Starting phenix.real_space_refine on Sun Jul 5 03:36:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bu3_44900/07_2026/9bu3_44900.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bu3_44900/07_2026/9bu3_44900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bu3_44900/07_2026/9bu3_44900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bu3_44900/07_2026/9bu3_44900.map" model { file = "/net/cci-nas-00/data/ceres_data/9bu3_44900/07_2026/9bu3_44900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bu3_44900/07_2026/9bu3_44900.cif" } resolution = 2.8 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9600 2.51 5 N 2290 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14630 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "C" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "D" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "E" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 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: 3.38, per 1000 atoms: 0.23 Number of scatterers: 14630 At special positions: 0 Unit cell: (100.1, 99, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2640 8.00 N 2290 7.00 C 9600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 209 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 38 " " NAG G 1 " - " ASN B 38 " " NAG H 1 " - " ASN C 38 " " NAG I 1 " - " ASN D 38 " " NAG J 1 " - " ASN E 38 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 669.5 milliseconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 39.7% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.710A pdb=" N PHE A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 93 removed outlier: 4.414A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.901A pdb=" N SER A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 248 through 270 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.706A pdb=" N ARG A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 421 removed outlier: 3.802A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.503A pdb=" N ILE A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.711A pdb=" N PHE B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 93 removed outlier: 4.414A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.901A pdb=" N SER B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 248 through 270 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.706A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 421 removed outlier: 3.802A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Proline residue: B 404 - end of helix removed outlier: 3.503A pdb=" N ILE B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 19 removed outlier: 3.710A pdb=" N PHE C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 86 through 93 removed outlier: 4.413A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 227 through 241 removed outlier: 3.900A pdb=" N SER C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 248 through 270 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.706A pdb=" N ARG C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.802A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Proline residue: C 404 - end of helix removed outlier: 3.502A pdb=" N ILE C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 19 removed outlier: 3.710A pdb=" N PHE D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 86 through 93 removed outlier: 4.414A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.901A pdb=" N SER D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 248 through 270 Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.707A pdb=" N ARG D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 421 removed outlier: 3.802A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Proline residue: D 404 - end of helix removed outlier: 3.502A pdb=" N ILE D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 19 removed outlier: 3.710A pdb=" N PHE E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 86 through 93 removed outlier: 4.414A pdb=" N ASP E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 227 through 241 removed outlier: 3.901A pdb=" N SER E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 248 through 270 Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.706A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 421 removed outlier: 3.802A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Proline residue: E 404 - end of helix removed outlier: 3.503A pdb=" N ILE E 417 " --> pdb=" O PHE E 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.242A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.148A 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 107 removed outlier: 6.457A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.388A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.388A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A 198 " --> pdb=" O CYS A 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 211 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 196 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 194 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.241A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.148A 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 107 removed outlier: 6.457A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.387A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.387A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 198 " --> pdb=" O CYS B 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 211 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 196 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 194 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.242A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.148A 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 107 removed outlier: 6.457A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.387A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.387A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS C 198 " --> pdb=" O CYS C 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 211 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 196 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 194 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 82 through 84 removed outlier: 4.242A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.148A 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 107 removed outlier: 6.457A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.388A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.388A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS D 198 " --> pdb=" O CYS D 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 211 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 196 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP D 194 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 84 removed outlier: 4.242A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL E 37 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU E 169 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.149A 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 107 removed outlier: 6.458A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.387A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.387A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS E 198 " --> pdb=" O CYS E 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU E 211 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E 196 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 194 " --> pdb=" O ARG E 213 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2688 1.33 - 1.45: 3756 1.45 - 1.58: 8081 1.58 - 1.70: 235 1.70 - 1.83: 165 Bond restraints: 14925 Sorted by residual: bond pdb=" C23 PX4 E 509 " pdb=" O7 PX4 E 509 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C23 PX4 C 508 " pdb=" O7 PX4 C 508 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C23 PX4 D 506 " pdb=" O7 PX4 D 506 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C23 PX4 C 506 " pdb=" O7 PX4 C 506 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C23 PX4 A 507 " pdb=" O7 PX4 A 507 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.73e+01 ... (remaining 14920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 18974 1.72 - 3.43: 730 3.43 - 5.15: 301 5.15 - 6.87: 40 6.87 - 8.59: 30 Bond angle restraints: 20075 Sorted by residual: angle pdb=" CA CYS C 209 " pdb=" CB CYS C 209 " pdb=" SG CYS C 209 " ideal model delta sigma weight residual 114.40 122.05 -7.65 2.30e+00 1.89e-01 1.11e+01 angle pdb=" CA CYS D 209 " pdb=" CB CYS D 209 " pdb=" SG CYS D 209 " ideal model delta sigma weight residual 114.40 122.02 -7.62 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA CYS E 209 " pdb=" CB CYS E 209 " pdb=" SG CYS E 209 " ideal model delta sigma weight residual 114.40 122.02 -7.62 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA CYS A 209 " pdb=" CB CYS A 209 " pdb=" SG CYS A 209 " ideal model delta sigma weight residual 114.40 122.01 -7.61 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA CYS B 209 " pdb=" CB CYS B 209 " pdb=" SG CYS B 209 " ideal model delta sigma weight residual 114.40 122.01 -7.61 2.30e+00 1.89e-01 1.09e+01 ... (remaining 20070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 8356 17.36 - 34.73: 618 34.73 - 52.09: 81 52.09 - 69.45: 10 69.45 - 86.81: 15 Dihedral angle restraints: 9080 sinusoidal: 4005 harmonic: 5075 Sorted by residual: dihedral pdb=" CA GLU E 110 " pdb=" C GLU E 110 " pdb=" N VAL E 111 " pdb=" CA VAL E 111 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLU D 110 " pdb=" C GLU D 110 " pdb=" N VAL D 111 " pdb=" CA VAL D 111 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLU A 110 " pdb=" C GLU A 110 " pdb=" N VAL A 111 " pdb=" CA VAL A 111 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 9077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1406 0.038 - 0.076: 569 0.076 - 0.114: 159 0.114 - 0.152: 71 0.152 - 0.190: 15 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CA LEU B 142 " pdb=" N LEU B 142 " pdb=" C LEU B 142 " pdb=" CB LEU B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA LEU A 142 " pdb=" N LEU A 142 " pdb=" C LEU A 142 " pdb=" CB LEU A 142 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA LEU D 142 " pdb=" N LEU D 142 " pdb=" C LEU D 142 " pdb=" CB LEU D 142 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 2217 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 399 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.34e+01 pdb=" C SER D 399 " 0.063 2.00e-02 2.50e+03 pdb=" O SER D 399 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG D 400 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 399 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C SER B 399 " -0.063 2.00e-02 2.50e+03 pdb=" O SER B 399 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG B 400 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 399 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C SER A 399 " 0.063 2.00e-02 2.50e+03 pdb=" O SER A 399 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 400 " -0.022 2.00e-02 2.50e+03 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4249 2.83 - 3.35: 12405 3.35 - 3.87: 22883 3.87 - 4.38: 27008 4.38 - 4.90: 46904 Nonbonded interactions: 113449 Sorted by model distance: nonbonded pdb=" OG1 THR A 55 " pdb=" OD1 ASP A 57 " model vdw 2.316 3.040 nonbonded pdb=" OG1 THR B 55 " pdb=" OD1 ASP B 57 " model vdw 2.316 3.040 nonbonded pdb=" OG1 THR C 55 " pdb=" OD1 ASP C 57 " model vdw 2.316 3.040 nonbonded pdb=" OG1 THR E 55 " pdb=" OD1 ASP E 57 " model vdw 2.316 3.040 nonbonded pdb=" OG1 THR D 55 " pdb=" OD1 ASP D 57 " model vdw 2.317 3.040 ... (remaining 113444 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 423 or resid 503 or resid 508 or (resid 511 and \ (name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C30 or name C31 or name C32 or name C33 or name C34 or name O7 or name \ O8 )))) selection = (chain 'B' and (resid 8 through 423 or resid 502 or resid 507 or (resid 510 and \ (name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C30 or name C31 or name C32 or name C33 or name C34 or name O7 or name \ O8 )))) selection = (chain 'C' and (resid 8 through 423 or resid 502 or resid 507 or (resid 510 and \ (name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C30 or name C31 or name C32 or name C33 or name C34 or name O7 or name \ O8 )))) selection = (chain 'D' and (resid 8 through 423 or resid 502 or resid 507 or (resid 510 and \ (name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C30 or name C31 or name C32 or name C33 or name C34 or name O7 or name \ O8 )))) selection = (chain 'E' and (resid 8 through 501 or (resid 506 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)) or resid 5 \ 09)) } 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.400 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.012 0.138 14940 Z= 0.603 Angle : 0.938 8.586 20115 Z= 0.443 Chirality : 0.048 0.190 2220 Planarity : 0.005 0.037 2485 Dihedral : 12.202 86.814 5765 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.23 (0.20), residues: 1690 helix: 0.88 (0.21), residues: 590 sheet: 0.82 (0.25), residues: 390 loop : -0.81 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 309 TYR 0.017 0.002 TYR D 301 PHE 0.016 0.001 PHE A 99 TRP 0.009 0.001 TRP B 170 HIS 0.001 0.000 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.01205 / 0.60 (14925) covalent geometry : angle 0.93231 / 0.44 (20075) SS BOND : bond 0.00246 / 0.13 ( 5) SS BOND : angle 4.89039 / 2.54 ( 10) hydrogen bonds : bond 0.20177 / 13.01 ( 690) hydrogen bonds : angle 6.88994 / 4.74 ( 2445) link_BETA1-4 : bond 0.00347 / 0.19 ( 5) link_BETA1-4 : angle 0.90092 / 0.53 ( 15) link_NAG-ASN : bond 0.00171 / 0.09 ( 5) link_NAG-ASN : angle 0.97129 / 0.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.557 Fit side-chains REVERT: C 287 MET cc_start: 0.8836 (mmt) cc_final: 0.8560 (mmm) REVERT: E 212 VAL cc_start: 0.9601 (t) cc_final: 0.9400 (m) outliers start: 0 outliers final: 3 residues processed: 143 average time/residue: 0.4893 time to fit residues: 78.3727 Evaluate side-chains 125 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 203 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.090738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.072504 restraints weight = 28051.236| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.65 r_work: 0.2893 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14940 Z= 0.126 Angle : 0.573 6.238 20115 Z= 0.297 Chirality : 0.043 0.148 2220 Planarity : 0.004 0.029 2485 Dihedral : 7.103 56.030 2416 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.81 % Allowed : 6.19 % Favored : 92.00 % 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: 1.68 (0.20), residues: 1690 helix: 2.31 (0.21), residues: 565 sheet: 1.25 (0.24), residues: 420 loop : 0.09 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 391 TYR 0.016 0.001 TYR E 301 PHE 0.015 0.001 PHE B 99 TRP 0.007 0.001 TRP C 68 HIS 0.001 0.000 HIS E 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (14925) covalent geometry : angle 0.56942 / 0.30 (20075) SS BOND : bond 0.00340 / 0.18 ( 5) SS BOND : angle 2.54882 / 1.32 ( 10) hydrogen bonds : bond 0.05472 / 3.62 ( 690) hydrogen bonds : angle 5.09801 / 3.50 ( 2445) link_BETA1-4 : bond 0.00503 / 0.27 ( 5) link_BETA1-4 : angle 1.48982 / 0.98 ( 15) link_NAG-ASN : bond 0.00220 / 0.12 ( 5) link_NAG-ASN : angle 0.53611 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.602 Fit side-chains REVERT: C 287 MET cc_start: 0.9290 (mmt) cc_final: 0.9079 (mmt) outliers start: 28 outliers final: 11 residues processed: 133 average time/residue: 0.5728 time to fit residues: 84.6900 Evaluate side-chains 127 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 240 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.065538 restraints weight = 28480.345| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.70 r_work: 0.2749 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14940 Z= 0.196 Angle : 0.607 7.548 20115 Z= 0.322 Chirality : 0.045 0.218 2220 Planarity : 0.005 0.046 2485 Dihedral : 7.270 48.646 2410 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.19 % Allowed : 7.55 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1690 helix: 2.17 (0.21), residues: 595 sheet: 1.40 (0.26), residues: 385 loop : -0.49 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 65 TYR 0.024 0.002 TYR A 301 PHE 0.020 0.002 PHE E 99 TRP 0.012 0.002 TRP E 239 HIS 0.004 0.001 HIS E 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (14925) covalent geometry : angle 0.60316 / 0.32 (20075) SS BOND : bond 0.00530 / 0.28 ( 5) SS BOND : angle 2.53822 / 1.32 ( 10) hydrogen bonds : bond 0.06625 / 4.48 ( 690) hydrogen bonds : angle 5.20980 / 3.59 ( 2445) link_BETA1-4 : bond 0.00394 / 0.21 ( 5) link_BETA1-4 : angle 1.66734 / 1.11 ( 15) link_NAG-ASN : bond 0.00108 / 0.05 ( 5) link_NAG-ASN : angle 0.70345 / 0.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.579 Fit side-chains REVERT: D 163 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8379 (mmm) REVERT: D 396 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8244 (t0) outliers start: 34 outliers final: 12 residues processed: 125 average time/residue: 0.6072 time to fit residues: 83.8361 Evaluate side-chains 124 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 8 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 417 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 23 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.086543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067853 restraints weight = 28449.866| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.71 r_work: 0.2798 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14940 Z= 0.127 Angle : 0.549 7.446 20115 Z= 0.286 Chirality : 0.042 0.152 2220 Planarity : 0.004 0.029 2485 Dihedral : 7.020 48.525 2410 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.13 % Allowed : 8.39 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.21), residues: 1690 helix: 2.40 (0.21), residues: 595 sheet: 1.32 (0.26), residues: 405 loop : -0.30 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 65 TYR 0.019 0.001 TYR D 301 PHE 0.016 0.001 PHE B 99 TRP 0.007 0.001 TRP D 170 HIS 0.002 0.000 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14925) covalent geometry : angle 0.54154 / 0.28 (20075) SS BOND : bond 0.01350 / 0.72 ( 5) SS BOND : angle 3.70332 / 1.92 ( 10) hydrogen bonds : bond 0.05274 / 3.57 ( 690) hydrogen bonds : angle 4.67533 / 3.24 ( 2445) link_BETA1-4 : bond 0.00448 / 0.24 ( 5) link_BETA1-4 : angle 1.46251 / 0.95 ( 15) link_NAG-ASN : bond 0.00150 / 0.08 ( 5) link_NAG-ASN : angle 0.43767 / 0.26 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.579 Fit side-chains REVERT: B 142 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9020 (mp) outliers start: 33 outliers final: 13 residues processed: 136 average time/residue: 0.6205 time to fit residues: 92.9546 Evaluate side-chains 132 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 8 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.068094 restraints weight = 28434.129| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.70 r_work: 0.2803 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14940 Z= 0.128 Angle : 0.554 11.255 20115 Z= 0.285 Chirality : 0.042 0.145 2220 Planarity : 0.004 0.033 2485 Dihedral : 6.844 50.138 2410 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.81 % Allowed : 8.97 % Favored : 89.23 % 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: 1.62 (0.21), residues: 1690 helix: 2.51 (0.21), residues: 595 sheet: 1.26 (0.26), residues: 405 loop : -0.32 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.021 0.001 TYR D 301 PHE 0.015 0.001 PHE B 99 TRP 0.008 0.001 TRP D 170 HIS 0.001 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14925) covalent geometry : angle 0.54486 / 0.28 (20075) SS BOND : bond 0.00787 / 0.42 ( 5) SS BOND : angle 4.28274 / 2.27 ( 10) hydrogen bonds : bond 0.05071 / 3.44 ( 690) hydrogen bonds : angle 4.53444 / 3.15 ( 2445) link_BETA1-4 : bond 0.00364 / 0.20 ( 5) link_BETA1-4 : angle 1.45040 / 0.96 ( 15) link_NAG-ASN : bond 0.00079 / 0.04 ( 5) link_NAG-ASN : angle 0.52944 / 0.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.602 Fit side-chains REVERT: B 56 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8766 (tpt) outliers start: 28 outliers final: 12 residues processed: 135 average time/residue: 0.6057 time to fit residues: 90.4024 Evaluate side-chains 133 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 8 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 ASN D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067744 restraints weight = 28375.671| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.70 r_work: 0.2799 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14940 Z= 0.133 Angle : 0.559 9.992 20115 Z= 0.287 Chirality : 0.042 0.145 2220 Planarity : 0.004 0.038 2485 Dihedral : 6.816 53.104 2410 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.61 % Allowed : 9.94 % Favored : 88.45 % 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: 1.63 (0.21), residues: 1690 helix: 2.55 (0.21), residues: 595 sheet: 1.26 (0.26), residues: 405 loop : -0.35 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 65 TYR 0.021 0.001 TYR D 301 PHE 0.015 0.001 PHE B 99 TRP 0.010 0.001 TRP E 239 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (14925) covalent geometry : angle 0.54803 / 0.28 (20075) SS BOND : bond 0.00714 / 0.37 ( 5) SS BOND : angle 4.64953 / 2.42 ( 10) hydrogen bonds : bond 0.05068 / 3.44 ( 690) hydrogen bonds : angle 4.51662 / 3.13 ( 2445) link_BETA1-4 : bond 0.00389 / 0.21 ( 5) link_BETA1-4 : angle 1.41198 / 0.93 ( 15) link_NAG-ASN : bond 0.00077 / 0.04 ( 5) link_NAG-ASN : angle 0.53332 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.699 Fit side-chains REVERT: B 56 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8757 (tpt) REVERT: B 142 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9051 (mp) REVERT: C 171 GLN cc_start: 0.8699 (tt0) cc_final: 0.8431 (mm-40) outliers start: 25 outliers final: 13 residues processed: 135 average time/residue: 0.6145 time to fit residues: 91.5582 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 8 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 127 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 149 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 ASN D 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.086767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.068211 restraints weight = 28207.536| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.69 r_work: 0.2808 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14940 Z= 0.123 Angle : 0.542 8.773 20115 Z= 0.278 Chirality : 0.042 0.156 2220 Planarity : 0.004 0.036 2485 Dihedral : 6.739 56.167 2410 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.29 % Allowed : 10.58 % Favored : 88.13 % 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: 1690 helix: 2.60 (0.21), residues: 595 sheet: 1.30 (0.26), residues: 405 loop : -0.36 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 65 TYR 0.021 0.001 TYR D 301 PHE 0.016 0.001 PHE B 121 TRP 0.011 0.001 TRP E 239 HIS 0.002 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (14925) covalent geometry : angle 0.53380 / 0.27 (20075) SS BOND : bond 0.00444 / 0.23 ( 5) SS BOND : angle 3.91902 / 2.04 ( 10) hydrogen bonds : bond 0.04865 / 3.31 ( 690) hydrogen bonds : angle 4.43597 / 3.08 ( 2445) link_BETA1-4 : bond 0.00372 / 0.20 ( 5) link_BETA1-4 : angle 1.37388 / 0.90 ( 15) link_NAG-ASN : bond 0.00094 / 0.05 ( 5) link_NAG-ASN : angle 0.50984 / 0.31 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.606 Fit side-chains REVERT: B 56 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8705 (tpt) REVERT: B 142 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9066 (mp) REVERT: C 171 GLN cc_start: 0.8698 (tt0) cc_final: 0.8440 (mm-40) outliers start: 20 outliers final: 15 residues processed: 130 average time/residue: 0.6349 time to fit residues: 90.8885 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 8 MET Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 0.0060 chunk 30 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 0.0040 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.069840 restraints weight = 28246.928| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.68 r_work: 0.2839 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14940 Z= 0.104 Angle : 0.522 10.513 20115 Z= 0.265 Chirality : 0.041 0.154 2220 Planarity : 0.003 0.036 2485 Dihedral : 6.481 59.674 2410 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.35 % Allowed : 10.65 % Favored : 88.00 % 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: 1.83 (0.21), residues: 1690 helix: 2.79 (0.21), residues: 590 sheet: 1.26 (0.25), residues: 425 loop : -0.25 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.020 0.001 TYR D 301 PHE 0.021 0.001 PHE A 121 TRP 0.010 0.001 TRP E 239 HIS 0.001 0.000 HIS E 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (14925) covalent geometry : angle 0.51599 / 0.26 (20075) SS BOND : bond 0.00372 / 0.20 ( 5) SS BOND : angle 3.40084 / 1.78 ( 10) hydrogen bonds : bond 0.04306 / 2.93 ( 690) hydrogen bonds : angle 4.23027 / 2.93 ( 2445) link_BETA1-4 : bond 0.00377 / 0.20 ( 5) link_BETA1-4 : angle 1.30612 / 0.85 ( 15) link_NAG-ASN : bond 0.00155 / 0.08 ( 5) link_NAG-ASN : angle 0.42215 / 0.26 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.559 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 141 average time/residue: 0.6017 time to fit residues: 93.6691 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 8 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 ASN D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069352 restraints weight = 28504.815| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.69 r_work: 0.2833 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14940 Z= 0.110 Angle : 0.527 8.813 20115 Z= 0.269 Chirality : 0.042 0.150 2220 Planarity : 0.003 0.036 2485 Dihedral : 6.354 59.605 2410 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.77 % Allowed : 11.81 % Favored : 87.42 % 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: 2.05 (0.21), residues: 1690 helix: 3.19 (0.21), residues: 560 sheet: 1.22 (0.25), residues: 425 loop : -0.06 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 65 TYR 0.020 0.001 TYR D 301 PHE 0.019 0.001 PHE B 121 TRP 0.013 0.001 TRP E 239 HIS 0.002 0.000 HIS E 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14925) covalent geometry : angle 0.52041 / 0.27 (20075) SS BOND : bond 0.00330 / 0.17 ( 5) SS BOND : angle 3.30531 / 1.73 ( 10) hydrogen bonds : bond 0.04423 / 3.00 ( 690) hydrogen bonds : angle 4.24300 / 2.94 ( 2445) link_BETA1-4 : bond 0.00363 / 0.19 ( 5) link_BETA1-4 : angle 1.32891 / 0.87 ( 15) link_NAG-ASN : bond 0.00106 / 0.06 ( 5) link_NAG-ASN : angle 0.50103 / 0.31 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.577 Fit side-chains REVERT: B 171 GLN cc_start: 0.8341 (tt0) cc_final: 0.8135 (mm-40) outliers start: 12 outliers final: 11 residues processed: 132 average time/residue: 0.6390 time to fit residues: 92.8228 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain E residue 8 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.066391 restraints weight = 28303.414| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.68 r_work: 0.2771 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14940 Z= 0.164 Angle : 0.571 9.061 20115 Z= 0.297 Chirality : 0.043 0.157 2220 Planarity : 0.004 0.038 2485 Dihedral : 6.646 50.178 2410 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.71 % Allowed : 11.94 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.21), residues: 1690 helix: 2.63 (0.21), residues: 595 sheet: 1.20 (0.26), residues: 405 loop : -0.51 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 65 TYR 0.023 0.002 TYR D 301 PHE 0.019 0.002 PHE C 99 TRP 0.025 0.002 TRP E 239 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (14925) covalent geometry : angle 0.56480 / 0.29 (20075) SS BOND : bond 0.00585 / 0.31 ( 5) SS BOND : angle 3.57076 / 1.88 ( 10) hydrogen bonds : bond 0.05521 / 3.76 ( 690) hydrogen bonds : angle 4.60027 / 3.18 ( 2445) link_BETA1-4 : bond 0.00305 / 0.16 ( 5) link_BETA1-4 : angle 1.40204 / 0.93 ( 15) link_NAG-ASN : bond 0.00047 / 0.03 ( 5) link_NAG-ASN : angle 0.70873 / 0.43 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.594 Fit side-chains REVERT: B 171 GLN cc_start: 0.8727 (tt0) cc_final: 0.8459 (mm-40) outliers start: 11 outliers final: 11 residues processed: 123 average time/residue: 0.6533 time to fit residues: 88.1973 Evaluate side-chains 130 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain E residue 8 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 5 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 119 optimal weight: 0.1980 chunk 47 optimal weight: 0.0870 chunk 159 optimal weight: 3.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.086800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068420 restraints weight = 28280.851| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.68 r_work: 0.2814 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14940 Z= 0.109 Angle : 0.531 9.446 20115 Z= 0.274 Chirality : 0.042 0.154 2220 Planarity : 0.003 0.034 2485 Dihedral : 6.404 49.018 2410 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.77 % Allowed : 12.13 % Favored : 87.10 % 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: 1.76 (0.21), residues: 1690 helix: 2.76 (0.21), residues: 590 sheet: 1.20 (0.25), residues: 435 loop : -0.34 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 65 TYR 0.020 0.001 TYR D 301 PHE 0.020 0.001 PHE B 121 TRP 0.022 0.001 TRP C 239 HIS 0.001 0.000 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14925) covalent geometry : angle 0.52555 / 0.27 (20075) SS BOND : bond 0.00321 / 0.17 ( 5) SS BOND : angle 3.06320 / 1.61 ( 10) hydrogen bonds : bond 0.04705 / 3.20 ( 690) hydrogen bonds : angle 4.39631 / 3.04 ( 2445) link_BETA1-4 : bond 0.00354 / 0.19 ( 5) link_BETA1-4 : angle 1.31503 / 0.87 ( 15) link_NAG-ASN : bond 0.00158 / 0.08 ( 5) link_NAG-ASN : angle 0.45664 / 0.27 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4277.85 seconds wall clock time: 73 minutes 56.77 seconds (4436.77 seconds total)