Starting phenix.real_space_refine on Sat Aug 23 16:54:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8r_36078/08_2025/8j8r_36078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8r_36078/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j8r_36078/08_2025/8j8r_36078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8r_36078/08_2025/8j8r_36078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j8r_36078/08_2025/8j8r_36078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8r_36078/08_2025/8j8r_36078.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLU: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: {'ARG:plan': 2, 'GLU:plan': 1} 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: 2.54, per 1000 atoms: 0.19 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: 0.72 Conformation dependent library (CDL) restraints added in 436.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.38 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: 1.59 Time building geometry restraints manager: 0.96 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: 1.420 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.240 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.080 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.000 ARG D 22 TYR 0.026 0.001 TYR C 48 PHE 0.039 0.001 PHE E 84 TRP 0.007 0.001 TRP D 106 HIS 0.006 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00440 (13735) covalent geometry : angle 0.63635 (18686) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.51000 ( 12) hydrogen bonds : bond 0.22546 ( 492) hydrogen bonds : angle 8.92969 ( 1398) *********************** 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 : 0.426 Fit side-chains outliers start: 33 outliers final: 33 residues processed: 224 average time/residue: 0.3950 time to fit residues: 99.1345 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 : 0.460 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110778 restraints weight = 19559.832| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.67 r_work: 0.3216 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13741 Z= 0.163 Angle : 0.595 7.754 18698 Z= 0.310 Chirality : 0.045 0.170 2109 Planarity : 0.004 0.054 2391 Dihedral : 6.076 59.264 1946 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.12 % Allowed : 16.74 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.21), residues: 1687 helix: 2.03 (0.84), residues: 36 sheet: 1.46 (0.19), residues: 789 loop : -0.38 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.013 0.001 TYR H 107 PHE 0.030 0.002 PHE E 84 TRP 0.008 0.001 TRP D 106 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00378 (13735) covalent geometry : angle 0.59482 (18686) SS BOND : bond 0.00451 ( 6) SS BOND : angle 0.66303 ( 12) hydrogen bonds : bond 0.03981 ( 492) hydrogen bonds : angle 5.88756 ( 1398) *********************** 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 259 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 0.549 Fit side-chains REVERT: A 282 ASN cc_start: 0.8569 (p0) cc_final: 0.8188 (p0) REVERT: B 316 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7921 (mt) REVERT: C 30 ASP cc_start: 0.8425 (t0) cc_final: 0.8093 (t0) REVERT: C 163 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7023 (p0) REVERT: C 200 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7322 (tp) REVERT: D 92 GLU cc_start: 0.7706 (pm20) cc_final: 0.7370 (pm20) outliers start: 60 outliers final: 39 residues processed: 243 average time/residue: 0.3726 time to fit residues: 101.7202 Evaluate side-chains 225 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 B residue 42 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 219 VAL 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 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 118 LEU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 84 PHE 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 M residue 53 SER Chi-restraints excluded: chain M residue 120 THR 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 91 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 8 optimal weight: 0.0040 chunk 85 optimal weight: 4.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN H 80 ASN N 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110670 restraints weight = 19706.259| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.69 r_work: 0.3217 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13741 Z= 0.151 Angle : 0.574 8.044 18698 Z= 0.297 Chirality : 0.045 0.159 2109 Planarity : 0.004 0.051 2391 Dihedral : 5.622 53.333 1927 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.46 % Allowed : 18.04 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.21), residues: 1687 helix: 2.07 (0.84), residues: 36 sheet: 1.34 (0.19), residues: 789 loop : -0.43 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 22 TYR 0.017 0.001 TYR C 48 PHE 0.028 0.002 PHE M 105 TRP 0.007 0.001 TRP D 106 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00350 (13735) covalent geometry : angle 0.57424 (18686) SS BOND : bond 0.00455 ( 6) SS BOND : angle 0.50727 ( 12) hydrogen bonds : bond 0.03632 ( 492) hydrogen bonds : angle 5.52026 ( 1398) *********************** 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 259 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 194 time to evaluate : 0.368 Fit side-chains REVERT: A 282 ASN cc_start: 0.8690 (p0) cc_final: 0.8487 (p0) REVERT: C 30 ASP cc_start: 0.8385 (t0) cc_final: 0.8082 (t0) REVERT: C 163 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7157 (p0) REVERT: C 200 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7512 (tp) REVERT: D 49 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: D 92 GLU cc_start: 0.7677 (pm20) cc_final: 0.7389 (pm20) REVERT: E 67 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8222 (ttt180) REVERT: E 89 CYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7487 (p) REVERT: H 49 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: H 92 GLU cc_start: 0.7743 (pm20) cc_final: 0.7507 (pm20) outliers start: 65 outliers final: 44 residues processed: 242 average time/residue: 0.4030 time to fit residues: 108.6250 Evaluate side-chains 235 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU 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 86 GLN 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 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 E residue 6 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 73 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 13 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 160 HIS B 218 ASN H 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107724 restraints weight = 19564.710| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.77 r_work: 0.3175 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13741 Z= 0.234 Angle : 0.642 6.819 18698 Z= 0.335 Chirality : 0.047 0.173 2109 Planarity : 0.005 0.053 2391 Dihedral : 5.701 48.920 1922 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.04 % Allowed : 17.90 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.21), residues: 1687 helix: 1.98 (0.84), residues: 36 sheet: 1.15 (0.19), residues: 784 loop : -0.50 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 77 TYR 0.016 0.002 TYR H 107 PHE 0.044 0.002 PHE M 105 TRP 0.012 0.002 TRP H 106 HIS 0.004 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00552 (13735) covalent geometry : angle 0.64226 (18686) SS BOND : bond 0.00492 ( 6) SS BOND : angle 0.62376 ( 12) hydrogen bonds : bond 0.03827 ( 492) hydrogen bonds : angle 5.51385 ( 1398) *********************** 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 276 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 188 time to evaluate : 0.451 Fit side-chains REVERT: A 282 ASN cc_start: 0.8906 (p0) cc_final: 0.8626 (p0) REVERT: C 30 ASP cc_start: 0.8444 (t0) cc_final: 0.8099 (t0) REVERT: C 163 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7103 (p0) REVERT: D 49 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: D 92 GLU cc_start: 0.7699 (pm20) cc_final: 0.7357 (pm20) REVERT: E 89 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7673 (p) REVERT: H 49 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: H 92 GLU cc_start: 0.7736 (pm20) cc_final: 0.7521 (pm20) REVERT: L 89 CYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7374 (p) outliers start: 88 outliers final: 57 residues processed: 257 average time/residue: 0.3670 time to fit residues: 106.0292 Evaluate side-chains 243 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 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 43 LYS Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 32 VAL 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 53 SER Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 107 ILE 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 109 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 C 296 HIS H 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112058 restraints weight = 19581.547| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.76 r_work: 0.3238 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13741 Z= 0.106 Angle : 0.545 11.286 18698 Z= 0.277 Chirality : 0.044 0.143 2109 Planarity : 0.004 0.051 2391 Dihedral : 5.154 41.741 1922 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.53 % Allowed : 20.03 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1687 helix: 2.10 (0.86), residues: 36 sheet: 1.20 (0.19), residues: 789 loop : -0.44 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 77 TYR 0.013 0.001 TYR H 107 PHE 0.019 0.001 PHE M 105 TRP 0.008 0.001 TRP M 106 HIS 0.011 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00238 (13735) covalent geometry : angle 0.54512 (18686) SS BOND : bond 0.00373 ( 6) SS BOND : angle 0.45647 ( 12) hydrogen bonds : bond 0.02992 ( 492) hydrogen bonds : angle 5.07619 ( 1398) *********************** 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 261 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 195 time to evaluate : 0.348 Fit side-chains REVERT: B 222 THR cc_start: 0.7759 (m) cc_final: 0.7423 (p) REVERT: C 30 ASP cc_start: 0.8317 (t0) cc_final: 0.7984 (t0) REVERT: C 163 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7101 (p0) REVERT: C 195 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: D 92 GLU cc_start: 0.7687 (pm20) cc_final: 0.7236 (pm20) REVERT: E 89 CYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7532 (p) REVERT: H 49 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: H 86 MET cc_start: 0.7695 (mtp) cc_final: 0.6388 (mtp) REVERT: H 92 GLU cc_start: 0.7733 (pm20) cc_final: 0.7471 (pm20) REVERT: L 89 CYS cc_start: 0.7271 (OUTLIER) cc_final: 0.7022 (p) REVERT: N 19 ARG cc_start: 0.7631 (ttt90) cc_final: 0.7061 (tmt90) outliers start: 66 outliers final: 43 residues processed: 248 average time/residue: 0.4278 time to fit residues: 119.0898 Evaluate side-chains 234 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 260 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU 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 190 HIS 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 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 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 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 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 118 LEU 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 69 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107519 restraints weight = 19552.625| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.76 r_work: 0.3171 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1582 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= 0.236 Angle : 0.646 7.891 18698 Z= 0.336 Chirality : 0.047 0.175 2109 Planarity : 0.005 0.053 2391 Dihedral : 5.407 39.327 1920 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.69 % Allowed : 19.62 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.21), residues: 1687 helix: 2.00 (0.86), residues: 36 sheet: 1.06 (0.19), residues: 782 loop : -0.52 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 22 TYR 0.015 0.002 TYR H 107 PHE 0.045 0.002 PHE M 105 TRP 0.013 0.002 TRP H 106 HIS 0.004 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00560 (13735) covalent geometry : angle 0.64636 (18686) SS BOND : bond 0.00470 ( 6) SS BOND : angle 0.69627 ( 12) hydrogen bonds : bond 0.03681 ( 492) hydrogen bonds : angle 5.31617 ( 1398) *********************** 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 269 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 186 time to evaluate : 0.569 Fit side-chains REVERT: A 77 ARG cc_start: 0.8685 (ttt-90) cc_final: 0.8393 (ttt-90) REVERT: B 86 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: B 207 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: B 267 SER cc_start: 0.7691 (p) cc_final: 0.7465 (p) REVERT: C 30 ASP cc_start: 0.8408 (t0) cc_final: 0.8097 (t0) REVERT: C 163 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7143 (p0) REVERT: C 195 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: D 49 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: D 92 GLU cc_start: 0.7695 (pm20) cc_final: 0.7333 (pm20) REVERT: E 89 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7710 (p) REVERT: H 49 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: L 89 CYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7350 (p) REVERT: L 93 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8879 (tmtm) REVERT: M 62 TYR cc_start: 0.8845 (m-80) cc_final: 0.8575 (m-80) outliers start: 83 outliers final: 51 residues processed: 252 average time/residue: 0.4304 time to fit residues: 121.6151 Evaluate side-chains 240 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 86 GLN 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 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 49 GLU 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 53 SER 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 89 CYS Chi-restraints excluded: chain L residue 93 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108090 restraints weight = 19452.963| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.76 r_work: 0.3178 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13741 Z= 0.209 Angle : 0.630 10.065 18698 Z= 0.324 Chirality : 0.046 0.164 2109 Planarity : 0.005 0.052 2391 Dihedral : 5.373 38.214 1919 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.28 % Allowed : 20.44 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.21), residues: 1687 helix: 1.98 (0.85), residues: 36 sheet: 1.01 (0.19), residues: 784 loop : -0.57 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 22 TYR 0.017 0.001 TYR H 107 PHE 0.040 0.002 PHE M 105 TRP 0.015 0.002 TRP M 106 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00493 (13735) covalent geometry : angle 0.62960 (18686) SS BOND : bond 0.00457 ( 6) SS BOND : angle 0.64364 ( 12) hydrogen bonds : bond 0.03497 ( 492) hydrogen bonds : angle 5.27711 ( 1398) *********************** 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 259 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 182 time to evaluate : 0.633 Fit side-chains REVERT: A 77 ARG cc_start: 0.8765 (ttt-90) cc_final: 0.8491 (ttt-90) REVERT: B 86 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: B 207 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: B 267 SER cc_start: 0.7720 (p) cc_final: 0.7494 (p) REVERT: B 298 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7984 (t0) REVERT: B 330 VAL cc_start: 0.6756 (m) cc_final: 0.6511 (m) REVERT: C 30 ASP cc_start: 0.8422 (t0) cc_final: 0.8103 (t0) REVERT: C 163 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7300 (p0) REVERT: C 195 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: D 49 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: D 92 GLU cc_start: 0.7729 (pm20) cc_final: 0.7355 (pm20) REVERT: E 89 CYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7712 (p) REVERT: H 49 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: H 92 GLU cc_start: 0.7737 (pm20) cc_final: 0.7519 (pm20) REVERT: L 89 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7325 (p) REVERT: M 62 TYR cc_start: 0.8861 (m-80) cc_final: 0.8558 (m-80) outliers start: 77 outliers final: 55 residues processed: 242 average time/residue: 0.4588 time to fit residues: 124.1359 Evaluate side-chains 244 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 86 GLN 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 295 LYS Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 320 VAL 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 258 GLU 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 C residue 340 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 GLU 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 89 CYS 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 117 optimal weight: 0.4980 chunk 79 optimal weight: 0.0070 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- 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 262 GLN C 296 HIS N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111504 restraints weight = 19465.514| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.66 r_work: 0.3223 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1630 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= 0.116 Angle : 0.559 12.186 18698 Z= 0.283 Chirality : 0.044 0.143 2109 Planarity : 0.004 0.051 2391 Dihedral : 4.976 38.517 1919 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.46 % Allowed : 21.81 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.21), residues: 1687 helix: 2.15 (0.86), residues: 36 sheet: 1.13 (0.19), residues: 786 loop : -0.49 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 22 TYR 0.014 0.001 TYR H 107 PHE 0.046 0.002 PHE E 84 TRP 0.011 0.001 TRP M 106 HIS 0.004 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00265 (13735) covalent geometry : angle 0.55911 (18686) SS BOND : bond 0.00357 ( 6) SS BOND : angle 0.51383 ( 12) hydrogen bonds : bond 0.02981 ( 492) hydrogen bonds : angle 5.01290 ( 1398) *********************** 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 255 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.463 Fit side-chains REVERT: B 222 THR cc_start: 0.7880 (m) cc_final: 0.7591 (p) REVERT: B 330 VAL cc_start: 0.6887 (m) cc_final: 0.6658 (m) REVERT: C 30 ASP cc_start: 0.8459 (t0) cc_final: 0.8173 (t0) REVERT: C 163 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7388 (p0) REVERT: C 195 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: D 92 GLU cc_start: 0.7704 (pm20) cc_final: 0.7289 (pm20) REVERT: E 89 CYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7613 (p) REVERT: H 49 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: H 92 GLU cc_start: 0.7733 (pm20) cc_final: 0.7479 (pm20) REVERT: M 62 TYR cc_start: 0.8800 (m-80) cc_final: 0.8541 (m-80) outliers start: 65 outliers final: 52 residues processed: 243 average time/residue: 0.3876 time to fit residues: 106.2626 Evaluate side-chains 240 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 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 321 SER 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 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 55 LEU Chi-restraints excluded: chain L residue 76 ILE 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 94 THR Chi-restraints excluded: chain M residue 118 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 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 118 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 190 HIS B 262 GLN C 296 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108489 restraints weight = 19598.194| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.77 r_work: 0.3186 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13741 Z= 0.192 Angle : 0.623 11.568 18698 Z= 0.320 Chirality : 0.046 0.174 2109 Planarity : 0.005 0.052 2391 Dihedral : 5.190 37.461 1919 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.87 % Allowed : 21.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.21), residues: 1687 helix: 2.06 (0.85), residues: 36 sheet: 1.17 (0.19), residues: 772 loop : -0.50 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.015 0.001 TYR H 107 PHE 0.039 0.002 PHE M 105 TRP 0.015 0.002 TRP M 106 HIS 0.004 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00454 (13735) covalent geometry : angle 0.61965 (18686) SS BOND : bond 0.00387 ( 6) SS BOND : angle 2.64177 ( 12) hydrogen bonds : bond 0.03363 ( 492) hydrogen bonds : angle 5.14590 ( 1398) *********************** 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 254 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 183 time to evaluate : 0.496 Fit side-chains REVERT: A 77 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8485 (ttt-90) REVERT: B 222 THR cc_start: 0.7836 (m) cc_final: 0.7455 (p) REVERT: B 267 SER cc_start: 0.7700 (p) cc_final: 0.7486 (p) REVERT: B 330 VAL cc_start: 0.6736 (m) cc_final: 0.6506 (m) REVERT: C 30 ASP cc_start: 0.8545 (t0) cc_final: 0.8157 (t0) REVERT: C 163 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7317 (p0) REVERT: C 195 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: D 49 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: D 92 GLU cc_start: 0.7721 (pm20) cc_final: 0.7340 (pm20) REVERT: E 89 CYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7714 (p) REVERT: H 49 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: H 92 GLU cc_start: 0.7735 (pm20) cc_final: 0.7449 (pm20) REVERT: M 62 TYR cc_start: 0.8885 (m-80) cc_final: 0.8627 (m-80) outliers start: 71 outliers final: 55 residues processed: 243 average time/residue: 0.4036 time to fit residues: 110.0279 Evaluate side-chains 240 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 77 ARG 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 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 190 HIS 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 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 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 32 VAL 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 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 SER 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 55 LEU 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 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 136 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 134 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN C 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110880 restraints weight = 19594.548| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.77 r_work: 0.3221 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13741 Z= 0.115 Angle : 0.578 13.172 18698 Z= 0.292 Chirality : 0.044 0.155 2109 Planarity : 0.004 0.051 2391 Dihedral : 4.956 38.319 1919 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.98 % Allowed : 22.77 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1687 helix: 2.19 (0.86), residues: 36 sheet: 1.20 (0.19), residues: 780 loop : -0.43 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 19 TYR 0.016 0.001 TYR H 107 PHE 0.046 0.002 PHE E 84 TRP 0.012 0.001 TRP M 106 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00267 (13735) covalent geometry : angle 0.57572 (18686) SS BOND : bond 0.00308 ( 6) SS BOND : angle 2.27723 ( 12) hydrogen bonds : bond 0.02929 ( 492) hydrogen bonds : angle 4.99428 ( 1398) ********************** 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 245 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.434 Fit side-chains REVERT: B 32 LEU cc_start: 0.7843 (mt) cc_final: 0.7583 (mm) REVERT: B 222 THR cc_start: 0.7790 (m) cc_final: 0.7455 (p) REVERT: B 330 VAL cc_start: 0.6719 (m) cc_final: 0.6511 (m) REVERT: C 30 ASP cc_start: 0.8485 (t0) cc_final: 0.8154 (t0) REVERT: C 163 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7377 (p0) REVERT: C 195 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: C 260 ASP cc_start: 0.6947 (m-30) cc_final: 0.6723 (m-30) REVERT: D 92 GLU cc_start: 0.7676 (pm20) cc_final: 0.7222 (pm20) REVERT: E 89 CYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7594 (p) REVERT: H 49 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: H 92 GLU cc_start: 0.7720 (pm20) cc_final: 0.7419 (pm20) outliers start: 58 outliers final: 54 residues processed: 234 average time/residue: 0.3933 time to fit residues: 103.9120 Evaluate side-chains 243 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 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 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 32 VAL 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 84 PHE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 SER 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 55 LEU 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 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 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 161 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 262 GLN B 262 GLN C 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110032 restraints weight = 19550.844| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.67 r_work: 0.3207 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13741 Z= 0.166 Angle : 0.607 11.973 18698 Z= 0.310 Chirality : 0.045 0.157 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.023 37.701 1919 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.39 % Allowed : 22.63 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.21), residues: 1687 helix: 2.13 (0.85), residues: 36 sheet: 1.23 (0.19), residues: 774 loop : -0.49 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 62 TYR 0.014 0.001 TYR H 107 PHE 0.052 0.002 PHE E 84 TRP 0.012 0.002 TRP M 106 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00391 (13735) covalent geometry : angle 0.60360 (18686) SS BOND : bond 0.00428 ( 6) SS BOND : angle 2.43425 ( 12) hydrogen bonds : bond 0.03189 ( 492) hydrogen bonds : angle 5.02085 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4374.17 seconds wall clock time: 75 minutes 10.93 seconds (4510.93 seconds total)