Starting phenix.real_space_refine on Sat May 17 11:04:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c9h_16510/05_2025/8c9h_16510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c9h_16510/05_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_16510/05_2025/8c9h_16510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c9h_16510/05_2025/8c9h_16510.map" model { file = "/net/cci-nas-00/data/ceres_data/8c9h_16510/05_2025/8c9h_16510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c9h_16510/05_2025/8c9h_16510.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.54, per 1000 atoms: 0.60 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: 4.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.41 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: 4.46 Time building geometry restraints manager: 4.99 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.170 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP D 177 HIS 0.002 0.001 HIS C 83 PHE 0.009 0.001 PHE E 37 TYR 0.018 0.001 TYR G 223 ARG 0.002 0.000 ARG G 106 Details of bonding type rmsd hydrogen bonds : bond 0.12901 ( 1061) hydrogen bonds : angle 4.74082 ( 3147) covalent geometry : bond 0.00512 (16248) covalent geometry : angle 0.59216 (22120) *********************** 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 : 1.641 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: 0.2989 time to fit residues: 81.9408 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 : 1.484 ------------------------------------------------------------------------------- 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 168 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130193 restraints weight = 18059.373| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.62 r_work: 0.3434 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0746 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= 0.132 Angle : 0.504 5.641 22120 Z= 0.273 Chirality : 0.038 0.125 2440 Planarity : 0.004 0.034 2752 Dihedral : 5.825 52.862 2252 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.20 % Allowed : 5.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.20), residues: 2008 helix: 2.57 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -0.26 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 253 HIS 0.002 0.001 HIS H 57 PHE 0.008 0.001 PHE A 172 TYR 0.020 0.001 TYR B 223 ARG 0.007 0.001 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.05449 ( 1061) hydrogen bonds : angle 3.87956 ( 3147) covalent geometry : bond 0.00285 (16248) covalent geometry : angle 0.50356 (22120) *********************** 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 212 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 1.487 Fit side-chains REVERT: A 74 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8016 (t80) REVERT: B 74 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7866 (t80) REVERT: C 74 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7857 (t80) REVERT: D 74 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7924 (t80) REVERT: E 74 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7890 (t80) REVERT: F 74 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7980 (t80) REVERT: G 74 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7971 (t80) outliers start: 35 outliers final: 26 residues processed: 198 average time/residue: 0.2864 time to fit residues: 82.9301 Evaluate side-chains 211 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.144383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119182 restraints weight = 18775.569| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.72 r_work: 0.3249 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 16248 Z= 0.283 Angle : 0.645 6.452 22120 Z= 0.356 Chirality : 0.044 0.144 2440 Planarity : 0.005 0.039 2752 Dihedral : 6.565 57.666 2248 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.58 % Allowed : 5.53 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 2008 helix: 2.30 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -0.47 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 177 HIS 0.004 0.001 HIS A 140 PHE 0.015 0.002 PHE E 172 TYR 0.029 0.003 TYR E 223 ARG 0.007 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.08337 ( 1061) hydrogen bonds : angle 4.23404 ( 3147) covalent geometry : bond 0.00707 (16248) covalent geometry : angle 0.64471 (22120) *********************** 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 224 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 1.584 Fit side-chains REVERT: A 74 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8185 (t80) REVERT: A 244 LYS cc_start: 0.8340 (ptpt) cc_final: 0.7536 (ttpp) REVERT: B 74 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8032 (t80) REVERT: B 244 LYS cc_start: 0.8394 (ptmt) cc_final: 0.7659 (ttpp) REVERT: C 74 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8141 (t80) REVERT: C 244 LYS cc_start: 0.8383 (ptmt) cc_final: 0.7649 (ttpp) REVERT: D 74 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8245 (t80) REVERT: D 244 LYS cc_start: 0.8364 (ptmt) cc_final: 0.7623 (ttpp) REVERT: E 74 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8096 (t80) REVERT: E 244 LYS cc_start: 0.8328 (ptpt) cc_final: 0.7530 (ttpp) REVERT: F 74 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8184 (t80) REVERT: F 244 LYS cc_start: 0.8377 (ptmt) cc_final: 0.7635 (ttpp) REVERT: G 74 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8243 (t80) REVERT: G 244 LYS cc_start: 0.8376 (ptmt) cc_final: 0.7633 (ttpp) REVERT: H 244 LYS cc_start: 0.8371 (ptmt) cc_final: 0.7624 (ttpp) outliers start: 41 outliers final: 32 residues processed: 216 average time/residue: 0.2746 time to fit residues: 88.4594 Evaluate side-chains 214 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 160 THR 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 142 SER Chi-restraints excluded: chain B residue 160 THR 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 160 THR 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 160 THR 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 160 THR 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 160 THR 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 142 SER Chi-restraints excluded: chain G residue 160 THR 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 160 THR 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 108 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.0670 chunk 131 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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** B 165 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS F 165 HIS G 165 HIS ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123384 restraints weight = 18362.404| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.66 r_work: 0.3368 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16248 Z= 0.124 Angle : 0.501 5.551 22120 Z= 0.272 Chirality : 0.037 0.122 2440 Planarity : 0.004 0.036 2752 Dihedral : 6.261 55.618 2248 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.39 % Allowed : 6.97 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.19), residues: 2008 helix: 2.52 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -0.33 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 169 HIS 0.003 0.001 HIS H 57 PHE 0.009 0.001 PHE F 172 TYR 0.014 0.001 TYR D 223 ARG 0.008 0.001 ARG F 106 Details of bonding type rmsd hydrogen bonds : bond 0.05418 ( 1061) hydrogen bonds : angle 3.85957 ( 3147) covalent geometry : bond 0.00252 (16248) covalent geometry : angle 0.50140 (22120) *********************** 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 225 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.522 Fit side-chains REVERT: A 74 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7990 (t80) REVERT: A 244 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7400 (ttpp) REVERT: B 74 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7794 (t80) REVERT: B 244 LYS cc_start: 0.8269 (ptmt) cc_final: 0.7513 (ttpp) REVERT: C 74 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7935 (t80) REVERT: C 244 LYS cc_start: 0.8240 (ptmt) cc_final: 0.7474 (ttpp) REVERT: D 74 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8171 (t80) REVERT: D 244 LYS cc_start: 0.8233 (ptmt) cc_final: 0.7463 (ttpp) REVERT: E 74 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7868 (t80) REVERT: E 244 LYS cc_start: 0.8155 (ptpt) cc_final: 0.7375 (ttpp) REVERT: F 74 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7987 (t80) REVERT: F 244 LYS cc_start: 0.8242 (ptmt) cc_final: 0.7462 (ttpp) REVERT: G 74 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8150 (t80) REVERT: G 244 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7478 (ttpp) REVERT: H 244 LYS cc_start: 0.8230 (ptmt) cc_final: 0.7462 (ttpp) outliers start: 38 outliers final: 26 residues processed: 218 average time/residue: 0.3080 time to fit residues: 95.8824 Evaluate side-chains 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 160 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 143 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.145399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120505 restraints weight = 18866.349| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.72 r_work: 0.3243 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 16248 Z= 0.264 Angle : 0.623 6.245 22120 Z= 0.342 Chirality : 0.044 0.146 2440 Planarity : 0.005 0.039 2752 Dihedral : 6.567 59.142 2248 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.70 % Allowed : 7.16 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.19), residues: 2008 helix: 2.36 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -0.54 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 169 HIS 0.004 0.002 HIS D 165 PHE 0.014 0.002 PHE B 74 TYR 0.028 0.002 TYR H 223 ARG 0.007 0.001 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.07842 ( 1061) hydrogen bonds : angle 4.14718 ( 3147) covalent geometry : bond 0.00662 (16248) covalent geometry : angle 0.62300 (22120) *********************** 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 229 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 3.438 Fit side-chains REVERT: A 74 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8209 (t80) REVERT: A 244 LYS cc_start: 0.8379 (ptpt) cc_final: 0.7563 (ttpp) REVERT: B 74 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7981 (t80) REVERT: B 244 LYS cc_start: 0.8395 (ptmt) cc_final: 0.7675 (ttpp) REVERT: C 74 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8119 (t80) REVERT: C 244 LYS cc_start: 0.8382 (ptmt) cc_final: 0.7660 (ttpp) REVERT: D 74 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8321 (t80) REVERT: D 244 LYS cc_start: 0.8369 (ptmt) cc_final: 0.7648 (ttpp) REVERT: E 74 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8131 (t80) REVERT: E 244 LYS cc_start: 0.8376 (ptpt) cc_final: 0.7551 (ttpp) REVERT: F 74 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8156 (t80) REVERT: F 244 LYS cc_start: 0.8379 (ptmt) cc_final: 0.7639 (ttpp) REVERT: G 74 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8321 (t80) REVERT: G 244 LYS cc_start: 0.8392 (ptmt) cc_final: 0.7664 (ttpp) REVERT: H 244 LYS cc_start: 0.8364 (ptmt) cc_final: 0.7632 (ttpp) outliers start: 43 outliers final: 27 residues processed: 219 average time/residue: 0.3399 time to fit residues: 106.7104 Evaluate side-chains 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 160 THR 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 160 THR 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 160 THR 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 160 THR 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 160 THR 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 160 THR 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 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 160 THR 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 109 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 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 = 0.3795 r_free = 0.3795 target = 0.152134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124829 restraints weight = 19007.212| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.89 r_work: 0.3316 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16248 Z= 0.136 Angle : 0.520 5.521 22120 Z= 0.282 Chirality : 0.038 0.127 2440 Planarity : 0.005 0.043 2752 Dihedral : 6.392 57.902 2248 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.32 % Allowed : 7.79 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.19), residues: 2008 helix: 2.65 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.56 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS C 57 PHE 0.008 0.001 PHE F 172 TYR 0.015 0.001 TYR H 223 ARG 0.011 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.05774 ( 1061) hydrogen bonds : angle 3.89630 ( 3147) covalent geometry : bond 0.00297 (16248) covalent geometry : angle 0.51951 (22120) *********************** 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 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 1.448 Fit side-chains REVERT: A 74 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8040 (t80) REVERT: A 244 LYS cc_start: 0.8274 (ptpt) cc_final: 0.7490 (ttpp) REVERT: B 74 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7799 (t80) REVERT: B 244 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7613 (ttpp) REVERT: C 74 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7961 (t80) REVERT: C 244 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7613 (ttpp) REVERT: D 47 MET cc_start: 0.8763 (tmm) cc_final: 0.8318 (ttt) REVERT: D 74 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8158 (t80) REVERT: D 244 LYS cc_start: 0.8308 (ptmt) cc_final: 0.7593 (ttpp) REVERT: E 74 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7928 (t80) REVERT: E 244 LYS cc_start: 0.8287 (ptpt) cc_final: 0.7514 (ttpp) REVERT: F 74 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7988 (t80) REVERT: F 244 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7593 (ttpp) REVERT: G 74 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8228 (t80) REVERT: G 244 LYS cc_start: 0.8313 (ptmt) cc_final: 0.7591 (ttpp) REVERT: H 47 MET cc_start: 0.8729 (tmm) cc_final: 0.8307 (ttt) REVERT: H 244 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7601 (ttpp) outliers start: 37 outliers final: 28 residues processed: 206 average time/residue: 0.2929 time to fit residues: 87.8577 Evaluate side-chains 218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 149 THR Chi-restraints excluded: chain B residue 160 THR 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 160 THR 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 149 THR Chi-restraints excluded: chain D residue 160 THR 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 149 THR 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 160 THR 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 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 160 THR 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 67 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.145255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119098 restraints weight = 19027.660| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.82 r_work: 0.3276 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16248 Z= 0.206 Angle : 0.573 5.934 22120 Z= 0.314 Chirality : 0.041 0.140 2440 Planarity : 0.005 0.045 2752 Dihedral : 6.480 59.464 2248 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.32 % Allowed : 8.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.19), residues: 2008 helix: 2.50 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.63 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 169 HIS 0.003 0.001 HIS F 57 PHE 0.012 0.002 PHE B 74 TYR 0.024 0.002 TYR H 223 ARG 0.009 0.001 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.06982 ( 1061) hydrogen bonds : angle 4.03323 ( 3147) covalent geometry : bond 0.00504 (16248) covalent geometry : angle 0.57251 (22120) *********************** 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: 37 poor density : 184 time to evaluate : 1.510 Fit side-chains REVERT: A 47 MET cc_start: 0.8837 (tmm) cc_final: 0.8371 (ttt) REVERT: A 74 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8171 (t80) REVERT: A 244 LYS cc_start: 0.8398 (ptpt) cc_final: 0.7577 (ttpp) REVERT: B 74 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7910 (t80) REVERT: B 244 LYS cc_start: 0.8403 (ptmt) cc_final: 0.7676 (ttpp) REVERT: C 47 MET cc_start: 0.8823 (tmm) cc_final: 0.8357 (ttt) REVERT: C 74 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8048 (t80) REVERT: C 244 LYS cc_start: 0.8388 (ptmt) cc_final: 0.7668 (ttpp) REVERT: D 47 MET cc_start: 0.8846 (tmm) cc_final: 0.8373 (ttt) REVERT: D 74 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8304 (t80) REVERT: D 244 LYS cc_start: 0.8366 (ptmt) cc_final: 0.7633 (ttpp) REVERT: E 47 MET cc_start: 0.8856 (tmm) cc_final: 0.8378 (ttt) REVERT: E 74 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8033 (t80) REVERT: E 244 LYS cc_start: 0.8390 (ptpt) cc_final: 0.7566 (ttpp) REVERT: F 47 MET cc_start: 0.8836 (tmm) cc_final: 0.8350 (ttt) REVERT: F 74 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8100 (t80) REVERT: F 244 LYS cc_start: 0.8374 (ptmt) cc_final: 0.7637 (ttpp) REVERT: G 47 MET cc_start: 0.8828 (tmm) cc_final: 0.8348 (ttt) REVERT: G 74 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8308 (t80) REVERT: G 244 LYS cc_start: 0.8377 (ptmt) cc_final: 0.7646 (ttpp) REVERT: H 47 MET cc_start: 0.8802 (tmm) cc_final: 0.8351 (ttt) REVERT: H 244 LYS cc_start: 0.8373 (ptmt) cc_final: 0.7633 (ttpp) outliers start: 37 outliers final: 28 residues processed: 210 average time/residue: 0.2933 time to fit residues: 89.1893 Evaluate side-chains 218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 160 THR 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 160 THR 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 87 ARG Chi-restraints excluded: chain C residue 160 THR 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 87 ARG Chi-restraints excluded: chain D residue 160 THR 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 160 THR 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 160 THR 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 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 160 THR 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 50 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 133 optimal weight: 0.0570 chunk 81 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.149487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124729 restraints weight = 18112.241| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.67 r_work: 0.3356 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1727 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= 0.137 Angle : 0.519 5.546 22120 Z= 0.281 Chirality : 0.038 0.126 2440 Planarity : 0.005 0.051 2752 Dihedral : 6.321 58.352 2248 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.14 % Allowed : 8.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.19), residues: 2008 helix: 2.68 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.61 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 169 HIS 0.003 0.001 HIS F 57 PHE 0.008 0.001 PHE F 172 TYR 0.016 0.001 TYR H 223 ARG 0.011 0.001 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.05640 ( 1061) hydrogen bonds : angle 3.86210 ( 3147) covalent geometry : bond 0.00306 (16248) covalent geometry : angle 0.51917 (22120) *********************** 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 218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.530 Fit side-chains REVERT: A 74 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.7979 (t80) REVERT: A 244 LYS cc_start: 0.8339 (ptpt) cc_final: 0.7532 (ttpp) REVERT: B 74 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7796 (t80) REVERT: B 244 LYS cc_start: 0.8346 (ptmt) cc_final: 0.7598 (ttpp) REVERT: C 74 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7948 (t80) REVERT: C 244 LYS cc_start: 0.8326 (ptmt) cc_final: 0.7584 (ttpp) REVERT: D 74 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8197 (t80) REVERT: D 244 LYS cc_start: 0.8335 (ptmt) cc_final: 0.7595 (ttpp) REVERT: E 74 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7922 (t80) REVERT: E 244 LYS cc_start: 0.8331 (ptpt) cc_final: 0.7529 (ttpp) REVERT: F 74 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7965 (t80) REVERT: F 244 LYS cc_start: 0.8352 (ptmt) cc_final: 0.7599 (ttpp) REVERT: G 74 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8188 (t80) REVERT: G 244 LYS cc_start: 0.8333 (ptmt) cc_final: 0.7601 (ttpp) REVERT: H 244 LYS cc_start: 0.8330 (ptmt) cc_final: 0.7607 (ttpp) outliers start: 34 outliers final: 26 residues processed: 209 average time/residue: 0.2942 time to fit residues: 89.0431 Evaluate side-chains 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 160 THR 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 160 THR 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 160 THR 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 160 THR 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 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 160 THR 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 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 160 THR 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 112 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.152522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125021 restraints weight = 18873.425| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.89 r_work: 0.3329 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1737 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= 0.140 Angle : 0.522 5.574 22120 Z= 0.284 Chirality : 0.038 0.130 2440 Planarity : 0.005 0.053 2752 Dihedral : 6.263 58.648 2248 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.95 % Allowed : 8.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.19), residues: 2008 helix: 2.74 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.59 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 169 HIS 0.003 0.001 HIS F 57 PHE 0.008 0.001 PHE B 172 TYR 0.018 0.001 TYR H 223 ARG 0.012 0.001 ARG F 106 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 1061) hydrogen bonds : angle 3.85451 ( 3147) covalent geometry : bond 0.00318 (16248) covalent geometry : angle 0.52210 (22120) *********************** 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 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 1.522 Fit side-chains REVERT: A 47 MET cc_start: 0.8818 (tmm) cc_final: 0.8350 (ttt) REVERT: A 74 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7969 (t80) REVERT: A 244 LYS cc_start: 0.8324 (ptpt) cc_final: 0.7513 (ttpp) REVERT: B 74 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7796 (t80) REVERT: B 244 LYS cc_start: 0.8343 (ptmt) cc_final: 0.7580 (ttpp) REVERT: C 47 MET cc_start: 0.8803 (tmm) cc_final: 0.8341 (ttt) REVERT: C 74 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7935 (t80) REVERT: C 244 LYS cc_start: 0.8312 (ptmt) cc_final: 0.7558 (ttpp) REVERT: D 74 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8220 (t80) REVERT: D 244 LYS cc_start: 0.8320 (ptmt) cc_final: 0.7545 (ttpp) REVERT: E 47 MET cc_start: 0.8812 (tmm) cc_final: 0.8332 (ttt) REVERT: E 74 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7914 (t80) REVERT: E 244 LYS cc_start: 0.8313 (ptpt) cc_final: 0.7497 (ttpp) REVERT: F 47 MET cc_start: 0.8805 (tmm) cc_final: 0.8324 (ttt) REVERT: F 74 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7957 (t80) REVERT: F 244 LYS cc_start: 0.8340 (ptmt) cc_final: 0.7569 (ttpp) REVERT: G 47 MET cc_start: 0.8798 (tmm) cc_final: 0.8310 (ttt) REVERT: G 74 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8197 (t80) REVERT: G 244 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7558 (ttpp) REVERT: H 47 MET cc_start: 0.8762 (tmm) cc_final: 0.8308 (ttt) REVERT: H 244 LYS cc_start: 0.8324 (ptmt) cc_final: 0.7576 (ttpp) outliers start: 31 outliers final: 23 residues processed: 209 average time/residue: 0.3225 time to fit residues: 95.9354 Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 160 THR 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 187 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 160 THR 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 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 160 THR 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 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 160 THR 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 49 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.3819 r_free = 0.3819 target = 0.150351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126269 restraints weight = 18348.064| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.67 r_work: 0.3403 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16248 Z= 0.112 Angle : 0.496 5.549 22120 Z= 0.266 Chirality : 0.037 0.120 2440 Planarity : 0.005 0.056 2752 Dihedral : 6.111 58.955 2248 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.57 % Allowed : 9.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.19), residues: 2008 helix: 2.86 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.53 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 169 HIS 0.003 0.001 HIS F 57 PHE 0.007 0.001 PHE G 41 TYR 0.013 0.001 TYR F 223 ARG 0.012 0.001 ARG C 106 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 1061) hydrogen bonds : angle 3.74600 ( 3147) covalent geometry : bond 0.00228 (16248) covalent geometry : angle 0.49617 (22120) ********************** 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 227 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 1.598 Fit side-chains REVERT: A 74 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7961 (t80) REVERT: A 244 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7357 (ttpp) REVERT: B 74 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7779 (t80) REVERT: B 244 LYS cc_start: 0.8248 (ptmt) cc_final: 0.7509 (ttpp) REVERT: C 74 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7847 (t80) REVERT: C 244 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7492 (ttpp) REVERT: D 74 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8181 (t80) REVERT: D 244 LYS cc_start: 0.8179 (ptmt) cc_final: 0.7435 (ttpp) REVERT: E 74 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7833 (t80) REVERT: E 244 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7356 (ttpp) REVERT: F 74 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7882 (t80) REVERT: F 244 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7478 (ttpp) REVERT: G 74 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8155 (t80) REVERT: G 244 LYS cc_start: 0.8217 (ptmt) cc_final: 0.7461 (ttpp) REVERT: H 244 LYS cc_start: 0.8226 (ptmt) cc_final: 0.7475 (ttpp) outliers start: 25 outliers final: 11 residues processed: 225 average time/residue: 0.3184 time to fit residues: 102.0561 Evaluate side-chains 210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE 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 187 PHE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain D residue 74 PHE 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 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 187 PHE 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 19 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.150315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125315 restraints weight = 18131.378| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.69 r_work: 0.3362 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1744 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= 0.142 Angle : 0.523 5.600 22120 Z= 0.283 Chirality : 0.039 0.128 2440 Planarity : 0.005 0.054 2752 Dihedral : 6.225 58.932 2248 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.51 % Allowed : 9.48 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.19), residues: 2008 helix: 2.77 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.47 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 169 HIS 0.003 0.001 HIS F 57 PHE 0.008 0.001 PHE D 236 TYR 0.019 0.001 TYR H 223 ARG 0.012 0.001 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.05586 ( 1061) hydrogen bonds : angle 3.80952 ( 3147) covalent geometry : bond 0.00325 (16248) covalent geometry : angle 0.52269 (22120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6734.70 seconds wall clock time: 118 minutes 5.49 seconds (7085.49 seconds total)