Starting phenix.real_space_refine on Wed Mar 4 17:54:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zd2_74049/03_2026/9zd2_74049.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zd2_74049/03_2026/9zd2_74049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zd2_74049/03_2026/9zd2_74049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zd2_74049/03_2026/9zd2_74049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zd2_74049/03_2026/9zd2_74049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zd2_74049/03_2026/9zd2_74049.map" } resolution = 3.1 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= 0.002 sd= 0.005 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 50 5.16 5 C 9604 2.51 5 N 2504 2.21 5 O 2641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14799 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 1821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1833 Chain: "B" Number of atoms: 1821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1833 Chain: "C" Number of atoms: 1821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1833 Chain: "A" Number of atoms: 1821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1833 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'CLR': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 234 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG D 234 " occ=0.47 residue: pdb=" N AARG B 234 " occ=0.75 ... (20 atoms not shown) pdb=" NH2BARG B 234 " occ=0.25 residue: pdb=" N AARG C 234 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG C 234 " occ=0.57 residue: pdb=" N AARG A 234 " occ=0.20 ... (20 atoms not shown) pdb=" NH2BARG A 234 " occ=0.80 Time building chain proxies: 4.33, per 1000 atoms: 0.29 Number of scatterers: 14799 At special positions: 0 Unit cell: (106.624, 137.445, 122.451, 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 50 16.00 O 2641 8.00 N 2504 7.00 C 9604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 688.2 milliseconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 16 sheets defined 65.1% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'D' and resid 3 through 6 removed outlier: 3.577A pdb=" N LYS D 6 " --> pdb=" O SER D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3 through 6' Processing helix chain 'D' and resid 7 through 34 removed outlier: 3.725A pdb=" N TRP D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 48 through 72 removed outlier: 5.747A pdb=" N HIS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 86 Processing helix chain 'D' and resid 90 through 116 Processing helix chain 'D' and resid 134 through 157 Processing helix chain 'D' and resid 167 through 188 removed outlier: 5.410A pdb=" N ASP D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 203 removed outlier: 3.505A pdb=" N SER D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.628A pdb=" N LYS D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TRP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 6 Processing helix chain 'B' and resid 7 through 33 removed outlier: 3.582A pdb=" N TRP B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 37 Processing helix chain 'B' and resid 48 through 72 removed outlier: 5.689A pdb=" N HIS B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 90 through 116 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 167 through 188 removed outlier: 5.346A pdb=" N ASP B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 removed outlier: 3.521A pdb=" N SER B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 237 through 248 removed outlier: 4.388A pdb=" N VAL B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.590A pdb=" N TRP C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'C' and resid 48 through 72 removed outlier: 5.998A pdb=" N HIS C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 90 through 116 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 167 through 188 removed outlier: 5.345A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.601A pdb=" N SER C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 230 removed outlier: 4.226A pdb=" N PHE C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP C 213 " --> pdb=" O HIS C 209 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.872A pdb=" N VAL C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 6 Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.732A pdb=" N TRP A 11 " --> pdb=" O LYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 Processing helix chain 'A' and resid 48 through 72 removed outlier: 5.538A pdb=" N HIS A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 90 through 116 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 167 through 188 removed outlier: 5.779A pdb=" N ASP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 210 through 230 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.744A pdb=" N LYS A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 12 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 28 through 45 Processing helix chain 'F' and resid 45 through 53 removed outlier: 5.398A pdb=" N TRP F 51 " --> pdb=" O PRO F 47 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 135 Processing helix chain 'F' and resid 138 through 157 removed outlier: 3.612A pdb=" N THR F 157 " --> pdb=" O ASN F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 166 through 183 Processing helix chain 'G' and resid 6 through 12 Processing helix chain 'G' and resid 14 through 19 removed outlier: 3.652A pdb=" N UNK G 18 " --> pdb=" O UNK G 14 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N UNK G 19 " --> pdb=" O UNK G 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 14 through 19' Processing helix chain 'G' and resid 28 through 45 Processing helix chain 'G' and resid 45 through 50 Processing helix chain 'G' and resid 128 through 135 Processing helix chain 'G' and resid 138 through 156 Processing helix chain 'G' and resid 159 through 166 Processing helix chain 'G' and resid 166 through 183 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.619A pdb=" N UNK E 13 " --> pdb=" O UNK E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 45 Processing helix chain 'E' and resid 45 through 53 removed outlier: 5.126A pdb=" N TRP E 51 " --> pdb=" O PRO E 47 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 138 through 157 removed outlier: 3.543A pdb=" N THR E 157 " --> pdb=" O ASN E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 166 Processing helix chain 'E' and resid 166 through 183 Processing helix chain 'I' and resid 6 through 11 Processing helix chain 'I' and resid 12 through 15 Processing helix chain 'I' and resid 28 through 45 Processing helix chain 'I' and resid 45 through 53 removed outlier: 5.189A pdb=" N TRP I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET I 52 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 135 Processing helix chain 'I' and resid 138 through 157 removed outlier: 3.513A pdb=" N THR I 157 " --> pdb=" O ASN I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 166 Processing helix chain 'I' and resid 166 through 183 Processing helix chain 'H' and resid 6 through 11 Processing helix chain 'H' and resid 12 through 19 Processing helix chain 'H' and resid 28 through 45 Processing helix chain 'H' and resid 45 through 53 removed outlier: 5.531A pdb=" N TRP H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET H 52 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 135 Processing helix chain 'H' and resid 138 through 157 removed outlier: 3.608A pdb=" N THR H 157 " --> pdb=" O ASN H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 166 Processing helix chain 'H' and resid 166 through 183 Processing sheet with id=AA1, first strand: chain 'F' and resid 54 through 57 Processing sheet with id=AA2, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AA3, first strand: chain 'F' and resid 99 through 102 Processing sheet with id=AA4, first strand: chain 'F' and resid 99 through 102 removed outlier: 7.587A pdb=" N THR F 115 " --> pdb=" O LYS F 198 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LYS F 198 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER F 117 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASP F 196 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP F 119 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE F 194 " --> pdb=" O ASP F 119 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL F 121 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL F 192 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR F 123 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 54 through 57 Processing sheet with id=AA6, first strand: chain 'G' and resid 61 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 99 through 109 removed outlier: 5.320A pdb=" N SER G 100 " --> pdb=" O TYR G 124 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR G 124 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASP G 102 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL G 122 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLY G 120 " --> pdb=" O PRO G 104 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP G 196 " --> pdb=" O ASP G 119 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL G 121 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE G 194 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR G 123 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL G 192 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ARG G 125 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU G 190 " --> pdb=" O ARG G 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'E' and resid 61 through 66 Processing sheet with id=AB1, first strand: chain 'E' and resid 99 through 109 removed outlier: 5.216A pdb=" N SER E 100 " --> pdb=" O TYR E 124 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR E 124 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP E 102 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 122 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY E 120 " --> pdb=" O PRO E 104 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR E 115 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS E 198 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER E 117 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP E 196 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP E 119 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE E 194 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 121 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL E 192 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR E 123 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 54 through 57 Processing sheet with id=AB3, first strand: chain 'I' and resid 61 through 66 Processing sheet with id=AB4, first strand: chain 'I' and resid 99 through 109 removed outlier: 3.807A pdb=" N GLY I 120 " --> pdb=" O ILE I 103 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL I 118 " --> pdb=" O PRO I 105 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU I 107 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE I 116 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR I 115 " --> pdb=" O LYS I 198 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS I 198 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER I 117 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP I 196 " --> pdb=" O SER I 117 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP I 119 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE I 194 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL I 121 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL I 192 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR I 123 " --> pdb=" O GLU I 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 54 through 57 Processing sheet with id=AB6, first strand: chain 'H' and resid 61 through 66 Processing sheet with id=AB7, first strand: chain 'H' and resid 99 through 109 removed outlier: 3.804A pdb=" N GLY H 120 " --> pdb=" O ILE H 103 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL H 118 " --> pdb=" O PRO H 105 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU H 107 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE H 116 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR H 115 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LYS H 198 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER H 117 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP H 196 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP H 119 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE H 194 " --> pdb=" O ASP H 119 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL H 121 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL H 192 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR H 123 " --> pdb=" O GLU H 190 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2688 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: 2.19 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4743 1.34 - 1.46: 3248 1.46 - 1.58: 7011 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 15071 Sorted by residual: bond pdb=" C1 PLM D 301 " pdb=" C2 PLM D 301 " ideal model delta sigma weight residual 1.542 1.498 0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" C1 PLM B 302 " pdb=" C2 PLM B 302 " ideal model delta sigma weight residual 1.542 1.499 0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 PLM C 303 " pdb=" C2 PLM C 303 " ideal model delta sigma weight residual 1.542 1.500 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C1 PLM A 302 " pdb=" C2 PLM A 302 " ideal model delta sigma weight residual 1.542 1.501 0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" N CYS A 87 " pdb=" CA CYS A 87 " ideal model delta sigma weight residual 1.462 1.439 0.023 1.31e-02 5.83e+03 2.98e+00 ... (remaining 15066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 19894 1.87 - 3.73: 510 3.73 - 5.60: 81 5.60 - 7.46: 21 7.46 - 9.33: 4 Bond angle restraints: 20510 Sorted by residual: angle pdb=" CA GLU E 169 " pdb=" CB GLU E 169 " pdb=" CG GLU E 169 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 angle pdb=" N GLN A 88 " pdb=" CA GLN A 88 " pdb=" C GLN A 88 " ideal model delta sigma weight residual 114.56 109.65 4.91 1.27e+00 6.20e-01 1.50e+01 angle pdb=" N GLN B 88 " pdb=" CA GLN B 88 " pdb=" C GLN B 88 " ideal model delta sigma weight residual 114.31 109.87 4.44 1.29e+00 6.01e-01 1.19e+01 angle pdb=" C THR E 45 " pdb=" N PHE E 46 " pdb=" CA PHE E 46 " ideal model delta sigma weight residual 120.09 124.34 -4.25 1.25e+00 6.40e-01 1.16e+01 angle pdb=" C THR H 45 " pdb=" N PHE H 46 " pdb=" CA PHE H 46 " ideal model delta sigma weight residual 120.26 124.80 -4.54 1.34e+00 5.57e-01 1.15e+01 ... (remaining 20505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8048 17.93 - 35.85: 802 35.85 - 53.78: 167 53.78 - 71.71: 22 71.71 - 89.64: 26 Dihedral angle restraints: 9065 sinusoidal: 3484 harmonic: 5581 Sorted by residual: dihedral pdb=" CA LEU A 182 " pdb=" C LEU A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual 180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU D 182 " pdb=" C LEU D 182 " pdb=" N ALA D 183 " pdb=" CA ALA D 183 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA LEU B 182 " pdb=" C LEU B 182 " pdb=" N ALA B 183 " pdb=" CA ALA B 183 " ideal model delta harmonic sigma weight residual -180.00 -160.30 -19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 9062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1596 0.038 - 0.075: 663 0.075 - 0.113: 203 0.113 - 0.150: 42 0.150 - 0.188: 4 Chirality restraints: 2508 Sorted by residual: chirality pdb=" CA CYS D 189 " pdb=" N CYS D 189 " pdb=" C CYS D 189 " pdb=" CB CYS D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CG LEU C 58 " pdb=" CB LEU C 58 " pdb=" CD1 LEU C 58 " pdb=" CD2 LEU C 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA PHE F 46 " pdb=" N PHE F 46 " pdb=" C PHE F 46 " pdb=" CB PHE F 46 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 2505 not shown) Planarity restraints: 2542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 189 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C CYS B 189 " -0.039 2.00e-02 2.50e+03 pdb=" O CYS B 189 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 190 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 180 " 0.015 2.00e-02 2.50e+03 1.63e-02 3.99e+00 pdb=" CG HIS A 180 " -0.035 2.00e-02 2.50e+03 pdb=" ND1 HIS A 180 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS A 180 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS A 180 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 180 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 197 " -0.013 2.00e-02 2.50e+03 1.43e-02 3.56e+00 pdb=" CG PHE C 197 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 197 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 197 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 197 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 197 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 197 " -0.000 2.00e-02 2.50e+03 ... (remaining 2539 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 6694 2.93 - 3.42: 16275 3.42 - 3.91: 25471 3.91 - 4.41: 28535 4.41 - 4.90: 47107 Nonbonded interactions: 124082 Sorted by model distance: nonbonded pdb=" O SER G 176 " pdb=" OD1 ASP G 179 " model vdw 2.432 3.040 nonbonded pdb=" O ASP F 102 " pdb=" OD1 ASP F 102 " model vdw 2.468 3.040 nonbonded pdb=" O SER G 176 " pdb=" OD2 ASP G 180 " model vdw 2.474 3.040 nonbonded pdb=" N GLU E 169 " pdb=" OE1 GLU E 169 " model vdw 2.489 3.120 nonbonded pdb=" O GLN G 175 " pdb=" OD1 ASP G 179 " model vdw 2.496 3.040 ... (remaining 124077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'B' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'C' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'D' and (resid 3 through 233 or resid 235 through 249)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.710 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.005 0.044 15075 Z= 0.226 Angle : 0.735 9.329 20510 Z= 0.398 Chirality : 0.045 0.188 2508 Planarity : 0.004 0.047 2542 Dihedral : 15.431 89.635 5467 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 2.05 % Allowed : 22.40 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.26 (0.19), residues: 1862 helix: 1.70 (0.16), residues: 1009 sheet: 1.22 (0.33), residues: 195 loop : -0.62 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 159 TYR 0.012 0.001 TYR D 37 PHE 0.033 0.002 PHE C 197 TRP 0.015 0.001 TRP A 11 HIS 0.018 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00467 (15071) covalent geometry : angle 0.73488 (20510) hydrogen bonds : bond 0.11306 ( 919) hydrogen bonds : angle 6.49112 ( 2688) Misc. bond : bond 0.03471 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 PHE cc_start: 0.8757 (m-80) cc_final: 0.8439 (m-80) REVERT: E 51 TRP cc_start: 0.7613 (m100) cc_final: 0.7376 (m100) REVERT: I 32 TRP cc_start: 0.6987 (m100) cc_final: 0.6366 (m100) REVERT: H 52 MET cc_start: 0.8525 (tpp) cc_final: 0.8158 (tpp) REVERT: H 107 GLU cc_start: 0.6249 (pm20) cc_final: 0.5920 (pm20) outliers start: 31 outliers final: 28 residues processed: 234 average time/residue: 0.1156 time to fit residues: 40.7103 Evaluate side-chains 231 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 133 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 40.0000 chunk 149 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN D 127 ASN D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 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 = 0.4022 r_free = 0.4022 target = 0.126139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090184 restraints weight = 120709.372| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 8.70 r_work: 0.3118 rms_B_bonded: 6.90 restraints_weight: 2.0000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15075 Z= 0.213 Angle : 0.619 6.761 20510 Z= 0.318 Chirality : 0.045 0.198 2508 Planarity : 0.004 0.051 2542 Dihedral : 7.411 59.500 2432 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.89 % Favored : 95.89 % Rotamer: Outliers : 3.11 % Allowed : 18.95 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.37 (0.20), residues: 1862 helix: 1.79 (0.16), residues: 1031 sheet: 0.96 (0.37), residues: 175 loop : -0.49 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 159 TYR 0.009 0.001 TYR A 227 PHE 0.025 0.002 PHE C 197 TRP 0.016 0.001 TRP A 11 HIS 0.017 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00475 (15071) covalent geometry : angle 0.61887 (20510) hydrogen bonds : bond 0.04314 ( 919) hydrogen bonds : angle 5.14664 ( 2688) Misc. bond : bond 0.00090 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8736 (mttp) REVERT: C 48 ASP cc_start: 0.8821 (t0) cc_final: 0.8559 (t0) REVERT: F 169 GLU cc_start: 0.8091 (tp30) cc_final: 0.7861 (tp30) REVERT: G 83 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: I 32 TRP cc_start: 0.6990 (m100) cc_final: 0.6250 (m100) REVERT: H 107 GLU cc_start: 0.6187 (pm20) cc_final: 0.5772 (pm20) outliers start: 47 outliers final: 29 residues processed: 253 average time/residue: 0.1131 time to fit residues: 42.5193 Evaluate side-chains 232 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 153 ASN Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 168 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 162 optimal weight: 0.3980 chunk 134 optimal weight: 30.0000 chunk 181 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN G 175 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** 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 = 0.4077 r_free = 0.4077 target = 0.130255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095301 restraints weight = 116140.249| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 8.61 r_work: 0.3196 rms_B_bonded: 6.98 restraints_weight: 2.0000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15075 Z= 0.115 Angle : 0.546 7.323 20510 Z= 0.282 Chirality : 0.042 0.193 2508 Planarity : 0.004 0.052 2542 Dihedral : 6.347 58.570 2405 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.73 % Favored : 96.05 % Rotamer: Outliers : 2.39 % Allowed : 19.62 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.47 (0.20), residues: 1862 helix: 1.87 (0.16), residues: 1039 sheet: 1.12 (0.37), residues: 165 loop : -0.50 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 126 TYR 0.010 0.001 TYR D 37 PHE 0.024 0.001 PHE G 41 TRP 0.013 0.001 TRP B 245 HIS 0.014 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00239 (15071) covalent geometry : angle 0.54562 (20510) hydrogen bonds : bond 0.03639 ( 919) hydrogen bonds : angle 4.89613 ( 2688) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: D 11 TRP cc_start: 0.9221 (m100) cc_final: 0.8977 (m100) REVERT: D 48 ASP cc_start: 0.8700 (t0) cc_final: 0.8447 (t0) REVERT: B 4 GLU cc_start: 0.8223 (mp0) cc_final: 0.7943 (mp0) REVERT: B 7 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8570 (mttp) REVERT: A 96 MET cc_start: 0.8746 (mmm) cc_final: 0.8421 (mmm) REVERT: A 178 LEU cc_start: 0.8908 (tp) cc_final: 0.8643 (tp) REVERT: F 33 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8898 (pt) REVERT: F 61 GLU cc_start: 0.7509 (pm20) cc_final: 0.7220 (pm20) REVERT: G 38 SER cc_start: 0.8384 (t) cc_final: 0.8116 (p) REVERT: G 83 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: H 107 GLU cc_start: 0.6043 (pm20) cc_final: 0.4653 (tt0) REVERT: H 193 GLU cc_start: 0.8848 (mp0) cc_final: 0.8526 (mp0) outliers start: 36 outliers final: 16 residues processed: 279 average time/residue: 0.1182 time to fit residues: 49.5730 Evaluate side-chains 227 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 118 optimal weight: 7.9990 chunk 100 optimal weight: 0.0040 chunk 166 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** 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 = 0.4019 r_free = 0.4019 target = 0.125951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.088865 restraints weight = 61934.360| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 4.63 r_work: 0.3221 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15075 Z= 0.235 Angle : 0.635 8.042 20510 Z= 0.325 Chirality : 0.045 0.185 2508 Planarity : 0.004 0.064 2542 Dihedral : 6.764 59.341 2397 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 2.98 % Allowed : 20.21 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.38 (0.20), residues: 1862 helix: 1.77 (0.16), residues: 1047 sheet: 0.86 (0.37), residues: 175 loop : -0.46 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 144 TYR 0.010 0.001 TYR E 60 PHE 0.030 0.002 PHE D 5 TRP 0.034 0.002 TRP B 11 HIS 0.016 0.002 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00528 (15071) covalent geometry : angle 0.63539 (20510) hydrogen bonds : bond 0.04261 ( 919) hydrogen bonds : angle 4.89895 ( 2688) Misc. bond : bond 0.00094 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 ASP cc_start: 0.8501 (t0) cc_final: 0.8246 (t70) REVERT: B 7 LYS cc_start: 0.8996 (mtmt) cc_final: 0.8712 (mttp) REVERT: C 197 PHE cc_start: 0.9476 (OUTLIER) cc_final: 0.9220 (t80) REVERT: A 96 MET cc_start: 0.8745 (mmm) cc_final: 0.8399 (mmm) REVERT: F 140 ASP cc_start: 0.9124 (p0) cc_final: 0.8819 (p0) REVERT: G 83 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: E 32 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.7210 (m-10) REVERT: I 32 TRP cc_start: 0.6863 (m100) cc_final: 0.6048 (m100) REVERT: H 107 GLU cc_start: 0.6167 (pm20) cc_final: 0.5765 (pm20) REVERT: H 193 GLU cc_start: 0.8644 (mp0) cc_final: 0.8159 (mp0) outliers start: 45 outliers final: 32 residues processed: 238 average time/residue: 0.1117 time to fit residues: 40.5550 Evaluate side-chains 230 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 153 ASN Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 119 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 173 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** 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 = 0.4019 r_free = 0.4019 target = 0.126366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091247 restraints weight = 130301.676| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 9.03 r_work: 0.3090 rms_B_bonded: 6.98 restraints_weight: 2.0000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15075 Z= 0.211 Angle : 0.615 9.213 20510 Z= 0.314 Chirality : 0.044 0.193 2508 Planarity : 0.004 0.063 2542 Dihedral : 6.695 57.348 2397 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.95 % Favored : 95.84 % Rotamer: Outliers : 3.51 % Allowed : 19.68 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.28 (0.20), residues: 1862 helix: 1.75 (0.16), residues: 1039 sheet: 0.79 (0.37), residues: 175 loop : -0.58 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 144 TYR 0.033 0.002 TYR A 97 PHE 0.021 0.002 PHE G 41 TRP 0.021 0.001 TRP H 51 HIS 0.015 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00473 (15071) covalent geometry : angle 0.61503 (20510) hydrogen bonds : bond 0.04093 ( 919) hydrogen bonds : angle 4.89260 ( 2688) Misc. bond : bond 0.00047 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: D 48 ASP cc_start: 0.8616 (t0) cc_final: 0.8326 (t70) REVERT: B 7 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8729 (mttp) REVERT: C 197 PHE cc_start: 0.9475 (OUTLIER) cc_final: 0.9255 (t80) REVERT: A 96 MET cc_start: 0.8923 (mmm) cc_final: 0.8606 (mmm) REVERT: G 83 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8334 (m-80) REVERT: E 32 TRP cc_start: 0.7497 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: I 32 TRP cc_start: 0.7159 (m100) cc_final: 0.6199 (m100) REVERT: I 46 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8290 (t80) REVERT: I 188 LYS cc_start: 0.9265 (tppt) cc_final: 0.8984 (tppt) REVERT: H 107 GLU cc_start: 0.6135 (pm20) cc_final: 0.5649 (pm20) REVERT: H 193 GLU cc_start: 0.8853 (mp0) cc_final: 0.8341 (mp0) outliers start: 53 outliers final: 35 residues processed: 250 average time/residue: 0.1097 time to fit residues: 42.3133 Evaluate side-chains 240 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 153 ASN Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 125 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** 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 = 0.4013 r_free = 0.4013 target = 0.125592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.090145 restraints weight = 107253.281| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 8.17 r_work: 0.3103 rms_B_bonded: 6.57 restraints_weight: 2.0000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15075 Z= 0.232 Angle : 0.640 9.594 20510 Z= 0.326 Chirality : 0.044 0.185 2508 Planarity : 0.004 0.062 2542 Dihedral : 6.757 57.355 2395 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.65 % Favored : 95.14 % Rotamer: Outliers : 3.45 % Allowed : 20.21 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.16 (0.20), residues: 1862 helix: 1.70 (0.16), residues: 1039 sheet: 0.63 (0.36), residues: 175 loop : -0.69 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 191 TYR 0.015 0.002 TYR A 97 PHE 0.019 0.002 PHE G 41 TRP 0.015 0.001 TRP H 51 HIS 0.016 0.002 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00522 (15071) covalent geometry : angle 0.63963 (20510) hydrogen bonds : bond 0.04246 ( 919) hydrogen bonds : angle 4.88725 ( 2688) Misc. bond : bond 0.00046 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: D 48 ASP cc_start: 0.8589 (t0) cc_final: 0.8263 (t70) REVERT: B 7 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8691 (mttp) REVERT: C 197 PHE cc_start: 0.9492 (OUTLIER) cc_final: 0.9210 (t80) REVERT: A 96 MET cc_start: 0.8947 (mmm) cc_final: 0.8709 (mmm) REVERT: F 59 GLU cc_start: 0.3649 (mp0) cc_final: 0.2994 (pm20) REVERT: F 140 ASP cc_start: 0.9166 (p0) cc_final: 0.8847 (p0) REVERT: G 51 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.7878 (p90) REVERT: G 83 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: E 32 TRP cc_start: 0.7469 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: I 32 TRP cc_start: 0.7358 (m100) cc_final: 0.6288 (m100) REVERT: I 46 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8362 (t80) REVERT: I 169 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8441 (tm-30) REVERT: H 107 GLU cc_start: 0.6250 (pm20) cc_final: 0.5748 (pm20) REVERT: H 193 GLU cc_start: 0.8883 (mp0) cc_final: 0.8374 (mp0) outliers start: 52 outliers final: 38 residues processed: 243 average time/residue: 0.1098 time to fit residues: 41.3092 Evaluate side-chains 241 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 13 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** 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 = 0.4059 r_free = 0.4059 target = 0.129211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094143 restraints weight = 126137.445| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 8.88 r_work: 0.3171 rms_B_bonded: 7.10 restraints_weight: 2.0000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15075 Z= 0.123 Angle : 0.576 10.418 20510 Z= 0.295 Chirality : 0.042 0.183 2508 Planarity : 0.004 0.062 2542 Dihedral : 6.258 58.852 2395 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.89 % Favored : 95.89 % Rotamer: Outliers : 2.19 % Allowed : 21.67 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1862 helix: 2.02 (0.16), residues: 1009 sheet: -0.09 (0.46), residues: 105 loop : -0.54 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 126 TYR 0.008 0.001 TYR D 37 PHE 0.025 0.001 PHE D 5 TRP 0.019 0.001 TRP H 51 HIS 0.013 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00266 (15071) covalent geometry : angle 0.57632 (20510) hydrogen bonds : bond 0.03675 ( 919) hydrogen bonds : angle 4.78134 ( 2688) Misc. bond : bond 0.00014 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: D 7 LYS cc_start: 0.8273 (mmmt) cc_final: 0.7616 (mttt) REVERT: D 48 ASP cc_start: 0.8573 (t0) cc_final: 0.8187 (t70) REVERT: B 7 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8741 (mttp) REVERT: C 197 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.9211 (t80) REVERT: A 96 MET cc_start: 0.8976 (mmm) cc_final: 0.8714 (mmm) REVERT: F 59 GLU cc_start: 0.3613 (mp0) cc_final: 0.3051 (pm20) REVERT: G 51 TRP cc_start: 0.7965 (OUTLIER) cc_final: 0.7691 (p90) REVERT: G 83 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: I 32 TRP cc_start: 0.7336 (m100) cc_final: 0.6283 (m100) REVERT: I 46 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8511 (t80) REVERT: I 169 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8491 (tm-30) REVERT: H 107 GLU cc_start: 0.6181 (pm20) cc_final: 0.5689 (pm20) REVERT: H 193 GLU cc_start: 0.8864 (mp0) cc_final: 0.8372 (mp0) outliers start: 33 outliers final: 18 residues processed: 252 average time/residue: 0.1121 time to fit residues: 43.4086 Evaluate side-chains 228 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain H residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 111 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** 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 = 0.4021 r_free = 0.4021 target = 0.126161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091308 restraints weight = 106985.963| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 8.02 r_work: 0.3129 rms_B_bonded: 6.66 restraints_weight: 2.0000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15075 Z= 0.212 Angle : 0.637 11.610 20510 Z= 0.324 Chirality : 0.044 0.186 2508 Planarity : 0.004 0.061 2542 Dihedral : 6.519 56.925 2394 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.49 % Favored : 95.30 % Rotamer: Outliers : 2.65 % Allowed : 21.54 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1862 helix: 1.97 (0.16), residues: 1009 sheet: -0.12 (0.47), residues: 105 loop : -0.59 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 191 TYR 0.020 0.001 TYR A 97 PHE 0.030 0.002 PHE E 46 TRP 0.016 0.001 TRP B 245 HIS 0.016 0.002 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00479 (15071) covalent geometry : angle 0.63747 (20510) hydrogen bonds : bond 0.04077 ( 919) hydrogen bonds : angle 4.82758 ( 2688) Misc. bond : bond 0.00048 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 ASP cc_start: 0.8596 (t0) cc_final: 0.8199 (t70) REVERT: B 7 LYS cc_start: 0.9117 (mtmt) cc_final: 0.8785 (mttp) REVERT: B 92 PHE cc_start: 0.7683 (t80) cc_final: 0.7473 (t80) REVERT: C 197 PHE cc_start: 0.9481 (OUTLIER) cc_final: 0.9216 (t80) REVERT: A 96 MET cc_start: 0.8984 (mmm) cc_final: 0.8735 (mmm) REVERT: F 59 GLU cc_start: 0.3702 (mp0) cc_final: 0.3069 (pm20) REVERT: G 51 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.7887 (p90) REVERT: G 83 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: G 174 MET cc_start: 0.9102 (mmm) cc_final: 0.8827 (mmp) REVERT: I 32 TRP cc_start: 0.7422 (m100) cc_final: 0.6335 (m100) REVERT: H 32 TRP cc_start: 0.7010 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: H 107 GLU cc_start: 0.6251 (pm20) cc_final: 0.5759 (pm20) REVERT: H 193 GLU cc_start: 0.8892 (mp0) cc_final: 0.8392 (mp0) outliers start: 40 outliers final: 31 residues processed: 232 average time/residue: 0.1067 time to fit residues: 38.0992 Evaluate side-chains 237 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.129590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093762 restraints weight = 95430.757| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 7.21 r_work: 0.3206 rms_B_bonded: 6.16 restraints_weight: 2.0000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15075 Z= 0.121 Angle : 0.606 12.599 20510 Z= 0.308 Chirality : 0.043 0.184 2508 Planarity : 0.004 0.063 2542 Dihedral : 6.034 59.051 2394 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.57 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 22.53 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.34 (0.20), residues: 1862 helix: 2.02 (0.16), residues: 1009 sheet: -0.14 (0.47), residues: 105 loop : -0.52 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 126 TYR 0.036 0.001 TYR A 97 PHE 0.029 0.001 PHE E 46 TRP 0.015 0.001 TRP H 51 HIS 0.013 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00260 (15071) covalent geometry : angle 0.60587 (20510) hydrogen bonds : bond 0.03566 ( 919) hydrogen bonds : angle 4.78028 ( 2688) Misc. bond : bond 0.00017 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7214 (mttt) REVERT: D 48 ASP cc_start: 0.8508 (t0) cc_final: 0.8078 (t70) REVERT: B 7 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8776 (mttp) REVERT: B 92 PHE cc_start: 0.7577 (t80) cc_final: 0.7338 (t80) REVERT: C 197 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.9247 (t80) REVERT: A 178 LEU cc_start: 0.8995 (tp) cc_final: 0.8771 (tp) REVERT: F 33 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8968 (pt) REVERT: F 59 GLU cc_start: 0.3739 (mp0) cc_final: 0.3065 (pm20) REVERT: G 51 TRP cc_start: 0.7871 (OUTLIER) cc_final: 0.7630 (p90) REVERT: G 83 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: E 174 MET cc_start: 0.9312 (mmm) cc_final: 0.9038 (mmp) REVERT: I 32 TRP cc_start: 0.7324 (m100) cc_final: 0.6238 (m100) REVERT: H 107 GLU cc_start: 0.6185 (pm20) cc_final: 0.5730 (pm20) REVERT: H 193 GLU cc_start: 0.8794 (mp0) cc_final: 0.8339 (mp0) outliers start: 28 outliers final: 22 residues processed: 242 average time/residue: 0.0998 time to fit residues: 37.4802 Evaluate side-chains 239 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain H residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 14 optimal weight: 0.0170 chunk 142 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 HIS ** 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 = 0.4050 r_free = 0.4050 target = 0.128494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093949 restraints weight = 113153.677| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 8.55 r_work: 0.3144 rms_B_bonded: 6.97 restraints_weight: 2.0000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15075 Z= 0.139 Angle : 0.609 12.270 20510 Z= 0.311 Chirality : 0.043 0.191 2508 Planarity : 0.004 0.063 2542 Dihedral : 5.925 58.332 2392 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.84 % Rotamer: Outliers : 1.86 % Allowed : 22.73 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.35 (0.20), residues: 1862 helix: 2.04 (0.16), residues: 1009 sheet: -0.15 (0.47), residues: 105 loop : -0.53 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 191 TYR 0.051 0.001 TYR A 97 PHE 0.032 0.002 PHE D 5 TRP 0.018 0.001 TRP D 11 HIS 0.015 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00311 (15071) covalent geometry : angle 0.60942 (20510) hydrogen bonds : bond 0.03668 ( 919) hydrogen bonds : angle 4.74992 ( 2688) Misc. bond : bond 0.00024 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 ASP cc_start: 0.8554 (t0) cc_final: 0.8149 (t70) REVERT: B 7 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8778 (mttp) REVERT: B 92 PHE cc_start: 0.7683 (t80) cc_final: 0.7450 (t80) REVERT: F 33 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8960 (pt) REVERT: F 59 GLU cc_start: 0.3679 (mp0) cc_final: 0.3047 (pm20) REVERT: G 51 TRP cc_start: 0.7943 (OUTLIER) cc_final: 0.7714 (p90) REVERT: G 83 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: E 174 MET cc_start: 0.9289 (mmm) cc_final: 0.8994 (mmp) REVERT: I 32 TRP cc_start: 0.7368 (m100) cc_final: 0.6298 (m100) REVERT: H 107 GLU cc_start: 0.6252 (pm20) cc_final: 0.5777 (pm20) REVERT: H 193 GLU cc_start: 0.8872 (mp0) cc_final: 0.8423 (mp0) outliers start: 28 outliers final: 22 residues processed: 230 average time/residue: 0.1036 time to fit residues: 36.9944 Evaluate side-chains 232 residues out of total 1537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain H residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 156 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 62 optimal weight: 40.0000 chunk 167 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 208 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.128388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.093881 restraints weight = 111415.260| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 8.38 r_work: 0.3144 rms_B_bonded: 6.87 restraints_weight: 2.0000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 15075 Z= 0.189 Angle : 0.845 59.073 20510 Z= 0.479 Chirality : 0.044 0.195 2508 Planarity : 0.004 0.063 2542 Dihedral : 5.945 58.305 2392 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.95 % Favored : 95.89 % Rotamer: Outliers : 1.86 % Allowed : 23.00 % Favored : 75.15 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.78 % 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: 1.34 (0.20), residues: 1862 helix: 2.03 (0.16), residues: 1009 sheet: -0.14 (0.47), residues: 105 loop : -0.54 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 191 TYR 0.032 0.001 TYR A 97 PHE 0.029 0.002 PHE E 46 TRP 0.016 0.001 TRP H 51 HIS 0.014 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00424 (15071) covalent geometry : angle 0.84507 (20510) hydrogen bonds : bond 0.03700 ( 919) hydrogen bonds : angle 4.74947 ( 2688) Misc. bond : bond 0.00034 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5326.69 seconds wall clock time: 91 minutes 26.09 seconds (5486.09 seconds total)