.003 0.032 2505 Dihedral : 6.913 53.641 2380 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.10 % Allowed : 11.08 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.21), residues: 1710 helix: 2.81 (0.20), residues: 575 sheet: 0.66 (0.26), residues: 435 loop : -0.04 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.002 0.001 HIS A 215 PHE 0.019 0.001 PHE C 295 TYR 0.022 0.001 TYR C 301 ARG 0.006 0.000 ARG C 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 5) link_NAG-ASN : angle 0.57196 ( 15) link_BETA1-4 : bond 0.00244 ( 5) link_BETA1-4 : angle 1.20885 ( 15) hydrogen bonds : bond 0.04204 ( 657) hydrogen bonds : angle 4.36826 ( 2160) metal coordination : bond 0.00106 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00286 (15010) covalent geometry : angle 0.50995 (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 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.932 Fit side-chains REVERT: A 8 MET cc_start: 0.7423 (tpt) cc_final: 0.7143 (tpp) REVERT: A 78 TYR cc_start: 0.7408 (t80) cc_final: 0.7088 (t80) REVERT: B 78 TYR cc_start: 0.7517 (t80) cc_final: 0.7300 (t80) REVERT: B 421 LEU cc_start: 0.8454 (tt) cc_final: 0.8226 (mp) REVERT: B 422 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8190 (mmm160) REVERT: C 78 TYR cc_start: 0.7474 (t80) cc_final: 0.7205 (t80) REVERT: C 422 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6508 (mtm180) REVERT: D 18 MET cc_start: 0.7730 (mtp) cc_final: 0.7351 (mtp) REVERT: D 78 TYR cc_start: 0.7553 (t80) cc_final: 0.7307 (t80) REVERT: E 78 TYR cc_start: 0.7416 (t80) cc_final: 0.7196 (t80) REVERT: E 422 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7881 (mmm160) outliers start: 33 outliers final: 20 residues processed: 159 average time/residue: 1.3381 time to fit residues: 235.5421 Evaluate side-chains 155 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 111 VAL 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 C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 117 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN E 171 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.073923 restraints weight = 20726.031| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.27 r_work: 0.2897 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1560 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= 0.139 Angle : 0.518 5.722 20262 Z= 0.274 Chirality : 0.041 0.157 2245 Planarity : 0.003 0.032 2505 Dihedral : 6.790 55.322 2380 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.23 % Allowed : 11.34 % Favored : 86.43 % 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: 1.73 (0.21), residues: 1710 helix: 2.88 (0.20), residues: 575 sheet: 0.73 (0.26), residues: 435 loop : -0.02 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 68 HIS 0.002 0.000 HIS D 109 PHE 0.018 0.002 PHE C 295 TYR 0.022 0.001 TYR C 301 ARG 0.006 0.000 ARG E 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 5) link_NAG-ASN : angle 0.64926 ( 15) link_BETA1-4 : bond 0.00191 ( 5) link_BETA1-4 : angle 1.22716 ( 15) hydrogen bonds : bond 0.04287 ( 657) hydrogen bonds : angle 4.35080 ( 2160) metal coordination : bond 0.00161 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00327 (15010) covalent geometry : angle 0.51714 (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 172 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.620 Fit side-chains REVERT: A 8 MET cc_start: 0.7429 (tpt) cc_final: 0.7211 (tpp) REVERT: A 78 TYR cc_start: 0.7431 (t80) cc_final: 0.7128 (t80) REVERT: B 8 MET cc_start: 0.7304 (tpt) cc_final: 0.6927 (tpp) REVERT: B 78 TYR cc_start: 0.7537 (t80) cc_final: 0.7330 (t80) REVERT: B 421 LEU cc_start: 0.8480 (tt) cc_final: 0.8266 (mp) REVERT: B 422 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7119 (mmm160) REVERT: C 8 MET cc_start: 0.7448 (tpt) cc_final: 0.7154 (tpp) REVERT: C 78 TYR cc_start: 0.7485 (t80) cc_final: 0.7199 (t80) REVERT: C 421 LEU cc_start: 0.8699 (tt) cc_final: 0.8316 (mp) REVERT: C 422 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.6512 (mtm180) REVERT: D 18 MET cc_start: 0.7724 (mtp) cc_final: 0.7335 (mtp) REVERT: E 8 MET cc_start: 0.7514 (tpt) cc_final: 0.7292 (tpp) REVERT: E 78 TYR cc_start: 0.7436 (t80) cc_final: 0.7144 (t80) REVERT: E 422 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7904 (mmm160) outliers start: 35 outliers final: 24 residues processed: 159 average time/residue: 1.2408 time to fit residues: 218.1362 Evaluate side-chains 160 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 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 C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain 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: 3.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 47 optimal weight: 0.0270 chunk 144 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN E 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.098932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.075483 restraints weight = 20628.860| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.26 r_work: 0.2929 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15035 Z= 0.102 Angle : 0.494 5.641 20262 Z= 0.260 Chirality : 0.040 0.154 2245 Planarity : 0.003 0.031 2505 Dihedral : 6.381 54.462 2380 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.78 % Allowed : 12.23 % Favored : 85.99 % 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: 1.90 (0.21), residues: 1710 helix: 3.03 (0.20), residues: 575 sheet: 0.83 (0.26), residues: 435 loop : 0.06 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.002 0.000 HIS C 215 PHE 0.019 0.001 PHE D 295 TYR 0.021 0.001 TYR D 301 ARG 0.007 0.000 ARG E 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 5) link_NAG-ASN : angle 0.44750 ( 15) link_BETA1-4 : bond 0.00240 ( 5) link_BETA1-4 : angle 1.20724 ( 15) hydrogen bonds : bond 0.03797 ( 657) hydrogen bonds : angle 4.18655 ( 2160) metal coordination : bond 0.00072 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00229 (15010) covalent geometry : angle 0.49355 (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 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.766 Fit side-chains REVERT: A 8 MET cc_start: 0.7347 (tpt) cc_final: 0.7130 (tpp) REVERT: A 78 TYR cc_start: 0.7400 (t80) cc_final: 0.7139 (t80) REVERT: B 8 MET cc_start: 0.7305 (tpt) cc_final: 0.6977 (tpp) REVERT: B 78 TYR cc_start: 0.7495 (t80) cc_final: 0.7281 (t80) REVERT: B 422 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7114 (mmm160) REVERT: C 78 TYR cc_start: 0.7474 (t80) cc_final: 0.7235 (t80) REVERT: C 421 LEU cc_start: 0.8683 (tt) cc_final: 0.8288 (mp) REVERT: C 422 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.6499 (mtm180) REVERT: D 18 MET cc_start: 0.7633 (mtp) cc_final: 0.7253 (mtp) REVERT: D 78 TYR cc_start: 0.7390 (t80) cc_final: 0.7189 (t80) REVERT: E 78 TYR cc_start: 0.7474 (t80) cc_final: 0.7177 (t80) REVERT: E 422 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7898 (mmm160) outliers start: 28 outliers final: 19 residues processed: 158 average time/residue: 1.5906 time to fit residues: 277.8888 Evaluate side-chains 156 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL 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 220 MET Chi-restraints excluded: chain B residue 422 ARG 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 C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain 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: 10.0000 chunk 46 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN E 171 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.095389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071358 restraints weight = 20538.132| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.28 r_work: 0.2850 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15035 Z= 0.258 Angle : 0.601 6.972 20262 Z= 0.320 Chirality : 0.046 0.160 2245 Planarity : 0.004 0.030 2505 Dihedral : 7.286 59.123 2380 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.10 % Allowed : 12.42 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.58 (0.21), residues: 1710 helix: 2.83 (0.20), residues: 570 sheet: 0.66 (0.26), residues: 435 loop : -0.16 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 239 HIS 0.003 0.001 HIS E 215 PHE 0.018 0.002 PHE E 48 TYR 0.024 0.002 TYR E 301 ARG 0.005 0.001 ARG E 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 5) link_NAG-ASN : angle 0.96352 ( 15) link_BETA1-4 : bond 0.00082 ( 5) link_BETA1-4 : angle 1.28637 ( 15) hydrogen bonds : bond 0.05276 ( 657) hydrogen bonds : angle 4.62575 ( 2160) metal coordination : bond 0.00381 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00628 (15010) covalent geometry : angle 0.60035 (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 169 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 2.064 Fit side-chains REVERT: A 8 MET cc_start: 0.7449 (tpt) cc_final: 0.7209 (tpp) REVERT: A 78 TYR cc_start: 0.7456 (t80) cc_final: 0.7185 (t80) REVERT: B 8 MET cc_start: 0.7242 (tpt) cc_final: 0.6825 (tpp) REVERT: B 422 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8107 (mtt-85) REVERT: C 8 MET cc_start: 0.7227 (tpt) cc_final: 0.7004 (tpp) REVERT: C 78 TYR cc_start: 0.7526 (t80) cc_final: 0.7291 (t80) REVERT: C 421 LEU cc_start: 0.8670 (tt) cc_final: 0.8319 (mp) REVERT: C 422 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.6597 (mtm180) REVERT: D 18 MET cc_start: 0.7816 (mtp) cc_final: 0.7404 (mtp) REVERT: D 220 MET cc_start: 0.8993 (mtp) cc_final: 0.8780 (mmm) REVERT: E 78 TYR cc_start: 0.7490 (t80) cc_final: 0.7209 (t80) REVERT: E 422 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7970 (mmm160) outliers start: 33 outliers final: 24 residues processed: 157 average time/residue: 2.2530 time to fit residues: 391.5706 Evaluate side-chains 160 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 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 C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 109 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.098394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074939 restraints weight = 20532.840| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.26 r_work: 0.2915 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15035 Z= 0.112 Angle : 0.518 6.818 20262 Z= 0.273 Chirality : 0.041 0.158 2245 Planarity : 0.003 0.032 2505 Dihedral : 6.639 58.359 2380 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.85 % Allowed : 12.99 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.21), residues: 1710 helix: 3.09 (0.20), residues: 570 sheet: 0.79 (0.26), residues: 435 loop : 0.00 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.002 0.000 HIS C 215 PHE 0.019 0.001 PHE C 295 TYR 0.020 0.001 TYR C 301 ARG 0.004 0.000 ARG E 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 5) link_NAG-ASN : angle 0.46536 ( 15) link_BETA1-4 : bond 0.00243 ( 5) link_BETA1-4 : angle 1.22665 ( 15) hydrogen bonds : bond 0.04005 ( 657) hydrogen bonds : angle 4.27615 ( 2160) metal coordination : bond 0.00081 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00254 (15010) covalent geometry : angle 0.51749 (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 165 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.615 Fit side-chains REVERT: A 8 MET cc_start: 0.7382 (tpt) cc_final: 0.7150 (tpp) REVERT: A 78 TYR cc_start: 0.7417 (t80) cc_final: 0.7142 (t80) REVERT: A 421 LEU cc_start: 0.8567 (tt) cc_final: 0.8207 (mp) REVERT: B 8 MET cc_start: 0.7300 (tpt) cc_final: 0.6986 (tpp) REVERT: B 78 TYR cc_start: 0.7478 (t80) cc_final: 0.7180 (t80) REVERT: B 422 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8094 (mtt-85) REVERT: C 78 TYR cc_start: 0.7480 (t80) cc_final: 0.7187 (t80) REVERT: C 421 LEU cc_start: 0.8675 (tt) cc_final: 0.8306 (mp) REVERT: C 422 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.6549 (mtm180) REVERT: D 18 MET cc_start: 0.7756 (mtp) cc_final: 0.7381 (mtp) REVERT: D 78 TYR cc_start: 0.7320 (t80) cc_final: 0.7058 (t80) REVERT: D 220 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8715 (mmm) REVERT: E 8 MET cc_start: 0.7486 (tpt) cc_final: 0.7193 (tpp) REVERT: E 78 TYR cc_start: 0.7470 (t80) cc_final: 0.7193 (t80) REVERT: E 422 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7729 (mmm160) outliers start: 29 outliers final: 19 residues processed: 157 average time/residue: 1.3409 time to fit residues: 234.1194 Evaluate side-chains 159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 2.271 ------------------------------------------------------------------------------- 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 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 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 C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 78 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 B 226 GLN C 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071826 restraints weight = 20963.575| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.25 r_work: 0.2855 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15035 Z= 0.234 Angle : 0.606 7.666 20262 Z= 0.320 Chirality : 0.045 0.157 2245 Planarity : 0.004 0.030 2505 Dihedral : 7.275 58.358 2380 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.72 % Allowed : 13.38 % 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: 1.65 (0.20), residues: 1710 helix: 2.86 (0.20), residues: 570 sheet: 0.69 (0.26), residues: 435 loop : -0.10 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 415 HIS 0.003 0.001 HIS E 215 PHE 0.017 0.002 PHE D 295 TYR 0.024 0.002 TYR E 301 ARG 0.004 0.001 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 5) link_NAG-ASN : angle 0.90293 ( 15) link_BETA1-4 : bond 0.00118 ( 5) link_BETA1-4 : angle 1.28993 ( 15) hydrogen bonds : bond 0.05118 ( 657) hydrogen bonds : angle 4.57298 ( 2160) metal coordination : bond 0.00329 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00567 (15010) covalent geometry : angle 0.60522 (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 159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.571 Fit side-chains REVERT: A 8 MET cc_start: 0.7479 (tpt) cc_final: 0.7244 (tpp) REVERT: A 78 TYR cc_start: 0.7448 (t80) cc_final: 0.7180 (t80) REVERT: B 8 MET cc_start: 0.7338 (tpt) cc_final: 0.7012 (tpp) REVERT: B 78 TYR cc_start: 0.7516 (t80) cc_final: 0.7262 (t80) REVERT: B 422 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8183 (mtt-85) REVERT: C 8 MET cc_start: 0.7304 (tpt) cc_final: 0.7040 (tpp) REVERT: C 78 TYR cc_start: 0.7533 (t80) cc_final: 0.7190 (t80) REVERT: C 422 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.6599 (mtm180) REVERT: D 18 MET cc_start: 0.7881 (mtp) cc_final: 0.7462 (mtp) REVERT: D 78 TYR cc_start: 0.7312 (t80) cc_final: 0.7085 (t80) REVERT: D 220 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8762 (mmm) REVERT: E 78 TYR cc_start: 0.7501 (t80) cc_final: 0.7266 (t80) REVERT: E 422 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8027 (mmm160) outliers start: 27 outliers final: 20 residues processed: 150 average time/residue: 1.3473 time to fit residues: 222.1454 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 : 1.820 ------------------------------------------------------------------------------- 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 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 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 C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074403 restraints weight = 20595.333| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.26 r_work: 0.2906 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15035 Z= 0.123 Angle : 0.541 8.315 20262 Z= 0.283 Chirality : 0.041 0.157 2245 Planarity : 0.003 0.034 2505 Dihedral : 6.806 59.399 2380 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.78 % Allowed : 13.44 % 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: 1.86 (0.21), residues: 1710 helix: 3.05 (0.20), residues: 570 sheet: 0.80 (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 0.001 0.000 HIS A 109 PHE 0.019 0.002 PHE D 295 TYR 0.021 0.001 TYR C 301 ARG 0.011 0.000 ARG C 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 5) link_NAG-ASN : angle 0.52105 ( 15) link_BETA1-4 : bond 0.00222 ( 5) link_BETA1-4 : angle 1.24951 ( 15) hydrogen bonds : bond 0.04152 ( 657) hydrogen bonds : angle 4.31297 ( 2160) metal coordination : bond 0.00114 ( 15) SS BOND : angle 0.00000 ( 7) covalent geometry : bond 0.00286 (15010) covalent geometry : angle 0.54008 (20225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13775.72 seconds wall clock time: 244 minutes 1.47 seconds (14641.47 seconds total)