Starting phenix.real_space_refine on Fri Feb 6 12:09:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwj_44976/02_2026/9bwj_44976.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwj_44976/02_2026/9bwj_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bwj_44976/02_2026/9bwj_44976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwj_44976/02_2026/9bwj_44976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bwj_44976/02_2026/9bwj_44976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwj_44976/02_2026/9bwj_44976.map" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13390 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 100 5.16 5 C 9630 2.51 5 N 2315 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14705 Number of models: 1 Model: "" Number of chains: 20 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: "B" 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: "C" 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: "D" 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: "G" 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: "H" 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: "I" 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: "J" 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: 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: "C" 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: "D" 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: "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} Time building chain proxies: 3.17, per 1000 atoms: 0.22 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=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 1.36 Conformation dependent library (CDL) restraints added in 597.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 215 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 427 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 109 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 109 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 215 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 427 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 109 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 215 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 427 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 109 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 427 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 215 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 109 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 215 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 427 " 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 20 sheets defined 38.6% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.764A pdb=" N ALA A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.585A pdb=" N VAL A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 71 through 74 removed outlier: 3.764A pdb=" N ALA B 74 " --> pdb=" O PRO B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 240 removed outlier: 3.584A pdb=" N VAL B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.764A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.584A pdb=" N VAL C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'D' and resid 9 through 18 Processing helix chain 'D' and resid 71 through 74 removed outlier: 3.764A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.584A pdb=" N VAL D 240 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 244 Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'E' and resid 9 through 18 Processing helix chain 'E' and resid 71 through 74 removed outlier: 3.765A pdb=" N ALA E 74 " --> pdb=" O PRO E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 74' Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.529A pdb=" N ILE E 93 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 227 through 240 removed outlier: 3.585A pdb=" N VAL E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.551A pdb=" N LEU E 298 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 420 removed outlier: 3.613A pdb=" N ASP E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Proline residue: E 404 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.236A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP A 57 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 51 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE A 63 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 45 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG A 65 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE A 43 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS A 67 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS A 41 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN A 69 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A 39 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE A 108 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ARG A 131 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP A 57 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 51 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE A 63 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 45 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG A 65 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE A 43 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS A 67 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS A 41 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN A 69 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A 39 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS A 215 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 192 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU A 217 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS A 190 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.237A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 57 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE B 51 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE B 63 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 45 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG B 65 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE B 43 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS B 67 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS B 41 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN B 69 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL B 39 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N PHE B 108 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ARG B 131 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 57 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE B 51 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE B 63 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 45 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG B 65 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE B 43 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS B 67 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS B 41 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN B 69 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL B 39 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS B 215 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU B 192 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU B 217 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS B 190 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.235A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP C 57 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE C 51 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE C 63 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE C 45 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG C 65 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE C 43 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS C 67 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS C 41 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN C 69 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL C 39 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 39 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N PHE C 108 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ARG C 131 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP C 57 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE C 51 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE C 63 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE C 45 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG C 65 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE C 43 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS C 67 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS C 41 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN C 69 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL C 39 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS C 215 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU C 192 " --> pdb=" O HIS C 215 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU C 217 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS C 190 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB4, first strand: chain 'D' and resid 82 through 84 removed outlier: 4.235A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP D 57 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE D 51 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE D 63 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE D 45 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG D 65 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE D 43 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS D 67 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS D 41 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN D 69 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL D 39 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE D 108 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ARG D 131 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP D 57 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE D 51 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE D 63 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE D 45 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG D 65 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE D 43 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS D 67 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS D 41 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASN D 69 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL D 39 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS D 215 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU D 192 " --> pdb=" O HIS D 215 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLU D 217 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS D 190 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 84 removed outlier: 4.236A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP E 57 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 51 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE E 63 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE E 45 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG E 65 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE E 43 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS E 67 " --> pdb=" O CYS E 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS E 41 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN E 69 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL E 39 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL E 37 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU E 169 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL E 39 " --> pdb=" O GLU E 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 103 through 108 removed outlier: 6.786A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE E 108 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ARG E 131 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP E 57 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 51 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE E 63 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE E 45 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG E 65 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE E 43 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS E 67 " --> pdb=" O CYS E 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS E 41 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN E 69 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL E 39 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.488A pdb=" N HIS E 215 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU E 192 " --> pdb=" O HIS E 215 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLU E 217 " --> pdb=" O LYS E 190 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS E 190 " --> pdb=" O GLU E 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 200 through 201 737 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.76 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: 8280 17.84 - 35.68: 618 35.68 - 53.51: 167 53.51 - 71.35: 40 71.35 - 89.19: 15 Dihedral angle restraints: 9120 sinusoidal: 3985 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 9117 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 506 or (resid 507 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C9 o \ r name O5 or name O6 )) or (resid 508 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C9 o \ r name O5 or name O6 )) or (resid 509 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C9 or name O5 or name O6 )))) selection = (chain 'B' and (resid 8 through 506 or (resid 507 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C9 o \ r name O5 or name O6 )) or (resid 508 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C9 o \ r name O5 or name O6 )) or (resid 509 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C9 or name O5 or name O6 )))) selection = (chain 'C' and (resid 8 through 506 or (resid 507 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C9 o \ r name O5 or name O6 )) or (resid 508 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C9 o \ r name O5 or name O6 )) or (resid 509 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C9 or name O5 or name O6 )))) selection = (chain 'D' and (resid 8 through 506 or (resid 507 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C9 o \ r name O5 or name O6 )) or (resid 508 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C9 o \ r name O5 or name O6 )) or (resid 509 and (name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C9 or name O5 or name O6 )))) selection = (chain 'E' and (resid 8 through 502 or (resid 503 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C9 or name O5 or name O6 )) or (resid 504 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C9 or name O5 or name O6 )) \ or (resid 505 and (name C10 or name C11 or name C12 or name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C9 or name O5 or \ name O6 )) or (resid 506 and (name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C9 or name O5 or \ name O6 )) or resid 507 through 509)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- 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 20255 Z= 0.518 Chirality : 0.049 0.180 2245 Planarity : 0.007 0.040 2505 Dihedral : 14.551 89.190 5780 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.51 % Allowed : 9.68 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1710 helix: -1.20 (0.18), residues: 575 sheet: -0.53 (0.25), residues: 440 loop : -0.59 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 27 TYR 0.014 0.002 TYR D 301 PHE 0.022 0.002 PHE B 295 TRP 0.020 0.002 TRP E 415 HIS 0.014 0.002 HIS E 215 Details of bonding type rmsd covalent geometry : bond 0.01453 (15010) covalent geometry : angle 1.02138 (20225) hydrogen bonds : bond 0.14393 ( 657) hydrogen bonds : angle 6.71307 ( 2160) metal coordination : bond 0.01908 ( 15) link_BETA1-4 : bond 0.00199 ( 5) link_BETA1-4 : angle 1.27887 ( 15) link_NAG-ASN : bond 0.00095 ( 5) link_NAG-ASN : angle 0.39120 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.569 Fit side-chains REVERT: A 14 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8234 (mp) REVERT: B 78 TYR cc_start: 0.7192 (t80) cc_final: 0.6970 (t80) REVERT: C 78 TYR cc_start: 0.7155 (t80) cc_final: 0.6884 (t80) REVERT: D 18 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7481 (mtp) REVERT: D 78 TYR cc_start: 0.7145 (t80) cc_final: 0.6880 (t80) REVERT: E 78 TYR cc_start: 0.7137 (t80) cc_final: 0.6919 (t80) outliers start: 8 outliers final: 2 residues processed: 145 average time/residue: 0.6353 time to fit residues: 101.3357 Evaluate side-chains 133 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain E residue 14 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 171 GLN B 155 GLN B 171 GLN B 226 GLN C 155 GLN D 155 GLN D 171 GLN E 155 GLN E 171 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073194 restraints weight = 20552.467| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.25 r_work: 0.2890 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15035 Z= 0.167 Angle : 0.579 5.439 20255 Z= 0.309 Chirality : 0.043 0.152 2245 Planarity : 0.004 0.031 2505 Dihedral : 7.880 52.315 2390 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.17 % Allowed : 8.15 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1710 helix: 1.42 (0.20), residues: 590 sheet: 0.05 (0.27), residues: 415 loop : -0.37 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 422 TYR 0.019 0.002 TYR B 301 PHE 0.016 0.002 PHE E 48 TRP 0.013 0.001 TRP D 415 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00391 (15010) covalent geometry : angle 0.57824 (20225) hydrogen bonds : bond 0.05093 ( 657) hydrogen bonds : angle 4.83465 ( 2160) metal coordination : bond 0.00241 ( 15) link_BETA1-4 : bond 0.00147 ( 5) link_BETA1-4 : angle 1.01791 ( 15) link_NAG-ASN : bond 0.00180 ( 5) link_NAG-ASN : angle 0.62986 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.454 Fit side-chains REVERT: A 78 TYR cc_start: 0.7178 (t80) cc_final: 0.6885 (t80) REVERT: B 144 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7393 (m110) REVERT: C 78 TYR cc_start: 0.7433 (t80) cc_final: 0.7092 (t80) REVERT: C 422 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6479 (mtm180) REVERT: D 18 MET cc_start: 0.7710 (mtp) cc_final: 0.7243 (mtp) REVERT: D 78 TYR cc_start: 0.7394 (t80) cc_final: 0.7159 (t80) REVERT: D 422 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7899 (mtt-85) REVERT: E 422 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7822 (mmm160) outliers start: 34 outliers final: 18 residues processed: 159 average time/residue: 0.6286 time to fit residues: 110.0095 Evaluate side-chains 150 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 422 ARG Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 14 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 171 GLN B 226 GLN C 171 GLN C 226 GLN D 171 GLN D 226 GLN E 171 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.097194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073357 restraints weight = 20793.132| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.27 r_work: 0.2882 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15035 Z= 0.162 Angle : 0.541 5.445 20255 Z= 0.289 Chirality : 0.042 0.155 2245 Planarity : 0.004 0.031 2505 Dihedral : 7.301 50.126 2382 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.29 % Allowed : 9.11 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1710 helix: 2.29 (0.20), residues: 575 sheet: 0.53 (0.26), residues: 435 loop : -0.11 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.022 0.001 TYR B 301 PHE 0.016 0.002 PHE E 48 TRP 0.010 0.001 TRP A 68 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00380 (15010) covalent geometry : angle 0.53991 (20225) hydrogen bonds : bond 0.04792 ( 657) hydrogen bonds : angle 4.59718 ( 2160) metal coordination : bond 0.00217 ( 15) link_BETA1-4 : bond 0.00171 ( 5) link_BETA1-4 : angle 1.10070 ( 15) link_NAG-ASN : bond 0.00155 ( 5) link_NAG-ASN : angle 0.71512 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.588 Fit side-chains REVERT: A 78 TYR cc_start: 0.7317 (t80) cc_final: 0.7023 (t80) REVERT: B 78 TYR cc_start: 0.7473 (t80) cc_final: 0.7231 (t80) REVERT: C 78 TYR cc_start: 0.7505 (t80) cc_final: 0.7194 (t80) REVERT: D 8 MET cc_start: 0.7481 (tpt) cc_final: 0.7245 (tpp) REVERT: D 18 MET cc_start: 0.7732 (mtp) cc_final: 0.7252 (mtp) REVERT: D 78 TYR cc_start: 0.7506 (t80) cc_final: 0.7248 (t80) REVERT: E 78 TYR cc_start: 0.7399 (t80) cc_final: 0.7188 (t80) outliers start: 36 outliers final: 21 residues processed: 158 average time/residue: 0.6478 time to fit residues: 112.7611 Evaluate side-chains 152 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 117 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 144 ASN B 171 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073979 restraints weight = 20597.084| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.26 r_work: 0.2895 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15035 Z= 0.140 Angle : 0.522 6.433 20255 Z= 0.277 Chirality : 0.042 0.157 2245 Planarity : 0.004 0.031 2505 Dihedral : 6.934 48.675 2380 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.23 % Allowed : 10.57 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1710 helix: 2.64 (0.20), residues: 575 sheet: 0.60 (0.26), residues: 435 loop : -0.03 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.022 0.001 TYR C 301 PHE 0.017 0.001 PHE C 295 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00328 (15010) covalent geometry : angle 0.52151 (20225) hydrogen bonds : bond 0.04392 ( 657) hydrogen bonds : angle 4.44111 ( 2160) metal coordination : bond 0.00160 ( 15) link_BETA1-4 : bond 0.00185 ( 5) link_BETA1-4 : angle 1.16487 ( 15) link_NAG-ASN : bond 0.00073 ( 5) link_NAG-ASN : angle 0.64008 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.708 Fit side-chains REVERT: A 78 TYR cc_start: 0.7354 (t80) cc_final: 0.7047 (t80) REVERT: B 78 TYR cc_start: 0.7507 (t80) cc_final: 0.7254 (t80) REVERT: B 421 LEU cc_start: 0.8442 (tt) cc_final: 0.8208 (mp) REVERT: B 422 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7954 (mtt-85) REVERT: C 78 TYR cc_start: 0.7497 (t80) cc_final: 0.7244 (t80) REVERT: C 422 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.6487 (mtm180) REVERT: D 8 MET cc_start: 0.7494 (tpt) cc_final: 0.7172 (tpp) REVERT: D 18 MET cc_start: 0.7711 (mtp) cc_final: 0.7299 (mtp) REVERT: D 78 TYR cc_start: 0.7519 (t80) cc_final: 0.7293 (t80) REVERT: D 220 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8746 (mmm) REVERT: E 78 TYR cc_start: 0.7412 (t80) cc_final: 0.7195 (t80) REVERT: E 417 ILE cc_start: 0.8676 (mm) cc_final: 0.8323 (mm) REVERT: E 422 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7872 (mmm160) outliers start: 35 outliers final: 22 residues processed: 158 average time/residue: 0.6266 time to fit residues: 108.9648 Evaluate side-chains 156 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 203 ASN D 226 GLN E 171 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.073923 restraints weight = 20679.073| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.26 r_work: 0.2893 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15035 Z= 0.142 Angle : 0.519 5.350 20255 Z= 0.275 Chirality : 0.041 0.154 2245 Planarity : 0.003 0.031 2505 Dihedral : 6.812 49.564 2380 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.17 % Allowed : 11.08 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.21), residues: 1710 helix: 2.80 (0.20), residues: 575 sheet: 0.68 (0.26), residues: 435 loop : -0.01 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.022 0.001 TYR C 301 PHE 0.017 0.002 PHE D 295 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00332 (15010) covalent geometry : angle 0.51760 (20225) hydrogen bonds : bond 0.04339 ( 657) hydrogen bonds : angle 4.39581 ( 2160) metal coordination : bond 0.00158 ( 15) link_BETA1-4 : bond 0.00188 ( 5) link_BETA1-4 : angle 1.19195 ( 15) link_NAG-ASN : bond 0.00086 ( 5) link_NAG-ASN : angle 0.63907 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.586 Fit side-chains REVERT: A 78 TYR cc_start: 0.7376 (t80) cc_final: 0.7067 (t80) REVERT: A 421 LEU cc_start: 0.8557 (tt) cc_final: 0.8151 (mp) REVERT: B 8 MET cc_start: 0.7251 (tpt) cc_final: 0.6937 (tpp) REVERT: B 78 TYR cc_start: 0.7485 (t80) cc_final: 0.7213 (t80) REVERT: B 226 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8320 (mm110) REVERT: B 421 LEU cc_start: 0.8412 (tt) cc_final: 0.8169 (mp) REVERT: C 78 TYR cc_start: 0.7478 (t80) cc_final: 0.7215 (t80) REVERT: C 422 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.6497 (mtm180) REVERT: D 8 MET cc_start: 0.7516 (tpt) cc_final: 0.7213 (tpp) REVERT: D 18 MET cc_start: 0.7670 (mtp) cc_final: 0.7265 (mtp) REVERT: D 78 TYR cc_start: 0.7528 (t80) cc_final: 0.7296 (t80) REVERT: D 220 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8771 (mmm) REVERT: E 78 TYR cc_start: 0.7420 (t80) cc_final: 0.6967 (t80) REVERT: E 417 ILE cc_start: 0.8768 (mm) cc_final: 0.8386 (mm) REVERT: E 422 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7859 (mmm160) outliers start: 34 outliers final: 22 residues processed: 158 average time/residue: 0.6203 time to fit residues: 107.8823 Evaluate side-chains 155 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 117 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN C 226 GLN D 171 GLN D 226 GLN E 171 GLN E 203 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.074469 restraints weight = 20530.190| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.25 r_work: 0.2907 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1536 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= 0.125 Angle : 0.509 5.391 20255 Z= 0.269 Chirality : 0.041 0.153 2245 Planarity : 0.003 0.031 2505 Dihedral : 6.607 49.664 2380 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.36 % Allowed : 11.34 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.21), residues: 1710 helix: 2.91 (0.20), residues: 575 sheet: 0.75 (0.26), residues: 435 loop : 0.02 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.022 0.001 TYR C 301 PHE 0.018 0.001 PHE C 295 TRP 0.009 0.001 TRP A 68 HIS 0.001 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00290 (15010) covalent geometry : angle 0.50770 (20225) hydrogen bonds : bond 0.04141 ( 657) hydrogen bonds : angle 4.31632 ( 2160) metal coordination : bond 0.00128 ( 15) link_BETA1-4 : bond 0.00236 ( 5) link_BETA1-4 : angle 1.21128 ( 15) link_NAG-ASN : bond 0.00034 ( 5) link_NAG-ASN : angle 0.57217 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.604 Fit side-chains REVERT: A 78 TYR cc_start: 0.7413 (t80) cc_final: 0.7088 (t80) REVERT: A 421 LEU cc_start: 0.8568 (tt) cc_final: 0.8178 (mp) REVERT: B 8 MET cc_start: 0.7289 (tpt) cc_final: 0.7027 (tpp) REVERT: B 78 TYR cc_start: 0.7504 (t80) cc_final: 0.7248 (t80) REVERT: B 421 LEU cc_start: 0.8470 (tt) cc_final: 0.8248 (mp) REVERT: B 422 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8022 (mtt-85) REVERT: C 78 TYR cc_start: 0.7477 (t80) cc_final: 0.7210 (t80) REVERT: C 421 LEU cc_start: 0.8689 (tt) cc_final: 0.8298 (mp) REVERT: C 422 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.6475 (mtm180) REVERT: D 8 MET cc_start: 0.7560 (tpt) cc_final: 0.7161 (tpp) REVERT: D 18 MET cc_start: 0.7626 (mtp) cc_final: 0.7217 (mtp) REVERT: D 78 TYR cc_start: 0.7526 (t80) cc_final: 0.7307 (t80) REVERT: D 220 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8744 (mmm) REVERT: E 78 TYR cc_start: 0.7428 (t80) cc_final: 0.7209 (t80) REVERT: E 417 ILE cc_start: 0.8806 (mm) cc_final: 0.8428 (mm) REVERT: E 422 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7879 (mmm160) outliers start: 37 outliers final: 23 residues processed: 163 average time/residue: 0.6180 time to fit residues: 111.2387 Evaluate side-chains 160 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 90 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.098327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074803 restraints weight = 20512.423| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.25 r_work: 0.2916 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15035 Z= 0.117 Angle : 0.504 5.449 20255 Z= 0.266 Chirality : 0.041 0.153 2245 Planarity : 0.003 0.031 2505 Dihedral : 6.417 49.326 2380 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.97 % Allowed : 11.91 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.21), residues: 1710 helix: 2.97 (0.20), residues: 575 sheet: 0.80 (0.26), residues: 435 loop : 0.05 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.021 0.001 TYR C 301 PHE 0.018 0.001 PHE C 295 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.000 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00270 (15010) covalent geometry : angle 0.50288 (20225) hydrogen bonds : bond 0.04008 ( 657) hydrogen bonds : angle 4.25343 ( 2160) metal coordination : bond 0.00109 ( 15) link_BETA1-4 : bond 0.00214 ( 5) link_BETA1-4 : angle 1.20580 ( 15) link_NAG-ASN : bond 0.00024 ( 5) link_NAG-ASN : angle 0.53850 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.572 Fit side-chains REVERT: A 78 TYR cc_start: 0.7441 (t80) cc_final: 0.7129 (t80) REVERT: A 421 LEU cc_start: 0.8561 (tt) cc_final: 0.8178 (mp) REVERT: B 8 MET cc_start: 0.7311 (tpt) cc_final: 0.7039 (tpp) REVERT: B 78 TYR cc_start: 0.7527 (t80) cc_final: 0.7290 (t80) REVERT: B 421 LEU cc_start: 0.8496 (tt) cc_final: 0.8275 (mp) REVERT: B 422 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8095 (mtt-85) REVERT: C 78 TYR cc_start: 0.7479 (t80) cc_final: 0.7215 (t80) REVERT: C 421 LEU cc_start: 0.8704 (tt) cc_final: 0.8319 (mp) REVERT: C 422 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.6497 (mtm180) REVERT: D 8 MET cc_start: 0.7588 (tpt) cc_final: 0.7176 (tpp) REVERT: D 18 MET cc_start: 0.7658 (mtp) cc_final: 0.7252 (mtp) REVERT: D 220 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8729 (mmm) REVERT: E 78 TYR cc_start: 0.7491 (t80) cc_final: 0.7261 (t80) REVERT: E 417 ILE cc_start: 0.8826 (mm) cc_final: 0.8605 (mm) REVERT: E 421 LEU cc_start: 0.8668 (tt) cc_final: 0.8200 (mp) outliers start: 31 outliers final: 21 residues processed: 158 average time/residue: 0.6287 time to fit residues: 109.5472 Evaluate side-chains 159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 62 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN E 203 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.073825 restraints weight = 20530.447| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.27 r_work: 0.2895 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15035 Z= 0.150 Angle : 0.529 5.843 20255 Z= 0.279 Chirality : 0.042 0.153 2245 Planarity : 0.003 0.030 2505 Dihedral : 6.527 50.934 2380 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.97 % Allowed : 12.74 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.21), residues: 1710 helix: 2.96 (0.20), residues: 575 sheet: 0.77 (0.26), residues: 435 loop : 0.01 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.023 0.001 TYR C 301 PHE 0.018 0.002 PHE C 295 TRP 0.008 0.001 TRP A 68 HIS 0.002 0.000 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00358 (15010) covalent geometry : angle 0.52815 (20225) hydrogen bonds : bond 0.04330 ( 657) hydrogen bonds : angle 4.33891 ( 2160) metal coordination : bond 0.00184 ( 15) link_BETA1-4 : bond 0.00182 ( 5) link_BETA1-4 : angle 1.22278 ( 15) link_NAG-ASN : bond 0.00106 ( 5) link_NAG-ASN : angle 0.65933 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.467 Fit side-chains REVERT: A 78 TYR cc_start: 0.7464 (t80) cc_final: 0.7132 (t80) REVERT: A 421 LEU cc_start: 0.8529 (tt) cc_final: 0.8150 (mp) REVERT: B 8 MET cc_start: 0.7253 (tpt) cc_final: 0.6967 (tpp) REVERT: B 78 TYR cc_start: 0.7518 (t80) cc_final: 0.7278 (t80) REVERT: B 421 LEU cc_start: 0.8475 (tt) cc_final: 0.8216 (mp) REVERT: B 422 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8153 (mtt-85) REVERT: C 8 MET cc_start: 0.7321 (tpt) cc_final: 0.7041 (tpp) REVERT: C 78 TYR cc_start: 0.7482 (t80) cc_final: 0.7245 (t80) REVERT: C 421 LEU cc_start: 0.8693 (tt) cc_final: 0.8315 (mp) REVERT: C 422 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.6554 (mtm180) REVERT: D 8 MET cc_start: 0.7475 (tpt) cc_final: 0.7217 (tpp) REVERT: D 18 MET cc_start: 0.7642 (mtp) cc_final: 0.7223 (mtp) REVERT: D 78 TYR cc_start: 0.7383 (t80) cc_final: 0.7144 (t80) REVERT: D 220 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8743 (mmm) REVERT: E 78 TYR cc_start: 0.7517 (t80) cc_final: 0.7238 (t80) REVERT: E 417 ILE cc_start: 0.8850 (mm) cc_final: 0.8615 (mm) REVERT: E 421 LEU cc_start: 0.8657 (tt) cc_final: 0.8193 (mp) REVERT: E 422 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7900 (mmm160) outliers start: 31 outliers final: 22 residues processed: 152 average time/residue: 0.6573 time to fit residues: 109.7265 Evaluate side-chains 158 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 72 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.098512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074869 restraints weight = 20655.436| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.27 r_work: 0.2916 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15035 Z= 0.114 Angle : 0.515 7.390 20255 Z= 0.270 Chirality : 0.041 0.153 2245 Planarity : 0.003 0.043 2505 Dihedral : 6.298 50.465 2380 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.78 % Allowed : 12.93 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.21), residues: 1710 helix: 3.12 (0.20), residues: 570 sheet: 0.83 (0.26), residues: 435 loop : 0.03 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 20 TYR 0.021 0.001 TYR C 301 PHE 0.019 0.001 PHE C 295 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.000 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00262 (15010) covalent geometry : angle 0.51443 (20225) hydrogen bonds : bond 0.03981 ( 657) hydrogen bonds : angle 4.23447 ( 2160) metal coordination : bond 0.00099 ( 15) link_BETA1-4 : bond 0.00221 ( 5) link_BETA1-4 : angle 1.21388 ( 15) link_NAG-ASN : bond 0.00050 ( 5) link_NAG-ASN : angle 0.50270 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.484 Fit side-chains REVERT: A 78 TYR cc_start: 0.7443 (t80) cc_final: 0.7174 (t80) REVERT: A 421 LEU cc_start: 0.8525 (tt) cc_final: 0.8167 (mp) REVERT: B 8 MET cc_start: 0.7239 (tpt) cc_final: 0.6913 (tpp) REVERT: B 78 TYR cc_start: 0.7518 (t80) cc_final: 0.7275 (t80) REVERT: B 421 LEU cc_start: 0.8516 (tt) cc_final: 0.8268 (mp) REVERT: B 422 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8176 (mtt-85) REVERT: C 8 MET cc_start: 0.7326 (tpt) cc_final: 0.7040 (tpp) REVERT: C 78 TYR cc_start: 0.7489 (t80) cc_final: 0.7240 (t80) REVERT: C 421 LEU cc_start: 0.8698 (tt) cc_final: 0.8322 (mp) REVERT: C 422 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6542 (mtm180) REVERT: D 8 MET cc_start: 0.7502 (tpt) cc_final: 0.7231 (tpp) REVERT: D 18 MET cc_start: 0.7663 (mtp) cc_final: 0.7270 (mtp) REVERT: D 78 TYR cc_start: 0.7408 (t80) cc_final: 0.7196 (t80) REVERT: D 220 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8717 (mmm) REVERT: E 78 TYR cc_start: 0.7458 (t80) cc_final: 0.7116 (t80) REVERT: E 417 ILE cc_start: 0.8863 (mm) cc_final: 0.8622 (mm) REVERT: E 421 LEU cc_start: 0.8670 (tt) cc_final: 0.8209 (mp) REVERT: E 422 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7954 (mmm160) outliers start: 28 outliers final: 21 residues processed: 157 average time/residue: 0.6396 time to fit residues: 110.1563 Evaluate side-chains 160 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073513 restraints weight = 20650.024| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.30 r_work: 0.2888 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15035 Z= 0.162 Angle : 0.556 8.454 20255 Z= 0.291 Chirality : 0.042 0.153 2245 Planarity : 0.003 0.030 2505 Dihedral : 6.503 52.596 2380 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.72 % Allowed : 13.18 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.21), residues: 1710 helix: 3.00 (0.20), residues: 575 sheet: 0.78 (0.26), residues: 435 loop : -0.00 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 20 TYR 0.023 0.001 TYR B 301 PHE 0.017 0.002 PHE C 295 TRP 0.008 0.001 TRP D 415 HIS 0.002 0.000 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00387 (15010) covalent geometry : angle 0.55540 (20225) hydrogen bonds : bond 0.04447 ( 657) hydrogen bonds : angle 4.35338 ( 2160) metal coordination : bond 0.00201 ( 15) link_BETA1-4 : bond 0.00195 ( 5) link_BETA1-4 : angle 1.24698 ( 15) link_NAG-ASN : bond 0.00133 ( 5) link_NAG-ASN : angle 0.68345 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.570 Fit side-chains REVERT: A 78 TYR cc_start: 0.7462 (t80) cc_final: 0.7157 (t80) REVERT: A 421 LEU cc_start: 0.8524 (tt) cc_final: 0.8178 (mp) REVERT: B 8 MET cc_start: 0.7222 (tpt) cc_final: 0.6881 (tpp) REVERT: B 78 TYR cc_start: 0.7536 (t80) cc_final: 0.7287 (t80) REVERT: B 421 LEU cc_start: 0.8483 (tt) cc_final: 0.8212 (mp) REVERT: B 422 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8148 (mtt-85) REVERT: C 8 MET cc_start: 0.7295 (tpt) cc_final: 0.6961 (tpp) REVERT: C 78 TYR cc_start: 0.7501 (t80) cc_final: 0.7246 (t80) REVERT: C 421 LEU cc_start: 0.8685 (tt) cc_final: 0.8312 (mp) REVERT: C 422 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.6564 (mtm180) REVERT: D 8 MET cc_start: 0.7514 (tpt) cc_final: 0.7214 (tpp) REVERT: D 18 MET cc_start: 0.7667 (mtp) cc_final: 0.7245 (mtp) REVERT: D 78 TYR cc_start: 0.7421 (t80) cc_final: 0.7206 (t80) REVERT: D 220 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8737 (mmm) REVERT: E 78 TYR cc_start: 0.7457 (t80) cc_final: 0.7166 (t80) REVERT: E 417 ILE cc_start: 0.8867 (mm) cc_final: 0.8607 (mm) REVERT: E 421 LEU cc_start: 0.8675 (tt) cc_final: 0.8218 (mp) REVERT: E 422 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7919 (mmm160) outliers start: 27 outliers final: 22 residues processed: 150 average time/residue: 0.6390 time to fit residues: 105.0720 Evaluate side-chains 158 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 422 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 153 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 226 GLN B 144 ASN B 171 GLN B 226 GLN C 226 GLN D 171 GLN D 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.075101 restraints weight = 20484.562| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.26 r_work: 0.2921 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1696 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= 0.111 Angle : 0.529 8.261 20255 Z= 0.275 Chirality : 0.041 0.153 2245 Planarity : 0.003 0.035 2505 Dihedral : 6.225 51.960 2380 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.72 % Allowed : 13.12 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.21), residues: 1710 helix: 3.13 (0.20), residues: 570 sheet: 0.86 (0.26), residues: 435 loop : 0.05 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 20 TYR 0.021 0.001 TYR C 301 PHE 0.019 0.001 PHE C 295 TRP 0.009 0.001 TRP A 68 HIS 0.001 0.000 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00255 (15010) covalent geometry : angle 0.52796 (20225) hydrogen bonds : bond 0.03958 ( 657) hydrogen bonds : angle 4.21963 ( 2160) metal coordination : bond 0.00082 ( 15) link_BETA1-4 : bond 0.00209 ( 5) link_BETA1-4 : angle 1.20995 ( 15) link_NAG-ASN : bond 0.00072 ( 5) link_NAG-ASN : angle 0.47965 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6864.61 seconds wall clock time: 117 minutes 26.02 seconds (7046.02 seconds total)