Starting phenix.real_space_refine on Sun Aug 24 00:05:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c9h_16510/08_2025/8c9h_16510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c9h_16510/08_2025/8c9h_16510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c9h_16510/08_2025/8c9h_16510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c9h_16510/08_2025/8c9h_16510.map" model { file = "/net/cci-nas-00/data/ceres_data/8c9h_16510/08_2025/8c9h_16510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c9h_16510/08_2025/8c9h_16510.cif" } resolution = 3.2 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= 0.003 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 10472 2.51 5 N 2568 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15776 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "B" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "C" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "D" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "E" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "G" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "H" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.73, per 1000 atoms: 0.24 Number of scatterers: 15776 At special positions: 0 Unit cell: (87.1792, 87.1792, 119.342, 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 104 16.00 O 2632 8.00 N 2568 7.00 C 10472 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=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 743.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 27 through 30 Processing helix chain 'A' and resid 31 through 61 removed outlier: 3.677A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 61 " --> pdb=" O HIS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 85 removed outlier: 4.147A pdb=" N VAL A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 removed outlier: 4.100A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.524A pdb=" N ILE A 157 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 167 through 191 Processing helix chain 'A' and resid 201 through 217 removed outlier: 3.529A pdb=" N VAL A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.696A pdb=" N SER A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 Proline residue: A 261 - end of helix Processing helix chain 'B' and resid 27 through 30 Processing helix chain 'B' and resid 31 through 61 removed outlier: 3.780A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 61 " --> pdb=" O HIS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 85 removed outlier: 4.207A pdb=" N VAL B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 removed outlier: 4.113A pdb=" N SER B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.525A pdb=" N ILE B 157 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 158 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 158' Processing helix chain 'B' and resid 167 through 191 Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.532A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.697A pdb=" N SER B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 Proline residue: B 261 - end of helix Processing helix chain 'C' and resid 27 through 30 Processing helix chain 'C' and resid 31 through 61 removed outlier: 3.673A pdb=" N GLU C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 61 " --> pdb=" O HIS C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 85 removed outlier: 4.302A pdb=" N VAL C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 4.096A pdb=" N SER C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.506A pdb=" N ILE C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 158' Processing helix chain 'C' and resid 167 through 191 removed outlier: 3.517A pdb=" N THR C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 217 removed outlier: 3.537A pdb=" N VAL C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 241 Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.696A pdb=" N SER C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 276 Proline residue: C 261 - end of helix Processing helix chain 'D' and resid 27 through 30 Processing helix chain 'D' and resid 31 through 61 removed outlier: 3.642A pdb=" N GLU D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 61 " --> pdb=" O HIS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 85 removed outlier: 4.271A pdb=" N VAL D 78 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 removed outlier: 4.104A pdb=" N SER D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.505A pdb=" N ILE D 157 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 158' Processing helix chain 'D' and resid 167 through 189 Processing helix chain 'D' and resid 201 through 217 removed outlier: 3.556A pdb=" N VAL D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 241 Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 244 through 253 removed outlier: 3.698A pdb=" N SER D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 Proline residue: D 261 - end of helix Processing helix chain 'E' and resid 27 through 30 Processing helix chain 'E' and resid 31 through 61 removed outlier: 3.728A pdb=" N GLU E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN E 61 " --> pdb=" O HIS E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 85 removed outlier: 4.240A pdb=" N VAL E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET E 80 " --> pdb=" O PHE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 90 removed outlier: 4.120A pdb=" N SER E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 154 through 158 removed outlier: 3.642A pdb=" N PHE E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 191 Processing helix chain 'E' and resid 201 through 217 removed outlier: 3.537A pdb=" N VAL E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 241 Proline residue: E 232 - end of helix Processing helix chain 'E' and resid 244 through 253 removed outlier: 3.695A pdb=" N SER E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY E 250 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 276 Proline residue: E 261 - end of helix Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 31 through 61 removed outlier: 3.774A pdb=" N GLU F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN F 61 " --> pdb=" O HIS F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 85 removed outlier: 4.219A pdb=" N VAL F 78 " --> pdb=" O PHE F 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET F 80 " --> pdb=" O PHE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 removed outlier: 4.103A pdb=" N SER F 89 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 134 through 143 Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.644A pdb=" N PHE F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 191 Processing helix chain 'F' and resid 201 through 217 removed outlier: 3.533A pdb=" N VAL F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 241 Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 244 through 253 removed outlier: 3.698A pdb=" N SER F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY F 250 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU F 251 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN F 252 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 276 Proline residue: F 261 - end of helix Processing helix chain 'G' and resid 27 through 30 Processing helix chain 'G' and resid 31 through 61 removed outlier: 3.574A pdb=" N ASN G 61 " --> pdb=" O HIS G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 85 removed outlier: 4.211A pdb=" N VAL G 78 " --> pdb=" O PHE G 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET G 80 " --> pdb=" O PHE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 90 removed outlier: 4.113A pdb=" N SER G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.643A pdb=" N PHE G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 191 Processing helix chain 'G' and resid 201 through 217 removed outlier: 3.534A pdb=" N VAL G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 241 Proline residue: G 232 - end of helix Processing helix chain 'G' and resid 244 through 253 removed outlier: 3.697A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY G 250 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU G 251 " --> pdb=" O PHE G 247 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN G 252 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 276 Proline residue: G 261 - end of helix Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 31 through 61 removed outlier: 3.665A pdb=" N GLU H 40 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN H 61 " --> pdb=" O HIS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 85 Processing helix chain 'H' and resid 85 through 90 removed outlier: 4.112A pdb=" N SER H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 111 through 134 Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.646A pdb=" N PHE H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 191 Processing helix chain 'H' and resid 201 through 217 removed outlier: 3.536A pdb=" N VAL H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 241 Proline residue: H 232 - end of helix Processing helix chain 'H' and resid 244 through 253 removed outlier: 3.697A pdb=" N SER H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY H 250 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU H 251 " --> pdb=" O PHE H 247 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN H 252 " --> pdb=" O SER H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 276 Proline residue: H 261 - end of helix 1061 hydrogen bonds defined for protein. 3147 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: 2.71 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2344 1.31 - 1.43: 4896 1.43 - 1.56: 8816 1.56 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 16248 Sorted by residual: bond pdb=" C11 T60 D 401 " pdb=" N13 T60 D 401 " ideal model delta sigma weight residual 1.355 1.452 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C11 T60 H 401 " pdb=" N13 T60 H 401 " ideal model delta sigma weight residual 1.355 1.452 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C11 T60 C 401 " pdb=" N13 T60 C 401 " ideal model delta sigma weight residual 1.355 1.451 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C11 T60 B 401 " pdb=" N13 T60 B 401 " ideal model delta sigma weight residual 1.355 1.451 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C11 T60 A 401 " pdb=" N13 T60 A 401 " ideal model delta sigma weight residual 1.355 1.451 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 16243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 21661 1.59 - 3.18: 291 3.18 - 4.77: 128 4.77 - 6.36: 25 6.36 - 7.95: 15 Bond angle restraints: 22120 Sorted by residual: angle pdb=" C06 T60 D 401 " pdb=" C04 T60 D 401 " pdb=" O03 T60 D 401 " ideal model delta sigma weight residual 112.45 120.40 -7.95 3.00e+00 1.11e-01 7.02e+00 angle pdb=" C06 T60 A 401 " pdb=" C04 T60 A 401 " pdb=" O03 T60 A 401 " ideal model delta sigma weight residual 112.45 120.40 -7.95 3.00e+00 1.11e-01 7.02e+00 angle pdb=" C06 T60 B 401 " pdb=" C04 T60 B 401 " pdb=" O03 T60 B 401 " ideal model delta sigma weight residual 112.45 120.40 -7.95 3.00e+00 1.11e-01 7.02e+00 angle pdb=" C06 T60 E 401 " pdb=" C04 T60 E 401 " pdb=" O03 T60 E 401 " ideal model delta sigma weight residual 112.45 120.39 -7.94 3.00e+00 1.11e-01 7.00e+00 angle pdb=" C06 T60 G 401 " pdb=" C04 T60 G 401 " pdb=" O03 T60 G 401 " ideal model delta sigma weight residual 112.45 120.38 -7.93 3.00e+00 1.11e-01 6.98e+00 ... (remaining 22115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.68: 8150 12.68 - 25.35: 532 25.35 - 38.03: 278 38.03 - 50.70: 77 50.70 - 63.38: 27 Dihedral angle restraints: 9064 sinusoidal: 3416 harmonic: 5648 Sorted by residual: dihedral pdb=" CA PHE D 76 " pdb=" C PHE D 76 " pdb=" N GLY D 77 " pdb=" CA GLY D 77 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG D 35 " pdb=" CD ARG D 35 " pdb=" NE ARG D 35 " pdb=" CZ ARG D 35 " ideal model delta sinusoidal sigma weight residual -90.00 -134.34 44.34 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG H 35 " pdb=" CD ARG H 35 " pdb=" NE ARG H 35 " pdb=" CZ ARG H 35 " ideal model delta sinusoidal sigma weight residual 180.00 -136.28 -43.72 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 9061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1407 0.025 - 0.050: 617 0.050 - 0.076: 317 0.076 - 0.101: 59 0.101 - 0.126: 40 Chirality restraints: 2440 Sorted by residual: chirality pdb=" CA LEU C 231 " pdb=" N LEU C 231 " pdb=" C LEU C 231 " pdb=" CB LEU C 231 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA LEU G 231 " pdb=" N LEU G 231 " pdb=" C LEU G 231 " pdb=" CB LEU G 231 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA LEU D 231 " pdb=" N LEU D 231 " pdb=" C LEU D 231 " pdb=" CB LEU D 231 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 2437 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 231 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO E 232 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 232 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 232 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 231 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO H 232 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO H 232 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 232 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 231 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO G 232 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO G 232 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 232 " -0.019 5.00e-02 4.00e+02 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5062 2.84 - 3.35: 15606 3.35 - 3.87: 26123 3.87 - 4.38: 28584 4.38 - 4.90: 53015 Nonbonded interactions: 128390 Sorted by model distance: nonbonded pdb=" OG1 THR C 79 " pdb=" O ALA C 203 " model vdw 2.324 3.040 nonbonded pdb=" O PHE F 275 " pdb=" NH1 ARG G 35 " model vdw 2.380 3.120 nonbonded pdb=" OG1 THR A 79 " pdb=" O ALA A 203 " model vdw 2.437 3.040 nonbonded pdb=" OG1 THR G 79 " pdb=" O ALA G 203 " model vdw 2.445 3.040 nonbonded pdb=" OG1 THR F 79 " pdb=" O ALA F 203 " model vdw 2.447 3.040 ... (remaining 128385 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 15.420 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 0.097 16248 Z= 0.256 Angle : 0.592 7.951 22120 Z= 0.279 Chirality : 0.036 0.126 2440 Planarity : 0.004 0.035 2752 Dihedral : 12.205 63.377 5512 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.44 % Allowed : 6.41 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.20), residues: 2008 helix: 2.48 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -0.14 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 106 TYR 0.018 0.001 TYR G 223 PHE 0.009 0.001 PHE E 37 TRP 0.009 0.001 TRP D 177 HIS 0.002 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00512 (16248) covalent geometry : angle 0.59216 (22120) hydrogen bonds : bond 0.12901 ( 1061) hydrogen bonds : angle 4.74082 ( 3147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 0.546 Fit side-chains REVERT: D 74 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7882 (t80) REVERT: G 74 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7849 (t80) outliers start: 7 outliers final: 4 residues processed: 191 average time/residue: 0.1374 time to fit residues: 37.6478 Evaluate side-chains 187 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain G residue 74 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 94 ASN E 94 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.155221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132182 restraints weight = 17931.425| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.63 r_work: 0.3459 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16248 Z= 0.120 Angle : 0.492 5.656 22120 Z= 0.265 Chirality : 0.037 0.123 2440 Planarity : 0.004 0.034 2752 Dihedral : 5.708 52.745 2252 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.07 % Allowed : 5.40 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.20), residues: 2008 helix: 2.57 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.13 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 106 TYR 0.018 0.001 TYR B 223 PHE 0.007 0.001 PHE F 37 TRP 0.009 0.001 TRP G 253 HIS 0.002 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00248 (16248) covalent geometry : angle 0.49191 (22120) hydrogen bonds : bond 0.05037 ( 1061) hydrogen bonds : angle 3.83839 ( 3147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.591 Fit side-chains REVERT: A 74 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7960 (t80) REVERT: B 74 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7789 (t80) REVERT: C 74 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7883 (t80) REVERT: D 74 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7943 (t80) REVERT: E 74 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.7907 (t80) REVERT: F 74 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7903 (t80) REVERT: G 74 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7907 (t80) outliers start: 33 outliers final: 25 residues processed: 196 average time/residue: 0.1343 time to fit residues: 38.9110 Evaluate side-chains 210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 30 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS G 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.154762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128366 restraints weight = 18868.379| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.82 r_work: 0.3338 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16248 Z= 0.162 Angle : 0.528 5.692 22120 Z= 0.289 Chirality : 0.039 0.133 2440 Planarity : 0.004 0.035 2752 Dihedral : 6.139 54.034 2248 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.89 % Allowed : 5.03 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.19), residues: 2008 helix: 2.70 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.39 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 106 TYR 0.023 0.002 TYR E 223 PHE 0.012 0.001 PHE B 172 TRP 0.008 0.001 TRP E 169 HIS 0.002 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00381 (16248) covalent geometry : angle 0.52751 (22120) hydrogen bonds : bond 0.06202 ( 1061) hydrogen bonds : angle 3.91034 ( 3147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.406 Fit side-chains REVERT: A 74 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8060 (t80) REVERT: B 74 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7868 (t80) REVERT: B 244 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7481 (ttpp) REVERT: C 74 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7947 (t80) REVERT: C 244 LYS cc_start: 0.8247 (ptmt) cc_final: 0.7477 (ttpp) REVERT: D 74 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8080 (t80) REVERT: D 244 LYS cc_start: 0.8236 (ptmt) cc_final: 0.7453 (ttpp) REVERT: E 74 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.7950 (t80) REVERT: E 244 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7439 (ttpp) REVERT: F 74 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7983 (t80) REVERT: F 244 LYS cc_start: 0.8238 (ptmt) cc_final: 0.7458 (ttpp) REVERT: G 74 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8137 (t80) REVERT: G 244 LYS cc_start: 0.8237 (ptmt) cc_final: 0.7457 (ttpp) outliers start: 46 outliers final: 32 residues processed: 214 average time/residue: 0.1494 time to fit residues: 46.4415 Evaluate side-chains 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 178 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126019 restraints weight = 18994.953| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.87 r_work: 0.3333 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16248 Z= 0.150 Angle : 0.520 5.676 22120 Z= 0.283 Chirality : 0.039 0.128 2440 Planarity : 0.004 0.035 2752 Dihedral : 6.164 55.572 2248 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.39 % Allowed : 6.72 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.19), residues: 2008 helix: 2.69 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.39 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 106 TYR 0.021 0.002 TYR F 223 PHE 0.010 0.001 PHE B 172 TRP 0.007 0.001 TRP B 169 HIS 0.003 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00346 (16248) covalent geometry : angle 0.51953 (22120) hydrogen bonds : bond 0.05861 ( 1061) hydrogen bonds : angle 3.87917 ( 3147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.503 Fit side-chains REVERT: A 74 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7989 (t80) REVERT: A 244 LYS cc_start: 0.8304 (ptmt) cc_final: 0.7494 (ttpp) REVERT: B 74 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7796 (t80) REVERT: B 244 LYS cc_start: 0.8288 (ptmt) cc_final: 0.7521 (ttpp) REVERT: C 74 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7889 (t80) REVERT: C 244 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7477 (ttpp) REVERT: D 74 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8144 (t80) REVERT: D 244 LYS cc_start: 0.8247 (ptmt) cc_final: 0.7470 (ttpp) REVERT: E 74 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7897 (t80) REVERT: E 244 LYS cc_start: 0.8187 (ptpt) cc_final: 0.7395 (ttpp) REVERT: F 74 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8021 (t80) REVERT: F 244 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7468 (ttpp) REVERT: G 74 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8160 (t80) REVERT: G 244 LYS cc_start: 0.8258 (ptmt) cc_final: 0.7479 (ttpp) REVERT: H 244 LYS cc_start: 0.8242 (ptmt) cc_final: 0.7465 (ttpp) outliers start: 38 outliers final: 28 residues processed: 210 average time/residue: 0.1355 time to fit residues: 41.1103 Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 181 optimal weight: 0.0070 chunk 137 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.130049 restraints weight = 18588.140| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.84 r_work: 0.3417 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16248 Z= 0.106 Angle : 0.475 5.628 22120 Z= 0.255 Chirality : 0.037 0.119 2440 Planarity : 0.004 0.035 2752 Dihedral : 5.934 57.438 2248 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.88 % Allowed : 8.04 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.00 (0.19), residues: 2008 helix: 2.94 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.32 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 106 TYR 0.015 0.001 TYR B 223 PHE 0.006 0.001 PHE E 37 TRP 0.007 0.001 TRP B 169 HIS 0.002 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00212 (16248) covalent geometry : angle 0.47503 (22120) hydrogen bonds : bond 0.04362 ( 1061) hydrogen bonds : angle 3.69111 ( 3147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.596 Fit side-chains REVERT: A 74 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7885 (t80) REVERT: C 74 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7794 (t80) REVERT: C 244 LYS cc_start: 0.8169 (ptmt) cc_final: 0.7404 (ttpp) REVERT: D 74 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8024 (t80) REVERT: E 74 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7781 (t80) REVERT: F 74 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7892 (t80) REVERT: F 244 LYS cc_start: 0.8144 (ptmt) cc_final: 0.7374 (ttpp) REVERT: G 74 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8022 (t80) REVERT: G 244 LYS cc_start: 0.8143 (ptmt) cc_final: 0.7369 (ttpp) outliers start: 30 outliers final: 20 residues processed: 209 average time/residue: 0.1325 time to fit residues: 40.1653 Evaluate side-chains 210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 116 optimal weight: 0.0170 chunk 154 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127604 restraints weight = 18554.892| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.84 r_work: 0.3385 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16248 Z= 0.120 Angle : 0.491 5.662 22120 Z= 0.264 Chirality : 0.037 0.125 2440 Planarity : 0.005 0.045 2752 Dihedral : 5.981 57.920 2248 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.51 % Allowed : 7.91 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.19), residues: 2008 helix: 2.95 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.28 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 106 TYR 0.019 0.001 TYR E 223 PHE 0.008 0.001 PHE E 172 TRP 0.007 0.001 TRP H 169 HIS 0.002 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00261 (16248) covalent geometry : angle 0.49061 (22120) hydrogen bonds : bond 0.04891 ( 1061) hydrogen bonds : angle 3.70558 ( 3147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.470 Fit side-chains REVERT: A 74 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7879 (t80) REVERT: A 244 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7392 (ttpp) REVERT: B 74 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7795 (t80) REVERT: B 244 LYS cc_start: 0.8190 (ptmt) cc_final: 0.7410 (ttpp) REVERT: C 74 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.7864 (t80) REVERT: C 244 LYS cc_start: 0.8149 (ptmt) cc_final: 0.7359 (ttpp) REVERT: D 74 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8092 (t80) REVERT: D 244 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7365 (ttpp) REVERT: E 74 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7867 (t80) REVERT: E 244 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7302 (ttpp) REVERT: F 74 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7893 (t80) REVERT: F 244 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7338 (ttpp) REVERT: G 74 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8087 (t80) REVERT: G 244 LYS cc_start: 0.8161 (ptmt) cc_final: 0.7359 (ttpp) REVERT: H 244 LYS cc_start: 0.8154 (ptmt) cc_final: 0.7361 (ttpp) outliers start: 40 outliers final: 24 residues processed: 217 average time/residue: 0.1397 time to fit residues: 44.0800 Evaluate side-chains 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 151 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126419 restraints weight = 18775.460| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.87 r_work: 0.3336 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16248 Z= 0.143 Angle : 0.516 5.680 22120 Z= 0.279 Chirality : 0.039 0.128 2440 Planarity : 0.005 0.047 2752 Dihedral : 6.124 57.778 2248 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.45 % Allowed : 8.17 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.19), residues: 2008 helix: 2.87 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.27 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 106 TYR 0.021 0.002 TYR D 223 PHE 0.010 0.001 PHE E 172 TRP 0.007 0.001 TRP D 169 HIS 0.002 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00331 (16248) covalent geometry : angle 0.51570 (22120) hydrogen bonds : bond 0.05610 ( 1061) hydrogen bonds : angle 3.78417 ( 3147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.652 Fit side-chains REVERT: A 74 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.7964 (t80) REVERT: A 244 LYS cc_start: 0.8277 (ptmt) cc_final: 0.7518 (ttpp) REVERT: B 74 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7814 (t80) REVERT: B 244 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7534 (ttpp) REVERT: C 74 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7951 (t80) REVERT: C 244 LYS cc_start: 0.8237 (ptmt) cc_final: 0.7526 (ttpp) REVERT: D 74 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8170 (t80) REVERT: D 244 LYS cc_start: 0.8226 (ptmt) cc_final: 0.7508 (ttpp) REVERT: E 74 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7949 (t80) REVERT: E 244 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7457 (ttpp) REVERT: F 74 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.7973 (t80) REVERT: F 244 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7498 (ttpp) REVERT: G 74 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8158 (t80) REVERT: G 244 LYS cc_start: 0.8233 (ptmt) cc_final: 0.7518 (ttpp) REVERT: H 244 LYS cc_start: 0.8223 (ptmt) cc_final: 0.7508 (ttpp) outliers start: 39 outliers final: 26 residues processed: 209 average time/residue: 0.1233 time to fit residues: 37.4120 Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 12 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122270 restraints weight = 19008.763| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.88 r_work: 0.3274 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16248 Z= 0.187 Angle : 0.563 5.832 22120 Z= 0.307 Chirality : 0.041 0.139 2440 Planarity : 0.005 0.050 2752 Dihedral : 6.367 58.515 2248 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.45 % Allowed : 8.42 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.19), residues: 2008 helix: 2.71 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.40 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 106 TYR 0.025 0.002 TYR H 223 PHE 0.012 0.002 PHE E 172 TRP 0.006 0.001 TRP C 169 HIS 0.003 0.001 HIS F 165 Details of bonding type rmsd covalent geometry : bond 0.00452 (16248) covalent geometry : angle 0.56347 (22120) hydrogen bonds : bond 0.06722 ( 1061) hydrogen bonds : angle 3.94888 ( 3147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.545 Fit side-chains REVERT: A 74 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8112 (t80) REVERT: A 244 LYS cc_start: 0.8351 (ptmt) cc_final: 0.7594 (ttpp) REVERT: B 74 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.7960 (t80) REVERT: B 244 LYS cc_start: 0.8291 (ptmt) cc_final: 0.7603 (ttpp) REVERT: C 74 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8070 (t80) REVERT: C 244 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7611 (ttpp) REVERT: D 74 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8239 (t80) REVERT: D 244 LYS cc_start: 0.8274 (ptmt) cc_final: 0.7580 (ttpp) REVERT: E 74 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8040 (t80) REVERT: E 244 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7502 (ttpp) REVERT: F 74 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8098 (t80) REVERT: F 244 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7573 (ttpp) REVERT: G 74 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8232 (t80) REVERT: G 244 LYS cc_start: 0.8291 (ptmt) cc_final: 0.7604 (ttpp) REVERT: H 47 MET cc_start: 0.8776 (tmm) cc_final: 0.8312 (ttt) REVERT: H 244 LYS cc_start: 0.8272 (ptmt) cc_final: 0.7586 (ttpp) outliers start: 39 outliers final: 25 residues processed: 209 average time/residue: 0.1281 time to fit residues: 38.6649 Evaluate side-chains 214 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 0.3980 chunk 125 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127638 restraints weight = 18832.378| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.88 r_work: 0.3359 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16248 Z= 0.120 Angle : 0.505 5.611 22120 Z= 0.272 Chirality : 0.037 0.123 2440 Planarity : 0.005 0.054 2752 Dihedral : 6.183 57.942 2248 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.07 % Allowed : 8.67 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.19), residues: 2008 helix: 2.89 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.32 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 106 TYR 0.016 0.001 TYR A 223 PHE 0.008 0.001 PHE F 172 TRP 0.008 0.001 TRP D 169 HIS 0.002 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00251 (16248) covalent geometry : angle 0.50499 (22120) hydrogen bonds : bond 0.05080 ( 1061) hydrogen bonds : angle 3.77039 ( 3147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.373 Fit side-chains REVERT: A 74 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 244 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7558 (ttpp) REVERT: B 74 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7786 (t80) REVERT: B 244 LYS cc_start: 0.8255 (ptmt) cc_final: 0.7566 (ttpp) REVERT: C 74 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7903 (t80) REVERT: C 244 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7556 (ttpp) REVERT: D 74 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8147 (t80) REVERT: D 244 LYS cc_start: 0.8228 (ptmt) cc_final: 0.7525 (ttpp) REVERT: E 74 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7809 (t80) REVERT: E 244 LYS cc_start: 0.8230 (ptpt) cc_final: 0.7461 (ttpp) REVERT: F 74 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7916 (t80) REVERT: F 244 LYS cc_start: 0.8227 (ptmt) cc_final: 0.7526 (ttpp) REVERT: G 74 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8143 (t80) REVERT: G 244 LYS cc_start: 0.8238 (ptmt) cc_final: 0.7547 (ttpp) REVERT: H 244 LYS cc_start: 0.8234 (ptmt) cc_final: 0.7541 (ttpp) outliers start: 33 outliers final: 23 residues processed: 212 average time/residue: 0.1358 time to fit residues: 40.9250 Evaluate side-chains 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 124 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 142 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131067 restraints weight = 18630.059| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.88 r_work: 0.3405 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16248 Z= 0.110 Angle : 0.490 5.610 22120 Z= 0.263 Chirality : 0.037 0.122 2440 Planarity : 0.005 0.057 2752 Dihedral : 5.990 59.423 2248 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.51 % Allowed : 9.17 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.09 (0.19), residues: 2008 helix: 3.02 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.35 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 106 TYR 0.017 0.001 TYR E 223 PHE 0.007 0.001 PHE G 41 TRP 0.008 0.001 TRP C 169 HIS 0.003 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00226 (16248) covalent geometry : angle 0.49037 (22120) hydrogen bonds : bond 0.04447 ( 1061) hydrogen bonds : angle 3.68937 ( 3147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.412 Fit side-chains REVERT: A 74 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7954 (t80) REVERT: A 244 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7444 (ttpp) REVERT: B 74 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7790 (t80) REVERT: B 244 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7501 (ttpp) REVERT: C 74 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.7816 (t80) REVERT: C 244 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7473 (ttpp) REVERT: D 74 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8125 (t80) REVERT: D 244 LYS cc_start: 0.8186 (ptmt) cc_final: 0.7463 (ttpp) REVERT: E 74 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7752 (t80) REVERT: E 244 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7373 (ttpp) REVERT: F 74 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7868 (t80) REVERT: F 244 LYS cc_start: 0.8193 (ptmt) cc_final: 0.7468 (ttpp) REVERT: G 74 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8125 (t80) REVERT: G 244 LYS cc_start: 0.8186 (ptmt) cc_final: 0.7471 (ttpp) REVERT: H 244 LYS cc_start: 0.8170 (ptmt) cc_final: 0.7451 (ttpp) outliers start: 24 outliers final: 17 residues processed: 217 average time/residue: 0.1447 time to fit residues: 44.5476 Evaluate side-chains 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 37 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129727 restraints weight = 18629.179| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.88 r_work: 0.3384 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16248 Z= 0.117 Angle : 0.495 5.624 22120 Z= 0.266 Chirality : 0.037 0.123 2440 Planarity : 0.005 0.056 2752 Dihedral : 6.030 59.726 2248 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.32 % Allowed : 9.55 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.06 (0.19), residues: 2008 helix: 3.00 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.35 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 106 TYR 0.017 0.001 TYR H 223 PHE 0.007 0.001 PHE D 172 TRP 0.007 0.001 TRP D 169 HIS 0.003 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00251 (16248) covalent geometry : angle 0.49525 (22120) hydrogen bonds : bond 0.04790 ( 1061) hydrogen bonds : angle 3.71129 ( 3147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2782.17 seconds wall clock time: 48 minutes 35.14 seconds (2915.14 seconds total)