Starting phenix.real_space_refine on Thu May 15 18:01:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8r_36078/05_2025/8j8r_36078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8r_36078/05_2025/8j8r_36078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8r_36078/05_2025/8j8r_36078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8r_36078/05_2025/8j8r_36078.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8r_36078/05_2025/8j8r_36078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8r_36078/05_2025/8j8r_36078.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.121 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 27 5.16 5 C 8522 2.51 5 N 2304 2.21 5 O 2562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13424 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2691 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2695 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 317} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2693 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 317} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 798 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 911 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 8.44, per 1000 atoms: 0.63 Number of scatterers: 13424 At special positions: 0 Unit cell: (148.664, 141.47, 91.1164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 9 15.00 O 2562 8.00 N 2304 7.00 C 8522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " distance=2.04 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 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 32 sheets defined 4.1% alpha, 48.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.754A pdb=" N LEU A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.080A pdb=" N ARG A 283 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.877A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.885A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 94 removed outlier: 3.921A pdb=" N THR M 94 " --> pdb=" O ALA M 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.793A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 144 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 54 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN A 86 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 56 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN A 84 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 58 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 82 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 60 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.793A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU A 141 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 190 removed outlier: 3.656A pdb=" N SER A 197 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 224 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.547A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU A 319 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A 240 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 321 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN A 238 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 323 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A 236 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 325 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 234 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS A 327 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 232 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 329 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE A 232 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU A 258 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL A 234 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN A 256 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 236 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 118 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.762A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS B 171 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N VAL B 143 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 144 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL B 54 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN B 86 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 56 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN B 84 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 58 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 82 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 60 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.762A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS B 171 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N VAL B 143 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU B 141 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 189 removed outlier: 3.501A pdb=" N LEU B 200 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.990A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU B 344 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL B 320 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 329 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS B 231 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE B 232 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU B 258 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 234 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN B 256 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 236 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AB3, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.834A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 54 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN C 86 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL C 56 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN C 84 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 58 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE C 82 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 60 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.834A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 141 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 190 removed outlier: 3.715A pdb=" N SER C 197 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN C 224 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.967A pdb=" N VAL C 336 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU C 344 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 320 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA C 240 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS C 251 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.557A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.217A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.217A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.641A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.894A pdb=" N LEU E 12 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.894A pdb=" N LEU E 12 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AC5, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.483A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.483A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC8, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.673A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA L 85 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.673A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA L 85 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 6 through 10 Processing sheet with id=AD2, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.434A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N SER M 35 " --> pdb=" O SER M 55 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER M 55 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE M 37 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP M 39 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.434A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR M 112 " --> pdb=" O ARG M 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 6 through 8 removed outlier: 3.535A pdb=" N VAL N 20 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.819A pdb=" N LEU N 12 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4326 1.34 - 1.46: 3188 1.46 - 1.58: 6151 1.58 - 1.70: 31 1.70 - 1.81: 39 Bond restraints: 13735 Sorted by residual: bond pdb=" OG1 TPO G 360 " pdb=" P TPO G 360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" OG1 TPO V 349 " pdb=" P TPO V 349 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" OG1 TPO U 307 " pdb=" P TPO U 307 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO G 363 " pdb=" P TPO G 363 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" OG1 TPO U 310 " pdb=" P TPO U 310 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.89e+01 ... (remaining 13730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 18485 2.56 - 5.12: 160 5.12 - 7.68: 29 7.68 - 10.24: 7 10.24 - 12.80: 5 Bond angle restraints: 18686 Sorted by residual: angle pdb=" C CYS B 69 " pdb=" N ASP B 70 " pdb=" CA ASP B 70 " ideal model delta sigma weight residual 123.03 115.87 7.16 1.34e+00 5.57e-01 2.85e+01 angle pdb=" C VAL B 71 " pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta sigma weight residual 122.93 115.81 7.12 1.45e+00 4.76e-01 2.41e+01 angle pdb=" CA PRO C 97 " pdb=" N PRO C 97 " pdb=" CD PRO C 97 " ideal model delta sigma weight residual 112.00 105.27 6.73 1.40e+00 5.10e-01 2.31e+01 angle pdb=" N VAL B 71 " pdb=" CA VAL B 71 " pdb=" C VAL B 71 " ideal model delta sigma weight residual 108.81 101.87 6.94 1.62e+00 3.81e-01 1.84e+01 angle pdb=" CB TPO G 363 " pdb=" OG1 TPO G 363 " pdb=" P TPO G 363 " ideal model delta sigma weight residual 119.31 106.51 12.80 3.00e+00 1.11e-01 1.82e+01 ... (remaining 18681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7347 17.79 - 35.58: 638 35.58 - 53.37: 197 53.37 - 71.16: 22 71.16 - 88.95: 23 Dihedral angle restraints: 8227 sinusoidal: 3187 harmonic: 5040 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 59.96 33.04 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS M 25 " pdb=" SG CYS M 25 " pdb=" SG CYS M 99 " pdb=" CB CYS M 99 " ideal model delta sinusoidal sigma weight residual 93.00 64.38 28.62 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ASP B 79 " pdb=" CB ASP B 79 " pdb=" CG ASP B 79 " pdb=" OD1 ASP B 79 " ideal model delta sinusoidal sigma weight residual -30.00 -89.02 59.02 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 8224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1808 0.058 - 0.116: 266 0.116 - 0.174: 33 0.174 - 0.232: 1 0.232 - 0.291: 1 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CA VAL B 71 " pdb=" N VAL B 71 " pdb=" C VAL B 71 " pdb=" CB VAL B 71 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB TPO V 352 " pdb=" CA TPO V 352 " pdb=" OG1 TPO V 352 " pdb=" CG2 TPO V 352 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA CYS B 69 " pdb=" N CYS B 69 " pdb=" C CYS B 69 " pdb=" CB CYS B 69 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2106 not shown) Planarity restraints: 2391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 96 " -0.051 5.00e-02 4.00e+02 7.40e-02 8.75e+00 pdb=" N PRO C 97 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 97 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 97 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 84 " 0.011 2.00e-02 2.50e+03 1.71e-02 5.13e+00 pdb=" CG PHE E 84 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 84 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE E 84 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 84 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 84 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 84 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 91 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO C 92 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 92 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 92 " -0.028 5.00e-02 4.00e+02 ... (remaining 2388 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 923 2.74 - 3.28: 12445 3.28 - 3.82: 21241 3.82 - 4.36: 25148 4.36 - 4.90: 46054 Nonbonded interactions: 105811 Sorted by model distance: nonbonded pdb=" OD1 ASP B 205 " pdb=" OH TYR B 209 " model vdw 2.199 3.040 nonbonded pdb=" N GLU C 177 " pdb=" OE1 GLU C 177 " model vdw 2.216 3.120 nonbonded pdb=" N ASN C 93 " pdb=" OD1 ASN C 93 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP A 136 " pdb=" NH1 ARG A 286 " model vdw 2.253 3.120 nonbonded pdb=" O THR C 222 " pdb=" OG1 THR C 222 " model vdw 2.262 3.040 ... (remaining 105806 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 7 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 157 or (resid 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 160 or \ (resid 161 through 162 and (name N or name CA or name C or name O or name CB )) \ or resid 163 through 191 or (resid 192 and (name N or name CA or name C or name \ O or name CB )) or resid 193 through 307 or (resid 308 and (name N or name CA o \ r name C or name O or name CB )) or resid 309 through 311 or (resid 312 through \ 314 and (name N or name CA or name C or name O or name CB )) or resid 315 throug \ h 350)) selection = (chain 'B' and (resid 7 through 48 or (resid 49 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 75 or (resid 76 and (n \ ame N or name CA or name C or name O or name CB )) or resid 77 through 110 or (r \ esid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 t \ hrough 157 or (resid 158 and (name N or name CA or name C or name O or name CB ) \ ) or resid 159 through 160 or (resid 161 through 162 and (name N or name CA or n \ ame C or name O or name CB )) or resid 163 through 307 or (resid 308 and (name N \ or name CA or name C or name O or name CB )) or resid 309 through 350)) selection = (chain 'C' and (resid 7 through 48 or (resid 49 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 65 or (resid 66 and (n \ ame N or name CA or name C or name O or name CB )) or resid 67 through 69 or (re \ sid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 thro \ ugh 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or \ resid 77 through 110 or (resid 111 and (name N or name CA or name C or name O or \ name CB )) or resid 112 through 311 or (resid 312 through 314 and (name N or na \ me CA or name C or name O or name CB )) or resid 315 through 350)) } ncs_group { reference = (chain 'D' and (resid 5 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 106 or (resid 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 122)) selection = (chain 'H' and (resid 5 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 122)) selection = (chain 'M' and (resid 5 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 122)) } ncs_group { reference = (chain 'E' and (resid 1 through 30 or resid 33 through 107)) selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'U' selection = chain 'V' } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.490 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.004 0.110 13741 Z= 0.209 Angle : 0.636 12.797 18698 Z= 0.307 Chirality : 0.044 0.291 2109 Planarity : 0.004 0.074 2391 Dihedral : 15.504 88.948 4971 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.26 % Allowed : 18.24 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1687 helix: 1.80 (0.82), residues: 36 sheet: 1.51 (0.20), residues: 790 loop : -0.24 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 106 HIS 0.006 0.001 HIS B 160 PHE 0.039 0.001 PHE E 84 TYR 0.026 0.001 TYR C 48 ARG 0.009 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.22546 ( 492) hydrogen bonds : angle 8.92969 ( 1398) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.51000 ( 12) covalent geometry : bond 0.00440 (13735) covalent geometry : angle 0.63635 (18686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.498 Fit side-chains outliers start: 33 outliers final: 33 residues processed: 224 average time/residue: 0.8762 time to fit residues: 221.1004 Evaluate side-chains 218 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 131 GLN B 218 ASN B 220 HIS B 281 ASN C 262 GLN D 6 GLN H 80 ASN L 7 GLN M 38 HIS U 306 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.148083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113222 restraints weight = 19498.432| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.68 r_work: 0.3250 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13741 Z= 0.111 Angle : 0.551 9.048 18698 Z= 0.285 Chirality : 0.044 0.172 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.789 58.761 1946 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.16 % Allowed : 17.01 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.21), residues: 1687 helix: 2.09 (0.85), residues: 36 sheet: 1.55 (0.19), residues: 784 loop : -0.34 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.005 0.001 HIS B 160 PHE 0.028 0.001 PHE E 84 TYR 0.012 0.001 TYR H 107 ARG 0.006 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 492) hydrogen bonds : angle 5.88822 ( 1398) SS BOND : bond 0.00331 ( 6) SS BOND : angle 0.65445 ( 12) covalent geometry : bond 0.00244 (13735) covalent geometry : angle 0.55063 (18686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 1.457 Fit side-chains REVERT: B 316 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7869 (mp) REVERT: C 30 ASP cc_start: 0.8401 (t0) cc_final: 0.8156 (t0) REVERT: C 163 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.6978 (p0) REVERT: C 200 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7299 (tp) REVERT: D 92 GLU cc_start: 0.7471 (pm20) cc_final: 0.7172 (pm20) outliers start: 46 outliers final: 26 residues processed: 231 average time/residue: 0.9145 time to fit residues: 237.1816 Evaluate side-chains 210 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 160 HIS B 218 ASN B 220 HIS H 80 ASN L 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108155 restraints weight = 19543.152| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.77 r_work: 0.3181 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13741 Z= 0.234 Angle : 0.639 6.865 18698 Z= 0.334 Chirality : 0.047 0.173 2109 Planarity : 0.005 0.053 2391 Dihedral : 5.723 53.404 1922 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.08 % Allowed : 17.35 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1687 helix: 2.06 (0.84), residues: 36 sheet: 1.30 (0.19), residues: 784 loop : -0.45 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 106 HIS 0.007 0.001 HIS B 112 PHE 0.042 0.002 PHE M 105 TYR 0.018 0.002 TYR C 48 ARG 0.006 0.001 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 492) hydrogen bonds : angle 5.65172 ( 1398) SS BOND : bond 0.00523 ( 6) SS BOND : angle 0.64296 ( 12) covalent geometry : bond 0.00550 (13735) covalent geometry : angle 0.63897 (18686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 193 time to evaluate : 1.511 Fit side-chains REVERT: C 30 ASP cc_start: 0.8444 (t0) cc_final: 0.8085 (t0) REVERT: C 163 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7114 (p0) REVERT: D 49 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: D 92 GLU cc_start: 0.7672 (pm20) cc_final: 0.7356 (pm20) REVERT: E 19 ARG cc_start: 0.7401 (ttt90) cc_final: 0.7177 (tmt90) REVERT: E 89 CYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7559 (p) REVERT: H 31 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8386 (m110) REVERT: H 92 GLU cc_start: 0.7741 (pm20) cc_final: 0.7477 (pm20) REVERT: L 93 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8929 (tmtm) outliers start: 74 outliers final: 48 residues processed: 247 average time/residue: 0.8945 time to fit residues: 248.2439 Evaluate side-chains 236 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain V residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 218 ASN B 220 HIS C 262 GLN H 80 ASN L 39 GLN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110463 restraints weight = 19405.679| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.66 r_work: 0.3213 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13741 Z= 0.155 Angle : 0.578 7.486 18698 Z= 0.298 Chirality : 0.045 0.156 2109 Planarity : 0.004 0.051 2391 Dihedral : 5.447 47.504 1920 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.08 % Allowed : 18.52 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1687 helix: 2.06 (0.85), residues: 36 sheet: 1.23 (0.19), residues: 786 loop : -0.47 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 106 HIS 0.005 0.001 HIS B 112 PHE 0.038 0.002 PHE E 84 TYR 0.016 0.001 TYR H 107 ARG 0.006 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 492) hydrogen bonds : angle 5.35367 ( 1398) SS BOND : bond 0.00416 ( 6) SS BOND : angle 0.50436 ( 12) covalent geometry : bond 0.00361 (13735) covalent geometry : angle 0.57768 (18686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 191 time to evaluate : 1.488 Fit side-chains REVERT: C 30 ASP cc_start: 0.8390 (t0) cc_final: 0.8093 (t0) REVERT: C 163 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7140 (p0) REVERT: C 200 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7512 (tp) REVERT: D 49 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: D 92 GLU cc_start: 0.7678 (pm20) cc_final: 0.7286 (pm20) REVERT: E 19 ARG cc_start: 0.7354 (ttt90) cc_final: 0.7150 (tmt90) REVERT: E 89 CYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7590 (p) REVERT: H 42 GLN cc_start: 0.8145 (tt0) cc_final: 0.7940 (tt0) REVERT: H 49 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: H 86 MET cc_start: 0.7862 (mtp) cc_final: 0.6614 (mtp) REVERT: L 89 CYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7231 (p) REVERT: M 62 TYR cc_start: 0.8729 (m-80) cc_final: 0.8522 (m-80) outliers start: 74 outliers final: 47 residues processed: 250 average time/residue: 0.9387 time to fit residues: 263.2035 Evaluate side-chains 234 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain V residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 86 GLN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 220 HIS B 262 GLN C 296 HIS H 80 ASN L 39 GLN N 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107359 restraints weight = 19532.204| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.76 r_work: 0.3169 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13741 Z= 0.259 Angle : 0.664 8.240 18698 Z= 0.346 Chirality : 0.047 0.175 2109 Planarity : 0.005 0.053 2391 Dihedral : 5.659 45.559 1920 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.97 % Allowed : 18.72 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1687 helix: 1.98 (0.85), residues: 36 sheet: 1.07 (0.19), residues: 784 loop : -0.58 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.009 0.002 HIS B 160 PHE 0.047 0.002 PHE M 105 TYR 0.015 0.002 TYR H 107 ARG 0.008 0.001 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 492) hydrogen bonds : angle 5.45646 ( 1398) SS BOND : bond 0.00518 ( 6) SS BOND : angle 0.68991 ( 12) covalent geometry : bond 0.00615 (13735) covalent geometry : angle 0.66386 (18686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 183 time to evaluate : 1.744 Fit side-chains REVERT: B 207 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: B 267 SER cc_start: 0.7720 (p) cc_final: 0.7493 (p) REVERT: C 30 ASP cc_start: 0.8446 (t0) cc_final: 0.8115 (t0) REVERT: C 163 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7162 (p0) REVERT: C 195 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: D 49 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: D 92 GLU cc_start: 0.7711 (pm20) cc_final: 0.7331 (pm20) REVERT: E 89 CYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7691 (p) REVERT: H 49 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: L 89 CYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7437 (p) outliers start: 87 outliers final: 56 residues processed: 252 average time/residue: 0.8895 time to fit residues: 252.2072 Evaluate side-chains 245 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 182 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 119 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 132 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 160 HIS B 218 ASN B 220 HIS C 296 HIS H 80 ASN L 39 GLN N 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110180 restraints weight = 19711.338| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.78 r_work: 0.3211 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13741 Z= 0.123 Angle : 0.568 9.587 18698 Z= 0.290 Chirality : 0.044 0.148 2109 Planarity : 0.004 0.051 2391 Dihedral : 5.176 39.647 1918 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.01 % Allowed : 20.44 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1687 helix: 2.06 (0.86), residues: 36 sheet: 1.13 (0.19), residues: 786 loop : -0.50 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 106 HIS 0.008 0.001 HIS B 160 PHE 0.044 0.002 PHE E 84 TYR 0.016 0.001 TYR H 107 ARG 0.006 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 492) hydrogen bonds : angle 5.16449 ( 1398) SS BOND : bond 0.00385 ( 6) SS BOND : angle 0.50873 ( 12) covalent geometry : bond 0.00281 (13735) covalent geometry : angle 0.56830 (18686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 191 time to evaluate : 1.658 Fit side-chains REVERT: A 30 ASP cc_start: 0.8506 (t0) cc_final: 0.8266 (t0) REVERT: C 30 ASP cc_start: 0.8490 (t0) cc_final: 0.8116 (t0) REVERT: C 163 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7171 (p0) REVERT: C 195 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: D 92 GLU cc_start: 0.7703 (pm20) cc_final: 0.7332 (pm20) REVERT: E 89 CYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7539 (p) REVERT: H 86 MET cc_start: 0.7834 (mtp) cc_final: 0.6391 (mtp) REVERT: L 89 CYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7194 (p) REVERT: N 19 ARG cc_start: 0.7622 (ttt90) cc_final: 0.7083 (tmt90) outliers start: 73 outliers final: 54 residues processed: 250 average time/residue: 0.9338 time to fit residues: 262.1754 Evaluate side-chains 241 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 218 ASN B 220 HIS B 262 GLN C 296 HIS L 39 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107190 restraints weight = 19540.332| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.76 r_work: 0.3168 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13741 Z= 0.252 Angle : 0.657 8.639 18698 Z= 0.342 Chirality : 0.047 0.176 2109 Planarity : 0.005 0.053 2391 Dihedral : 5.476 39.550 1918 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.83 % Allowed : 19.68 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1687 helix: 1.97 (0.85), residues: 36 sheet: 1.04 (0.19), residues: 776 loop : -0.59 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 106 HIS 0.006 0.001 HIS C 346 PHE 0.047 0.002 PHE M 105 TYR 0.015 0.002 TYR H 107 ARG 0.009 0.001 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 492) hydrogen bonds : angle 5.34771 ( 1398) SS BOND : bond 0.00493 ( 6) SS BOND : angle 0.69697 ( 12) covalent geometry : bond 0.00597 (13735) covalent geometry : angle 0.65671 (18686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 184 time to evaluate : 1.667 Fit side-chains REVERT: A 30 ASP cc_start: 0.8603 (t0) cc_final: 0.8369 (t0) REVERT: B 267 SER cc_start: 0.7736 (p) cc_final: 0.7516 (p) REVERT: B 298 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8025 (t0) REVERT: C 30 ASP cc_start: 0.8588 (t0) cc_final: 0.8186 (t0) REVERT: C 163 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7302 (p0) REVERT: C 195 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: D 49 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: D 92 GLU cc_start: 0.7716 (pm20) cc_final: 0.7328 (pm20) REVERT: E 89 CYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7668 (p) REVERT: H 49 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: L 89 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7380 (p) REVERT: L 93 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8903 (tmtm) outliers start: 85 outliers final: 62 residues processed: 251 average time/residue: 0.8895 time to fit residues: 251.6987 Evaluate side-chains 250 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 51 optimal weight: 0.1980 chunk 152 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 86 GLN B 218 ASN B 220 HIS B 262 GLN C 262 GLN C 296 HIS L 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110950 restraints weight = 19562.275| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.67 r_work: 0.3223 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13741 Z= 0.121 Angle : 0.566 10.264 18698 Z= 0.288 Chirality : 0.044 0.152 2109 Planarity : 0.004 0.051 2391 Dihedral : 5.067 39.500 1917 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.87 % Allowed : 21.19 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1687 helix: 2.10 (0.86), residues: 36 sheet: 1.09 (0.19), residues: 786 loop : -0.51 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 106 HIS 0.004 0.001 HIS B 112 PHE 0.024 0.002 PHE B 269 TYR 0.016 0.001 TYR H 107 ARG 0.007 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 492) hydrogen bonds : angle 5.06389 ( 1398) SS BOND : bond 0.00367 ( 6) SS BOND : angle 0.53265 ( 12) covalent geometry : bond 0.00280 (13735) covalent geometry : angle 0.56646 (18686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 187 time to evaluate : 2.399 Fit side-chains REVERT: B 207 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: B 222 THR cc_start: 0.7853 (m) cc_final: 0.7528 (p) REVERT: B 330 VAL cc_start: 0.6772 (m) cc_final: 0.6528 (m) REVERT: C 30 ASP cc_start: 0.8500 (t0) cc_final: 0.8185 (t0) REVERT: C 163 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7412 (p0) REVERT: C 195 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: D 92 GLU cc_start: 0.7709 (pm20) cc_final: 0.7280 (pm20) REVERT: E 89 CYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7593 (p) REVERT: L 89 CYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7118 (p) outliers start: 71 outliers final: 52 residues processed: 244 average time/residue: 1.0104 time to fit residues: 283.4045 Evaluate side-chains 244 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 220 HIS B 262 GLN C 296 HIS H 80 ASN L 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109080 restraints weight = 19386.519| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.76 r_work: 0.3195 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13741 Z= 0.169 Angle : 0.600 10.608 18698 Z= 0.308 Chirality : 0.045 0.155 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.133 38.066 1917 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.14 % Allowed : 21.19 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1687 helix: 2.08 (0.85), residues: 36 sheet: 1.11 (0.19), residues: 780 loop : -0.55 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 106 HIS 0.004 0.001 HIS B 112 PHE 0.047 0.002 PHE E 84 TYR 0.013 0.001 TYR H 107 ARG 0.005 0.000 ARG M 22 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 492) hydrogen bonds : angle 5.09325 ( 1398) SS BOND : bond 0.00394 ( 6) SS BOND : angle 0.60635 ( 12) covalent geometry : bond 0.00398 (13735) covalent geometry : angle 0.60046 (18686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 190 time to evaluate : 1.611 Fit side-chains REVERT: A 77 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.8375 (ttt-90) REVERT: B 207 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: B 222 THR cc_start: 0.7820 (m) cc_final: 0.7435 (p) REVERT: B 267 SER cc_start: 0.7722 (p) cc_final: 0.7519 (p) REVERT: B 330 VAL cc_start: 0.6625 (m) cc_final: 0.6380 (m) REVERT: C 30 ASP cc_start: 0.8539 (t0) cc_final: 0.8138 (t0) REVERT: C 163 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7299 (p0) REVERT: D 49 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: D 92 GLU cc_start: 0.7705 (pm20) cc_final: 0.7308 (pm20) REVERT: E 89 CYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7642 (p) REVERT: H 49 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: L 89 CYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7260 (p) outliers start: 75 outliers final: 57 residues processed: 249 average time/residue: 0.8507 time to fit residues: 239.6844 Evaluate side-chains 248 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 165 optimal weight: 0.0770 chunk 130 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 218 ASN B 220 HIS B 262 GLN C 296 HIS H 80 ASN L 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109479 restraints weight = 19501.515| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.76 r_work: 0.3203 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13741 Z= 0.153 Angle : 0.595 12.080 18698 Z= 0.303 Chirality : 0.045 0.153 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.079 37.938 1917 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.60 % Allowed : 21.88 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1687 helix: 2.05 (0.84), residues: 36 sheet: 1.10 (0.19), residues: 781 loop : -0.53 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 106 HIS 0.004 0.001 HIS B 112 PHE 0.031 0.002 PHE M 105 TYR 0.016 0.001 TYR H 107 ARG 0.004 0.000 ARG M 22 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 492) hydrogen bonds : angle 5.05623 ( 1398) SS BOND : bond 0.00383 ( 6) SS BOND : angle 0.56465 ( 12) covalent geometry : bond 0.00360 (13735) covalent geometry : angle 0.59547 (18686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 1.553 Fit side-chains REVERT: B 207 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: B 222 THR cc_start: 0.7788 (m) cc_final: 0.7448 (p) REVERT: B 267 SER cc_start: 0.7706 (p) cc_final: 0.7504 (p) REVERT: B 330 VAL cc_start: 0.6589 (m) cc_final: 0.6353 (m) REVERT: C 30 ASP cc_start: 0.8530 (t0) cc_final: 0.8163 (t0) REVERT: C 163 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7297 (p0) REVERT: D 92 GLU cc_start: 0.7697 (pm20) cc_final: 0.7301 (pm20) REVERT: E 89 CYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7623 (p) REVERT: H 49 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: L 89 CYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7301 (p) outliers start: 67 outliers final: 55 residues processed: 238 average time/residue: 0.8839 time to fit residues: 237.2120 Evaluate side-chains 242 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 220 HIS B 262 GLN C 296 HIS L 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.144986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109400 restraints weight = 19596.213| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.77 r_work: 0.3199 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13741 Z= 0.159 Angle : 0.603 11.805 18698 Z= 0.308 Chirality : 0.045 0.155 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.086 37.868 1917 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.80 % Allowed : 22.02 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1687 helix: 2.02 (0.84), residues: 36 sheet: 1.14 (0.19), residues: 775 loop : -0.54 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 106 HIS 0.004 0.001 HIS B 112 PHE 0.042 0.002 PHE E 84 TYR 0.015 0.001 TYR H 107 ARG 0.004 0.000 ARG M 22 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 492) hydrogen bonds : angle 5.06012 ( 1398) SS BOND : bond 0.00374 ( 6) SS BOND : angle 0.61707 ( 12) covalent geometry : bond 0.00373 (13735) covalent geometry : angle 0.60273 (18686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9803.11 seconds wall clock time: 169 minutes 32.97 seconds (10172.97 seconds total)