Starting phenix.real_space_refine on Sun May 3 12:03:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lev_63035/05_2026/9lev_63035.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lev_63035/05_2026/9lev_63035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lev_63035/05_2026/9lev_63035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lev_63035/05_2026/9lev_63035.map" model { file = "/net/cci-nas-00/data/ceres_data/9lev_63035/05_2026/9lev_63035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lev_63035/05_2026/9lev_63035.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8255 2.51 5 N 2070 2.21 5 O 2305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12685 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.68, per 1000 atoms: 0.29 Number of scatterers: 12685 At special positions: 0 Unit cell: (131.412, 107.18, 100.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2305 8.00 N 2070 7.00 C 8255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 394 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG F 1 " - " ASN C 55 " " NAG G 1 " - " ASN C 170 " " NAG H 1 " - " ASN A 55 " " NAG I 1 " - " ASN A 170 " " NAG J 1 " - " ASN B 55 " " NAG K 1 " - " ASN B 170 " " NAG L 1 " - " ASN D 55 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 55 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 708.4 milliseconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3020 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 20 sheets defined 36.1% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.774A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 259 through 283 removed outlier: 4.184A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 322 removed outlier: 3.925A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 391 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.676A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 259 through 282 removed outlier: 4.232A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.940A pdb=" N TYR A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 391 Processing helix chain 'B' and resid 94 through 97 removed outlier: 3.574A pdb=" N ALA B 97 " --> pdb=" O THR B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.599A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 259 through 282 removed outlier: 4.311A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 322 removed outlier: 3.953A pdb=" N TYR B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 391 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 231 through 252 removed outlier: 4.677A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 259 through 282 removed outlier: 4.137A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 322 removed outlier: 3.954A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 391 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 231 through 252 removed outlier: 4.616A pdb=" N VAL E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 258 through 282 removed outlier: 4.590A pdb=" N ILE E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 322 removed outlier: 3.967A pdb=" N TYR E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 391 Processing sheet with id=AA1, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.880A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 138 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA C 150 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL C 128 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.880A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 138 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 151 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 80 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL C 74 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C 86 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL C 68 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ARG C 88 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL C 66 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER C 90 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL C 64 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N LEU C 92 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL C 62 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C 68 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AA4, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AA5, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.108A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 128 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.108A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR A 80 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN A 73 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER A 82 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL A 71 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET A 84 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU A 92 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 61 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 68 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.890A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL B 128 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.890A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 80 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL B 74 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 86 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL B 68 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG B 88 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL B 66 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N SER B 90 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 64 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LEU B 92 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N VAL B 62 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 192 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 68 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AB3, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.861A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL D 128 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU D 154 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.861A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR D 80 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL D 74 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN D 70 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU D 86 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL D 68 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ARG D 88 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL D 66 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER D 90 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL D 64 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N LEU D 92 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL D 62 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL D 68 " --> pdb=" O VAL D 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB7, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB8, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.200A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA E 150 " --> pdb=" O TRP E 130 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP E 130 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL E 128 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.200A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR E 80 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN E 73 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER E 82 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL E 71 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N MET E 84 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU E 92 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU E 61 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL E 68 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AC2, first strand: chain 'E' and resid 121 through 122 756 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3185 1.33 - 1.45: 2450 1.45 - 1.57: 7275 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 12985 Sorted by residual: bond pdb=" CA LEU D 87 " pdb=" C LEU D 87 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.23e-02 6.61e+03 1.39e+01 bond pdb=" C PHE A 164 " pdb=" N PRO A 165 " ideal model delta sigma weight residual 1.335 1.365 -0.031 1.28e-02 6.10e+03 5.69e+00 bond pdb=" N ARG D 88 " pdb=" CA ARG D 88 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.23e-02 6.61e+03 4.60e+00 bond pdb=" C LEU D 87 " pdb=" O LEU D 87 " ideal model delta sigma weight residual 1.236 1.212 0.024 1.19e-02 7.06e+03 3.91e+00 bond pdb=" N LEU D 87 " pdb=" CA LEU D 87 " ideal model delta sigma weight residual 1.458 1.434 0.023 1.22e-02 6.72e+03 3.70e+00 ... (remaining 12980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 17320 1.92 - 3.84: 363 3.84 - 5.76: 77 5.76 - 7.68: 10 7.68 - 9.59: 5 Bond angle restraints: 17775 Sorted by residual: angle pdb=" C PHE A 164 " pdb=" N PRO A 165 " pdb=" CA PRO A 165 " ideal model delta sigma weight residual 119.28 115.05 4.23 1.10e+00 8.26e-01 1.48e+01 angle pdb=" N ILE B 50 " pdb=" CA ILE B 50 " pdb=" C ILE B 50 " ideal model delta sigma weight residual 112.80 108.43 4.37 1.15e+00 7.56e-01 1.44e+01 angle pdb=" N VAL C 280 " pdb=" CA VAL C 280 " pdb=" C VAL C 280 " ideal model delta sigma weight residual 110.62 114.09 -3.47 1.02e+00 9.61e-01 1.16e+01 angle pdb=" C VAL B 66 " pdb=" CA VAL B 66 " pdb=" CB VAL B 66 " ideal model delta sigma weight residual 111.31 106.21 5.10 1.51e+00 4.39e-01 1.14e+01 angle pdb=" N ILE C 50 " pdb=" CA ILE C 50 " pdb=" C ILE C 50 " ideal model delta sigma weight residual 112.80 109.38 3.42 1.15e+00 7.56e-01 8.82e+00 ... (remaining 17770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 7445 21.76 - 43.51: 464 43.51 - 65.27: 51 65.27 - 87.03: 50 87.03 - 108.79: 20 Dihedral angle restraints: 8030 sinusoidal: 3420 harmonic: 4610 Sorted by residual: dihedral pdb=" CB CYS D 289 " pdb=" SG CYS D 289 " pdb=" SG CYS D 394 " pdb=" CB CYS D 394 " ideal model delta sinusoidal sigma weight residual 93.00 164.96 -71.96 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS E 289 " pdb=" SG CYS E 289 " pdb=" SG CYS E 394 " pdb=" CB CYS E 394 " ideal model delta sinusoidal sigma weight residual 93.00 164.50 -71.50 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS B 289 " pdb=" SG CYS B 289 " pdb=" SG CYS B 394 " pdb=" CB CYS B 394 " ideal model delta sinusoidal sigma weight residual 93.00 164.04 -71.04 1 1.00e+01 1.00e-02 6.48e+01 ... (remaining 8027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1844 0.055 - 0.111: 332 0.111 - 0.166: 41 0.166 - 0.222: 7 0.222 - 0.277: 6 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2227 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 264 " 0.018 2.00e-02 2.50e+03 1.81e-02 6.58e+00 pdb=" CG TYR E 264 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR E 264 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR E 264 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR E 264 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR E 264 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 264 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 264 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 86 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C LEU D 86 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU D 86 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 87 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 112 " -0.014 2.00e-02 2.50e+03 1.33e-02 4.39e+00 pdb=" CG TRP D 112 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP D 112 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP D 112 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 112 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 112 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 112 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 112 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 112 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 112 " -0.001 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1206 2.75 - 3.29: 12642 3.29 - 3.82: 21465 3.82 - 4.36: 24205 4.36 - 4.90: 42822 Nonbonded interactions: 102340 Sorted by model distance: nonbonded pdb=" O PRO D 165 " pdb=" ND2 ASN D 228 " model vdw 2.209 3.120 nonbonded pdb=" NH2 ARG B 131 " pdb=" OG1 THR B 152 " model vdw 2.214 3.120 nonbonded pdb=" NH2 ARG D 78 " pdb=" OE2 GLU D 154 " model vdw 2.225 3.120 nonbonded pdb=" OE2 GLU B 242 " pdb=" OH TYR B 296 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASP A 167 " pdb=" ND2 ASN A 228 " model vdw 2.234 3.120 ... (remaining 102335 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } 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: 2.430 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.310 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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 0.046 13020 Z= 0.183 Angle : 0.709 9.595 17870 Z= 0.347 Chirality : 0.046 0.277 2230 Planarity : 0.004 0.033 2150 Dihedral : 15.980 108.786 4980 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1535 helix: 2.85 (0.22), residues: 470 sheet: 0.81 (0.25), residues: 470 loop : -0.44 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 257 TYR 0.044 0.002 TYR E 264 PHE 0.032 0.002 PHE A 370 TRP 0.036 0.001 TRP D 112 HIS 0.010 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00359 (12985) covalent geometry : angle 0.70462 (17775) SS BOND : bond 0.00274 ( 10) SS BOND : angle 1.03931 ( 20) hydrogen bonds : bond 0.15050 ( 672) hydrogen bonds : angle 6.89248 ( 2211) link_BETA1-4 : bond 0.00377 ( 15) link_BETA1-4 : angle 1.38444 ( 45) link_NAG-ASN : bond 0.00232 ( 10) link_NAG-ASN : angle 1.31179 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: C 93 ASP cc_start: 0.7705 (t70) cc_final: 0.7374 (t70) REVERT: C 242 GLU cc_start: 0.8452 (mp0) cc_final: 0.8212 (mp0) REVERT: C 285 SER cc_start: 0.7897 (t) cc_final: 0.7217 (p) REVERT: B 88 ARG cc_start: 0.7470 (ptt180) cc_final: 0.6460 (ttm-80) REVERT: B 383 PHE cc_start: 0.7936 (m-80) cc_final: 0.7650 (t80) REVERT: D 232 LYS cc_start: 0.8393 (ptpt) cc_final: 0.7954 (ptpt) REVERT: D 250 CYS cc_start: 0.7562 (m) cc_final: 0.7360 (m) REVERT: D 380 CYS cc_start: 0.8718 (t) cc_final: 0.8467 (t) REVERT: E 246 LEU cc_start: 0.8374 (tt) cc_final: 0.7984 (tt) REVERT: E 367 ASP cc_start: 0.8207 (t70) cc_final: 0.7891 (t70) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.0979 time to fit residues: 59.9316 Evaluate side-chains 326 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 GLN C 281 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN B 136 GLN D 163 HIS D 322 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.149842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124448 restraints weight = 19392.527| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.30 r_work: 0.3534 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13020 Z= 0.171 Angle : 0.699 10.745 17870 Z= 0.334 Chirality : 0.043 0.162 2230 Planarity : 0.004 0.034 2150 Dihedral : 9.431 65.454 2180 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.52 % Allowed : 10.61 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.22), residues: 1535 helix: 2.79 (0.21), residues: 480 sheet: 0.72 (0.25), residues: 470 loop : -0.54 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 257 TYR 0.018 0.002 TYR E 272 PHE 0.031 0.002 PHE B 305 TRP 0.021 0.001 TRP D 112 HIS 0.008 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00383 (12985) covalent geometry : angle 0.69085 (17775) SS BOND : bond 0.00308 ( 10) SS BOND : angle 0.84393 ( 20) hydrogen bonds : bond 0.04700 ( 672) hydrogen bonds : angle 4.91592 ( 2211) link_BETA1-4 : bond 0.00402 ( 15) link_BETA1-4 : angle 1.88459 ( 45) link_NAG-ASN : bond 0.00240 ( 10) link_NAG-ASN : angle 1.50277 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 357 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 ASP cc_start: 0.7763 (t70) cc_final: 0.7397 (t70) REVERT: C 136 GLN cc_start: 0.6754 (mm-40) cc_final: 0.6134 (mt0) REVERT: C 272 TYR cc_start: 0.8619 (t80) cc_final: 0.8316 (t80) REVERT: C 285 SER cc_start: 0.8295 (t) cc_final: 0.7992 (p) REVERT: C 362 TRP cc_start: 0.7889 (t60) cc_final: 0.7621 (t60) REVERT: A 276 HIS cc_start: 0.8256 (t70) cc_final: 0.7935 (t-170) REVERT: A 300 LEU cc_start: 0.9266 (mp) cc_final: 0.9015 (mp) REVERT: A 391 TRP cc_start: 0.6336 (m-90) cc_final: 0.6025 (p-90) REVERT: B 86 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8551 (tp) REVERT: B 88 ARG cc_start: 0.7674 (ptt180) cc_final: 0.6532 (ttm-80) REVERT: B 176 TYR cc_start: 0.8033 (m-80) cc_final: 0.7822 (m-80) REVERT: B 364 GLU cc_start: 0.8518 (mp0) cc_final: 0.8110 (pt0) REVERT: B 383 PHE cc_start: 0.8257 (m-80) cc_final: 0.7753 (t80) REVERT: D 310 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 380 CYS cc_start: 0.9029 (t) cc_final: 0.8784 (t) REVERT: E 113 GLU cc_start: 0.8846 (mp0) cc_final: 0.8641 (mp0) REVERT: E 227 LYS cc_start: 0.7977 (mttm) cc_final: 0.7326 (mmtt) REVERT: E 305 PHE cc_start: 0.9121 (m-80) cc_final: 0.8888 (m-80) REVERT: E 367 ASP cc_start: 0.8262 (t70) cc_final: 0.8043 (t70) outliers start: 21 outliers final: 11 residues processed: 365 average time/residue: 0.0888 time to fit residues: 50.1685 Evaluate side-chains 325 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 313 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 150 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN B 51 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120680 restraints weight = 19791.497| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.31 r_work: 0.3487 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13020 Z= 0.197 Angle : 0.695 9.808 17870 Z= 0.334 Chirality : 0.044 0.184 2230 Planarity : 0.004 0.036 2150 Dihedral : 5.869 32.853 2180 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.96 % Allowed : 13.86 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.22), residues: 1535 helix: 2.76 (0.22), residues: 480 sheet: 0.40 (0.25), residues: 475 loop : -0.76 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 131 TYR 0.020 0.002 TYR E 272 PHE 0.037 0.002 PHE B 305 TRP 0.022 0.001 TRP D 112 HIS 0.007 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00447 (12985) covalent geometry : angle 0.68713 (17775) SS BOND : bond 0.00642 ( 10) SS BOND : angle 0.81242 ( 20) hydrogen bonds : bond 0.04601 ( 672) hydrogen bonds : angle 4.64247 ( 2211) link_BETA1-4 : bond 0.00406 ( 15) link_BETA1-4 : angle 1.83967 ( 45) link_NAG-ASN : bond 0.00224 ( 10) link_NAG-ASN : angle 1.58760 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 360 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: C 93 ASP cc_start: 0.7949 (t70) cc_final: 0.7579 (t70) REVERT: C 136 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6254 (mt0) REVERT: C 238 LEU cc_start: 0.8848 (mt) cc_final: 0.8444 (mt) REVERT: C 272 TYR cc_start: 0.8705 (t80) cc_final: 0.8474 (t80) REVERT: C 285 SER cc_start: 0.8453 (t) cc_final: 0.8171 (p) REVERT: C 362 TRP cc_start: 0.8064 (t60) cc_final: 0.7773 (t60) REVERT: A 276 HIS cc_start: 0.8376 (t70) cc_final: 0.8096 (t-170) REVERT: A 391 TRP cc_start: 0.6484 (m-90) cc_final: 0.5947 (p-90) REVERT: B 51 GLN cc_start: 0.7980 (mm110) cc_final: 0.7495 (mp10) REVERT: B 88 ARG cc_start: 0.7789 (ptt180) cc_final: 0.6520 (ttm-80) REVERT: B 176 TYR cc_start: 0.8016 (m-80) cc_final: 0.7694 (m-80) REVERT: B 188 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6678 (tm-30) REVERT: B 295 TYR cc_start: 0.8369 (m-80) cc_final: 0.7893 (m-10) REVERT: B 302 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8508 (mm) REVERT: B 383 PHE cc_start: 0.8318 (m-80) cc_final: 0.7871 (t80) REVERT: D 158 ASN cc_start: 0.7977 (t0) cc_final: 0.7458 (p0) REVERT: D 310 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7896 (tm-30) REVERT: D 380 CYS cc_start: 0.9024 (t) cc_final: 0.8759 (t) REVERT: E 124 GLU cc_start: 0.7354 (tp30) cc_final: 0.7016 (mm-30) REVERT: E 140 ASP cc_start: 0.8057 (m-30) cc_final: 0.7591 (m-30) outliers start: 41 outliers final: 27 residues processed: 378 average time/residue: 0.0861 time to fit residues: 50.1771 Evaluate side-chains 351 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 380 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 13 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN B 136 GLN D 141 GLN D 322 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.121227 restraints weight = 19898.557| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.11 r_work: 0.3497 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13020 Z= 0.142 Angle : 0.662 10.064 17870 Z= 0.315 Chirality : 0.043 0.283 2230 Planarity : 0.004 0.032 2150 Dihedral : 4.913 24.042 2180 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.89 % Allowed : 16.68 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.22), residues: 1535 helix: 2.88 (0.22), residues: 475 sheet: 0.54 (0.25), residues: 465 loop : -0.88 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 257 TYR 0.025 0.002 TYR E 264 PHE 0.036 0.002 PHE B 305 TRP 0.017 0.001 TRP D 112 HIS 0.005 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00316 (12985) covalent geometry : angle 0.65455 (17775) SS BOND : bond 0.00541 ( 10) SS BOND : angle 1.04339 ( 20) hydrogen bonds : bond 0.04380 ( 672) hydrogen bonds : angle 4.51389 ( 2211) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.65991 ( 45) link_NAG-ASN : bond 0.00225 ( 10) link_NAG-ASN : angle 1.48844 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 ASP cc_start: 0.7901 (t70) cc_final: 0.7546 (t70) REVERT: C 136 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6050 (mt0) REVERT: C 232 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7462 (ttmm) REVERT: C 272 TYR cc_start: 0.8656 (t80) cc_final: 0.8429 (t80) REVERT: C 362 TRP cc_start: 0.8134 (t60) cc_final: 0.7833 (t60) REVERT: A 112 TRP cc_start: 0.8554 (p-90) cc_final: 0.8204 (p-90) REVERT: A 183 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7115 (tmm) REVERT: A 276 HIS cc_start: 0.8390 (t70) cc_final: 0.8146 (t-170) REVERT: A 300 LEU cc_start: 0.9226 (mp) cc_final: 0.8953 (mp) REVERT: A 391 TRP cc_start: 0.6428 (m-90) cc_final: 0.6128 (p-90) REVERT: B 86 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8480 (tp) REVERT: B 88 ARG cc_start: 0.7673 (ptt180) cc_final: 0.6576 (ttm-80) REVERT: B 302 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8461 (mm) REVERT: B 383 PHE cc_start: 0.8221 (m-80) cc_final: 0.7832 (t80) REVERT: D 116 TRP cc_start: 0.8251 (t60) cc_final: 0.7336 (t60) REVERT: D 158 ASN cc_start: 0.7789 (t0) cc_final: 0.7449 (p0) REVERT: D 299 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8783 (mp) REVERT: D 380 CYS cc_start: 0.9016 (t) cc_final: 0.8780 (t) REVERT: E 140 ASP cc_start: 0.8070 (m-30) cc_final: 0.7744 (m-30) REVERT: E 260 GLU cc_start: 0.8290 (pm20) cc_final: 0.7828 (pm20) outliers start: 40 outliers final: 21 residues processed: 355 average time/residue: 0.0839 time to fit residues: 46.5281 Evaluate side-chains 337 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 312 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 383 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 380 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 4.9990 chunk 117 optimal weight: 0.0040 chunk 107 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN D 141 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 HIS E 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117572 restraints weight = 19790.444| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.27 r_work: 0.3444 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13020 Z= 0.246 Angle : 0.740 11.300 17870 Z= 0.358 Chirality : 0.046 0.420 2230 Planarity : 0.004 0.037 2150 Dihedral : 4.823 20.941 2180 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.62 % Allowed : 16.68 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.22), residues: 1535 helix: 2.54 (0.22), residues: 480 sheet: 0.15 (0.24), residues: 470 loop : -0.93 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 257 TYR 0.029 0.002 TYR E 264 PHE 0.033 0.003 PHE B 305 TRP 0.026 0.002 TRP D 112 HIS 0.004 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00563 (12985) covalent geometry : angle 0.73364 (17775) SS BOND : bond 0.00923 ( 10) SS BOND : angle 1.06559 ( 20) hydrogen bonds : bond 0.04769 ( 672) hydrogen bonds : angle 4.69037 ( 2211) link_BETA1-4 : bond 0.00394 ( 15) link_BETA1-4 : angle 1.56099 ( 45) link_NAG-ASN : bond 0.00293 ( 10) link_NAG-ASN : angle 1.74488 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 340 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 ASP cc_start: 0.8173 (t70) cc_final: 0.7818 (t70) REVERT: C 136 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6214 (mt0) REVERT: C 162 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8008 (tt) REVERT: C 194 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: C 362 TRP cc_start: 0.8141 (t60) cc_final: 0.7838 (t60) REVERT: C 369 ILE cc_start: 0.9295 (mt) cc_final: 0.8936 (tt) REVERT: A 112 TRP cc_start: 0.8602 (p-90) cc_final: 0.8248 (p-90) REVERT: A 300 LEU cc_start: 0.9310 (mp) cc_final: 0.8995 (mp) REVERT: A 391 TRP cc_start: 0.6595 (m-90) cc_final: 0.6047 (p-90) REVERT: B 262 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7655 (mm) REVERT: B 302 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8419 (mm) REVERT: B 383 PHE cc_start: 0.8338 (m-80) cc_final: 0.7891 (t80) REVERT: D 158 ASN cc_start: 0.7932 (t0) cc_final: 0.7363 (p0) REVERT: D 299 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8750 (mp) REVERT: D 380 CYS cc_start: 0.9140 (t) cc_final: 0.8914 (t) REVERT: E 140 ASP cc_start: 0.7965 (m-30) cc_final: 0.7624 (m-30) REVERT: E 227 LYS cc_start: 0.8333 (mttt) cc_final: 0.7810 (mptt) REVERT: E 260 GLU cc_start: 0.8408 (pm20) cc_final: 0.7906 (pm20) outliers start: 64 outliers final: 37 residues processed: 373 average time/residue: 0.0912 time to fit residues: 52.8552 Evaluate side-chains 357 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 383 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 380 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 94 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN D 141 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.146981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.121767 restraints weight = 19696.678| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.30 r_work: 0.3500 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13020 Z= 0.134 Angle : 0.689 14.507 17870 Z= 0.323 Chirality : 0.043 0.278 2230 Planarity : 0.004 0.040 2150 Dihedral : 4.567 22.261 2180 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.39 % Allowed : 19.42 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.22), residues: 1535 helix: 2.64 (0.22), residues: 475 sheet: 0.51 (0.25), residues: 445 loop : -0.91 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 257 TYR 0.035 0.002 TYR E 264 PHE 0.031 0.002 PHE A 370 TRP 0.021 0.001 TRP D 116 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00293 (12985) covalent geometry : angle 0.68288 (17775) SS BOND : bond 0.00469 ( 10) SS BOND : angle 1.15306 ( 20) hydrogen bonds : bond 0.04463 ( 672) hydrogen bonds : angle 4.47301 ( 2211) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 1.41671 ( 45) link_NAG-ASN : bond 0.00154 ( 10) link_NAG-ASN : angle 1.50516 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 352 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 ASP cc_start: 0.8108 (t70) cc_final: 0.7739 (t70) REVERT: C 136 GLN cc_start: 0.7154 (mm-40) cc_final: 0.6218 (mt0) REVERT: C 141 GLN cc_start: 0.8505 (tt0) cc_final: 0.8263 (tt0) REVERT: C 232 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7457 (ttmm) REVERT: C 238 LEU cc_start: 0.8953 (mt) cc_final: 0.8752 (mm) REVERT: C 272 TYR cc_start: 0.8661 (t80) cc_final: 0.8322 (t80) REVERT: C 362 TRP cc_start: 0.8154 (t60) cc_final: 0.7834 (t60) REVERT: C 369 ILE cc_start: 0.9298 (mt) cc_final: 0.8921 (tt) REVERT: A 112 TRP cc_start: 0.8535 (p-90) cc_final: 0.8138 (p-90) REVERT: A 183 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7229 (tmm) REVERT: A 300 LEU cc_start: 0.9269 (mp) cc_final: 0.8979 (mp) REVERT: A 391 TRP cc_start: 0.6505 (m-90) cc_final: 0.5964 (p-90) REVERT: B 86 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8627 (tp) REVERT: B 88 ARG cc_start: 0.7652 (ptt180) cc_final: 0.6391 (ttm-80) REVERT: B 188 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6762 (tm-30) REVERT: B 302 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8371 (mm) REVERT: B 383 PHE cc_start: 0.8275 (m-80) cc_final: 0.7813 (t80) REVERT: D 116 TRP cc_start: 0.8296 (t60) cc_final: 0.7375 (t60) REVERT: D 158 ASN cc_start: 0.7865 (t0) cc_final: 0.7448 (p0) REVERT: D 299 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8760 (mp) REVERT: D 310 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7662 (tm-30) REVERT: D 380 CYS cc_start: 0.9102 (t) cc_final: 0.8868 (t) REVERT: E 140 ASP cc_start: 0.7957 (m-30) cc_final: 0.7598 (m-30) outliers start: 47 outliers final: 29 residues processed: 379 average time/residue: 0.0915 time to fit residues: 53.9054 Evaluate side-chains 364 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 331 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 383 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 145 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN D 215 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.142354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119040 restraints weight = 20274.717| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.02 r_work: 0.3488 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13020 Z= 0.190 Angle : 0.722 14.742 17870 Z= 0.344 Chirality : 0.044 0.456 2230 Planarity : 0.004 0.042 2150 Dihedral : 4.602 17.000 2180 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.32 % Allowed : 20.51 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1535 helix: 2.53 (0.22), residues: 475 sheet: 0.45 (0.25), residues: 445 loop : -0.97 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 257 TYR 0.020 0.002 TYR B 374 PHE 0.032 0.002 PHE A 370 TRP 0.022 0.001 TRP D 112 HIS 0.003 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00439 (12985) covalent geometry : angle 0.71666 (17775) SS BOND : bond 0.00442 ( 10) SS BOND : angle 1.18458 ( 20) hydrogen bonds : bond 0.04581 ( 672) hydrogen bonds : angle 4.49900 ( 2211) link_BETA1-4 : bond 0.00422 ( 15) link_BETA1-4 : angle 1.42064 ( 45) link_NAG-ASN : bond 0.00206 ( 10) link_NAG-ASN : angle 1.59887 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 337 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 ASP cc_start: 0.8188 (t70) cc_final: 0.7894 (t70) REVERT: C 136 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6186 (mt0) REVERT: C 141 GLN cc_start: 0.8510 (tt0) cc_final: 0.8282 (tt0) REVERT: C 194 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7223 (pt0) REVERT: C 232 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7605 (ttmm) REVERT: C 272 TYR cc_start: 0.8735 (t80) cc_final: 0.8445 (t80) REVERT: C 362 TRP cc_start: 0.8206 (t60) cc_final: 0.7888 (t60) REVERT: C 369 ILE cc_start: 0.9349 (mt) cc_final: 0.8959 (tt) REVERT: A 391 TRP cc_start: 0.6599 (m-90) cc_final: 0.6117 (p-90) REVERT: B 88 ARG cc_start: 0.7612 (ptt180) cc_final: 0.6537 (ttm-80) REVERT: B 188 GLN cc_start: 0.7331 (tm-30) cc_final: 0.6878 (tm-30) REVERT: B 262 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7555 (mm) REVERT: B 302 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8277 (mm) REVERT: B 383 PHE cc_start: 0.8241 (m-80) cc_final: 0.7935 (t80) REVERT: D 158 ASN cc_start: 0.7717 (t0) cc_final: 0.7484 (p0) REVERT: D 299 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8802 (mp) REVERT: D 310 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7548 (tm-30) REVERT: D 380 CYS cc_start: 0.8894 (t) cc_final: 0.8687 (t) REVERT: E 140 ASP cc_start: 0.8017 (m-30) cc_final: 0.7778 (m-30) outliers start: 46 outliers final: 32 residues processed: 362 average time/residue: 0.0874 time to fit residues: 49.0846 Evaluate side-chains 356 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 383 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 113 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 0.0570 chunk 21 optimal weight: 0.0010 chunk 52 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.6906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN D 215 GLN D 221 GLN ** E 51 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 = 0.3936 r_free = 0.3936 target = 0.147048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122304 restraints weight = 19526.740| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.25 r_work: 0.3506 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13020 Z= 0.132 Angle : 0.699 16.064 17870 Z= 0.328 Chirality : 0.043 0.345 2230 Planarity : 0.004 0.044 2150 Dihedral : 4.446 17.170 2180 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.03 % Allowed : 21.08 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.22), residues: 1535 helix: 2.44 (0.22), residues: 480 sheet: 0.51 (0.25), residues: 445 loop : -0.85 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 257 TYR 0.017 0.002 TYR A 176 PHE 0.030 0.002 PHE A 370 TRP 0.020 0.001 TRP D 116 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00292 (12985) covalent geometry : angle 0.69347 (17775) SS BOND : bond 0.00274 ( 10) SS BOND : angle 1.22035 ( 20) hydrogen bonds : bond 0.04400 ( 672) hydrogen bonds : angle 4.39757 ( 2211) link_BETA1-4 : bond 0.00370 ( 15) link_BETA1-4 : angle 1.34970 ( 45) link_NAG-ASN : bond 0.00166 ( 10) link_NAG-ASN : angle 1.47102 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 341 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 ASP cc_start: 0.8178 (t70) cc_final: 0.7833 (t70) REVERT: C 136 GLN cc_start: 0.7107 (mm-40) cc_final: 0.6122 (mt0) REVERT: C 141 GLN cc_start: 0.8547 (tt0) cc_final: 0.8322 (tt0) REVERT: C 194 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7122 (pt0) REVERT: C 232 LYS cc_start: 0.7716 (ttmm) cc_final: 0.7413 (ttmm) REVERT: C 272 TYR cc_start: 0.8655 (t80) cc_final: 0.8363 (t80) REVERT: C 362 TRP cc_start: 0.8160 (t60) cc_final: 0.7863 (t60) REVERT: C 369 ILE cc_start: 0.9301 (mt) cc_final: 0.8927 (tt) REVERT: A 310 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8480 (tm-30) REVERT: A 391 TRP cc_start: 0.6460 (m-90) cc_final: 0.6029 (p-90) REVERT: B 86 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8613 (tp) REVERT: B 88 ARG cc_start: 0.7635 (ptt180) cc_final: 0.6410 (ttm-80) REVERT: B 188 GLN cc_start: 0.7345 (tm-30) cc_final: 0.6809 (tm-30) REVERT: B 302 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8197 (mm) REVERT: B 383 PHE cc_start: 0.8300 (m-80) cc_final: 0.7851 (t80) REVERT: D 158 ASN cc_start: 0.7813 (t0) cc_final: 0.7495 (p0) REVERT: D 299 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8806 (mp) REVERT: D 310 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7709 (tm-30) REVERT: D 380 CYS cc_start: 0.9092 (t) cc_final: 0.8868 (t) REVERT: E 113 GLU cc_start: 0.8856 (mp0) cc_final: 0.8647 (mp0) REVERT: E 140 ASP cc_start: 0.7941 (m-30) cc_final: 0.7678 (m-30) outliers start: 42 outliers final: 32 residues processed: 364 average time/residue: 0.0914 time to fit residues: 51.5740 Evaluate side-chains 357 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 321 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 383 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.138803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114030 restraints weight = 20162.387| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.23 r_work: 0.3394 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 13020 Z= 0.355 Angle : 0.858 12.817 17870 Z= 0.421 Chirality : 0.050 0.495 2230 Planarity : 0.006 0.060 2150 Dihedral : 5.202 20.314 2180 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.97 % Allowed : 20.58 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1535 helix: 2.12 (0.22), residues: 480 sheet: -0.16 (0.24), residues: 470 loop : -1.14 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 257 TYR 0.024 0.003 TYR E 205 PHE 0.037 0.004 PHE A 370 TRP 0.032 0.002 TRP D 112 HIS 0.005 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00816 (12985) covalent geometry : angle 0.85168 (17775) SS BOND : bond 0.00821 ( 10) SS BOND : angle 1.59627 ( 20) hydrogen bonds : bond 0.05176 ( 672) hydrogen bonds : angle 4.82652 ( 2211) link_BETA1-4 : bond 0.00467 ( 15) link_BETA1-4 : angle 1.53368 ( 45) link_NAG-ASN : bond 0.00410 ( 10) link_NAG-ASN : angle 2.00047 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 321 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 ASP cc_start: 0.8379 (t70) cc_final: 0.8002 (t70) REVERT: C 136 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6585 (mm110) REVERT: C 141 GLN cc_start: 0.8584 (tt0) cc_final: 0.8311 (tt0) REVERT: C 362 TRP cc_start: 0.8135 (t60) cc_final: 0.7881 (t60) REVERT: C 369 ILE cc_start: 0.9305 (mt) cc_final: 0.8952 (tt) REVERT: A 206 ASP cc_start: 0.7601 (m-30) cc_final: 0.6951 (t0) REVERT: A 391 TRP cc_start: 0.6615 (m-90) cc_final: 0.6088 (p-90) REVERT: B 302 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8320 (mm) REVERT: D 108 ILE cc_start: 0.6917 (tt) cc_final: 0.6570 (tt) REVERT: D 158 ASN cc_start: 0.7849 (t0) cc_final: 0.7263 (p0) REVERT: D 264 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.8105 (t80) REVERT: D 275 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8910 (tt) REVERT: D 299 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8759 (mp) REVERT: D 380 CYS cc_start: 0.9084 (t) cc_final: 0.8857 (t) REVERT: E 260 GLU cc_start: 0.8447 (pm20) cc_final: 0.7917 (pm20) outliers start: 55 outliers final: 37 residues processed: 355 average time/residue: 0.0885 time to fit residues: 48.9502 Evaluate side-chains 351 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 383 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 380 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 3.9990 chunk 137 optimal weight: 0.0570 chunk 143 optimal weight: 0.0970 chunk 112 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 151 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.144785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.121723 restraints weight = 20253.911| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.02 r_work: 0.3530 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13020 Z= 0.135 Angle : 0.766 18.794 17870 Z= 0.357 Chirality : 0.044 0.352 2230 Planarity : 0.004 0.041 2150 Dihedral : 4.698 23.190 2180 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.17 % Allowed : 22.96 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1535 helix: 2.21 (0.22), residues: 480 sheet: 0.28 (0.24), residues: 455 loop : -0.94 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 257 TYR 0.018 0.002 TYR E 202 PHE 0.033 0.002 PHE B 305 TRP 0.030 0.002 TRP D 116 HIS 0.005 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00300 (12985) covalent geometry : angle 0.75783 (17775) SS BOND : bond 0.00477 ( 10) SS BOND : angle 2.57226 ( 20) hydrogen bonds : bond 0.04556 ( 672) hydrogen bonds : angle 4.47322 ( 2211) link_BETA1-4 : bond 0.00370 ( 15) link_BETA1-4 : angle 1.33805 ( 45) link_NAG-ASN : bond 0.00185 ( 10) link_NAG-ASN : angle 1.51305 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 340 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 ASP cc_start: 0.8188 (t70) cc_final: 0.7889 (t70) REVERT: C 114 SER cc_start: 0.8990 (m) cc_final: 0.8686 (t) REVERT: C 136 GLN cc_start: 0.6838 (mm-40) cc_final: 0.6285 (mm110) REVERT: C 141 GLN cc_start: 0.8506 (tt0) cc_final: 0.8279 (tt0) REVERT: C 184 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7865 (mp0) REVERT: C 232 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7646 (ttmm) REVERT: C 272 TYR cc_start: 0.8644 (t80) cc_final: 0.8273 (t80) REVERT: C 362 TRP cc_start: 0.8150 (t60) cc_final: 0.7878 (t60) REVERT: C 369 ILE cc_start: 0.9332 (mt) cc_final: 0.8934 (tt) REVERT: A 300 LEU cc_start: 0.9151 (mp) cc_final: 0.8892 (mp) REVERT: A 310 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8511 (tm-30) REVERT: A 391 TRP cc_start: 0.6546 (m-90) cc_final: 0.6177 (p-90) REVERT: B 86 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8599 (tp) REVERT: B 88 ARG cc_start: 0.7602 (ptt180) cc_final: 0.6553 (ttm-80) REVERT: B 188 GLN cc_start: 0.7290 (tm-30) cc_final: 0.6886 (tm-30) REVERT: B 302 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8247 (mm) REVERT: D 275 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8930 (tt) REVERT: D 299 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8815 (mp) REVERT: D 380 CYS cc_start: 0.8816 (t) cc_final: 0.8611 (t) REVERT: E 227 LYS cc_start: 0.8601 (mttt) cc_final: 0.8319 (mtmm) REVERT: E 260 GLU cc_start: 0.8283 (pm20) cc_final: 0.7774 (pm20) outliers start: 30 outliers final: 23 residues processed: 357 average time/residue: 0.0838 time to fit residues: 47.0964 Evaluate side-chains 348 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 321 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 383 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 145 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 117 optimal weight: 0.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.142881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119871 restraints weight = 20232.463| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.01 r_work: 0.3498 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13020 Z= 0.165 Angle : 0.757 16.636 17870 Z= 0.356 Chirality : 0.044 0.338 2230 Planarity : 0.004 0.044 2150 Dihedral : 4.620 23.201 2180 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.09 % Allowed : 23.54 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1535 helix: 2.21 (0.22), residues: 480 sheet: 0.26 (0.24), residues: 455 loop : -0.97 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 257 TYR 0.038 0.002 TYR E 264 PHE 0.031 0.002 PHE B 305 TRP 0.038 0.002 TRP D 116 HIS 0.005 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00381 (12985) covalent geometry : angle 0.74980 (17775) SS BOND : bond 0.00533 ( 10) SS BOND : angle 2.11558 ( 20) hydrogen bonds : bond 0.04592 ( 672) hydrogen bonds : angle 4.46723 ( 2211) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.34746 ( 45) link_NAG-ASN : bond 0.00139 ( 10) link_NAG-ASN : angle 1.56440 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2762.27 seconds wall clock time: 48 minutes 12.05 seconds (2892.05 seconds total)