Starting phenix.real_space_refine on Mon Nov 18 05:46:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/11_2024/8c9h_16510.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/11_2024/8c9h_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/11_2024/8c9h_16510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/11_2024/8c9h_16510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/11_2024/8c9h_16510.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/11_2024/8c9h_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.62, per 1000 atoms: 0.55 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: 3.90 Conformation dependent library (CDL) restraints added in 1.8 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: 1.31 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: 4.43 Time building geometry restraints manager: 4.49 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.970 Find NCS groups from input model: 0.840 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.090 ------------------------------------------------------------------------------- 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= 0.344 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 *********************** 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 : 1.652 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: 0.3132 time to fit residues: 86.1440 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 : 1.642 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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= 0.186 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 *********************** 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 : 1.693 Fit side-chains REVERT: A 74 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8047 (t80) REVERT: B 74 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7920 (t80) REVERT: C 74 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7892 (t80) REVERT: D 74 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.7961 (t80) REVERT: E 74 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7936 (t80) REVERT: F 74 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8014 (t80) REVERT: G 74 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8000 (t80) outliers start: 35 outliers final: 26 residues processed: 198 average time/residue: 0.3047 time to fit residues: 88.5390 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 : 1.612 ------------------------------------------------------------------------------- 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 100 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 196 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** G 165 HIS ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16248 Z= 0.270 Angle : 0.550 5.868 22120 Z= 0.302 Chirality : 0.040 0.139 2440 Planarity : 0.005 0.036 2752 Dihedral : 6.298 55.137 2248 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.64 % Allowed : 5.34 % Favored : 92.02 % 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: 2.54 (0.19), residues: 2008 helix: 2.57 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.39 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS A 57 PHE 0.013 0.002 PHE G 172 TYR 0.024 0.002 TYR A 223 ARG 0.007 0.001 ARG A 106 *********************** 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 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 1.710 Fit side-chains REVERT: A 74 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 244 LYS cc_start: 0.8287 (ptpt) cc_final: 0.7568 (ttpp) REVERT: B 74 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7923 (t80) REVERT: B 244 LYS cc_start: 0.8348 (ptmt) cc_final: 0.7656 (ttpp) REVERT: C 74 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8048 (t80) REVERT: C 244 LYS cc_start: 0.8347 (ptmt) cc_final: 0.7666 (ttpp) REVERT: D 74 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8175 (t80) REVERT: D 244 LYS cc_start: 0.8346 (ptmt) cc_final: 0.7663 (ttpp) REVERT: E 74 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7991 (t80) REVERT: E 244 LYS cc_start: 0.8290 (ptpt) cc_final: 0.7583 (ttpp) REVERT: F 74 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8068 (t80) REVERT: F 244 LYS cc_start: 0.8331 (ptmt) cc_final: 0.7639 (ttpp) REVERT: G 74 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8163 (t80) REVERT: G 244 LYS cc_start: 0.8335 (ptmt) cc_final: 0.7639 (ttpp) REVERT: H 244 LYS cc_start: 0.8347 (ptmt) cc_final: 0.7634 (ttpp) outliers start: 42 outliers final: 30 residues processed: 212 average time/residue: 0.3089 time to fit residues: 95.5811 Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 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 187 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS 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 ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16248 Z= 0.260 Angle : 0.539 5.667 22120 Z= 0.295 Chirality : 0.039 0.131 2440 Planarity : 0.005 0.037 2752 Dihedral : 6.311 56.242 2248 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.51 % Allowed : 6.60 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.52 (0.19), residues: 2008 helix: 2.57 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.44 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 169 HIS 0.003 0.001 HIS G 165 PHE 0.011 0.001 PHE B 172 TYR 0.021 0.002 TYR B 223 ARG 0.009 0.001 ARG G 106 *********************** 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 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.658 Fit side-chains REVERT: A 74 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8074 (t80) REVERT: A 244 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7581 (ttpp) REVERT: B 74 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7886 (t80) REVERT: B 244 LYS cc_start: 0.8357 (ptmt) cc_final: 0.7666 (ttpp) REVERT: C 74 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7981 (t80) REVERT: C 244 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7703 (ttpp) REVERT: D 74 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8237 (t80) REVERT: D 244 LYS cc_start: 0.8343 (ptmt) cc_final: 0.7665 (ttpp) REVERT: E 74 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.7990 (t80) REVERT: E 244 LYS cc_start: 0.8294 (ptpt) cc_final: 0.7587 (ttpp) REVERT: F 74 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8002 (t80) REVERT: F 244 LYS cc_start: 0.8351 (ptmt) cc_final: 0.7661 (ttpp) REVERT: G 74 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8237 (t80) REVERT: G 244 LYS cc_start: 0.8346 (ptmt) cc_final: 0.7655 (ttpp) REVERT: H 244 LYS cc_start: 0.8343 (ptmt) cc_final: 0.7654 (ttpp) outliers start: 40 outliers final: 33 residues processed: 212 average time/residue: 0.3045 time to fit residues: 93.3029 Evaluate side-chains 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 133 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.3804 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1454 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= 0.192 Angle : 0.506 5.578 22120 Z= 0.275 Chirality : 0.038 0.126 2440 Planarity : 0.005 0.036 2752 Dihedral : 6.178 56.528 2248 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.58 % Allowed : 7.29 % 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: 2.72 (0.19), residues: 2008 helix: 2.76 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.003 0.001 HIS C 57 PHE 0.009 0.001 PHE F 172 TYR 0.018 0.001 TYR B 223 ARG 0.010 0.001 ARG D 106 *********************** 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 230 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.679 Fit side-chains REVERT: A 74 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8034 (t80) REVERT: A 244 LYS cc_start: 0.8251 (ptpt) cc_final: 0.7520 (ttpp) REVERT: B 74 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7782 (t80) REVERT: B 244 LYS cc_start: 0.8344 (ptmt) cc_final: 0.7654 (ttpp) REVERT: C 74 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7918 (t80) REVERT: C 244 LYS cc_start: 0.8328 (ptmt) cc_final: 0.7659 (ttpp) REVERT: D 74 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8170 (t80) REVERT: D 244 LYS cc_start: 0.8325 (ptmt) cc_final: 0.7647 (ttpp) REVERT: E 74 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7942 (t80) REVERT: E 244 LYS cc_start: 0.8265 (ptpt) cc_final: 0.7559 (ttpp) REVERT: F 74 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7953 (t80) REVERT: F 244 LYS cc_start: 0.8333 (ptmt) cc_final: 0.7644 (ttpp) REVERT: G 74 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8161 (t80) REVERT: G 244 LYS cc_start: 0.8322 (ptmt) cc_final: 0.7630 (ttpp) REVERT: H 244 LYS cc_start: 0.8326 (ptmt) cc_final: 0.7641 (ttpp) outliers start: 41 outliers final: 29 residues processed: 222 average time/residue: 0.3223 time to fit residues: 103.0080 Evaluate side-chains 223 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 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 187 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16248 Z= 0.227 Angle : 0.526 5.597 22120 Z= 0.286 Chirality : 0.039 0.131 2440 Planarity : 0.005 0.042 2752 Dihedral : 6.230 57.184 2248 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.58 % Allowed : 7.98 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.19), residues: 2008 helix: 2.73 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 169 HIS 0.003 0.001 HIS F 57 PHE 0.010 0.001 PHE A 172 TYR 0.021 0.002 TYR H 223 ARG 0.010 0.001 ARG B 106 *********************** 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 229 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 2.143 Fit side-chains REVERT: A 74 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8081 (t80) REVERT: A 244 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7560 (ttpp) REVERT: B 74 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7840 (t80) REVERT: B 244 LYS cc_start: 0.8356 (ptmt) cc_final: 0.7679 (ttpp) REVERT: C 74 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7982 (t80) REVERT: C 244 LYS cc_start: 0.8344 (ptmt) cc_final: 0.7683 (ttpp) REVERT: D 74 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8202 (t80) REVERT: D 244 LYS cc_start: 0.8331 (ptmt) cc_final: 0.7671 (ttpp) REVERT: E 74 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7980 (t80) REVERT: E 244 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7602 (ttpp) REVERT: F 74 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8007 (t80) REVERT: F 244 LYS cc_start: 0.8345 (ptmt) cc_final: 0.7671 (ttpp) REVERT: G 74 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8194 (t80) REVERT: G 244 LYS cc_start: 0.8338 (ptmt) cc_final: 0.7655 (ttpp) REVERT: H 244 LYS cc_start: 0.8328 (ptmt) cc_final: 0.7659 (ttpp) outliers start: 41 outliers final: 34 residues processed: 221 average time/residue: 0.3353 time to fit residues: 106.9408 Evaluate side-chains 229 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.754 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 192 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16248 Z= 0.235 Angle : 0.530 5.613 22120 Z= 0.288 Chirality : 0.039 0.131 2440 Planarity : 0.005 0.047 2752 Dihedral : 6.274 57.858 2248 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.64 % Allowed : 8.10 % 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: 2.65 (0.19), residues: 2008 helix: 2.72 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.56 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 169 HIS 0.003 0.001 HIS D 57 PHE 0.009 0.001 PHE F 172 TYR 0.020 0.002 TYR F 223 ARG 0.010 0.001 ARG H 106 *********************** 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 229 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.727 Fit side-chains REVERT: A 74 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 244 LYS cc_start: 0.8293 (ptpt) cc_final: 0.7578 (ttpp) REVERT: B 74 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7849 (t80) REVERT: B 244 LYS cc_start: 0.8355 (ptmt) cc_final: 0.7693 (ttpp) REVERT: C 74 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8005 (t80) REVERT: C 244 LYS cc_start: 0.8370 (ptmt) cc_final: 0.7713 (ttpp) REVERT: D 74 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8217 (t80) REVERT: D 244 LYS cc_start: 0.8337 (ptmt) cc_final: 0.7686 (ttpp) REVERT: E 74 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7990 (t80) REVERT: E 244 LYS cc_start: 0.8306 (ptpt) cc_final: 0.7616 (ttpp) REVERT: F 74 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8018 (t80) REVERT: F 244 LYS cc_start: 0.8344 (ptmt) cc_final: 0.7681 (ttpp) REVERT: G 74 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8225 (t80) REVERT: G 244 LYS cc_start: 0.8350 (ptmt) cc_final: 0.7681 (ttpp) REVERT: H 244 LYS cc_start: 0.8335 (ptmt) cc_final: 0.7676 (ttpp) outliers start: 42 outliers final: 34 residues processed: 220 average time/residue: 0.3363 time to fit residues: 105.4583 Evaluate side-chains 229 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16248 Z= 0.273 Angle : 0.551 5.669 22120 Z= 0.300 Chirality : 0.040 0.136 2440 Planarity : 0.005 0.047 2752 Dihedral : 6.372 58.834 2248 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.64 % Allowed : 8.23 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.65 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.51 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 169 HIS 0.003 0.001 HIS D 57 PHE 0.010 0.001 PHE F 172 TYR 0.022 0.002 TYR H 223 ARG 0.010 0.001 ARG G 106 *********************** 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 230 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 1.676 Fit side-chains REVERT: A 74 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8062 (t80) REVERT: A 244 LYS cc_start: 0.8355 (ptpt) cc_final: 0.7618 (ttpp) REVERT: B 74 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7883 (t80) REVERT: B 244 LYS cc_start: 0.8379 (ptmt) cc_final: 0.7714 (ttpp) REVERT: C 74 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8055 (t80) REVERT: C 244 LYS cc_start: 0.8373 (ptmt) cc_final: 0.7721 (ttpp) REVERT: D 74 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8259 (t80) REVERT: D 244 LYS cc_start: 0.8367 (ptmt) cc_final: 0.7716 (ttpp) REVERT: E 74 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8030 (t80) REVERT: E 244 LYS cc_start: 0.8366 (ptpt) cc_final: 0.7623 (ttpp) REVERT: F 74 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8072 (t80) REVERT: F 244 LYS cc_start: 0.8371 (ptmt) cc_final: 0.7704 (ttpp) REVERT: G 74 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8256 (t80) REVERT: G 244 LYS cc_start: 0.8362 (ptmt) cc_final: 0.7694 (ttpp) REVERT: H 244 LYS cc_start: 0.8361 (ptmt) cc_final: 0.7700 (ttpp) outliers start: 42 outliers final: 27 residues processed: 221 average time/residue: 0.3262 time to fit residues: 102.6815 Evaluate side-chains 222 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 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 87 ARG 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 184 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 55 optimal weight: 0.4980 chunk 162 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1664 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= 0.179 Angle : 0.511 5.578 22120 Z= 0.276 Chirality : 0.038 0.124 2440 Planarity : 0.005 0.054 2752 Dihedral : 6.242 57.857 2248 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.95 % Allowed : 8.54 % Favored : 89.51 % 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: 2.80 (0.19), residues: 2008 helix: 2.85 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.53 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 169 HIS 0.002 0.001 HIS F 57 PHE 0.008 0.001 PHE F 172 TYR 0.016 0.001 TYR D 223 ARG 0.012 0.001 ARG F 106 *********************** 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 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 1.487 Fit side-chains REVERT: A 74 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7957 (t80) REVERT: A 244 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7576 (ttpp) REVERT: B 74 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.7809 (t80) REVERT: B 244 LYS cc_start: 0.8351 (ptmt) cc_final: 0.7686 (ttpp) REVERT: C 74 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7934 (t80) REVERT: C 244 LYS cc_start: 0.8354 (ptmt) cc_final: 0.7703 (ttpp) REVERT: D 74 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8198 (t80) REVERT: D 244 LYS cc_start: 0.8349 (ptmt) cc_final: 0.7692 (ttpp) REVERT: E 74 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7919 (t80) REVERT: E 244 LYS cc_start: 0.8307 (ptpt) cc_final: 0.7604 (ttpp) REVERT: F 74 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7963 (t80) REVERT: F 244 LYS cc_start: 0.8338 (ptmt) cc_final: 0.7672 (ttpp) REVERT: G 74 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8194 (t80) REVERT: G 244 LYS cc_start: 0.8336 (ptmt) cc_final: 0.7665 (ttpp) REVERT: H 244 LYS cc_start: 0.8317 (ptmt) cc_final: 0.7661 (ttpp) outliers start: 31 outliers final: 19 residues processed: 213 average time/residue: 0.3313 time to fit residues: 99.8540 Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 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 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 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 115 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16248 Z= 0.267 Angle : 0.550 5.610 22120 Z= 0.299 Chirality : 0.040 0.135 2440 Planarity : 0.005 0.054 2752 Dihedral : 6.354 59.112 2248 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.88 % Allowed : 8.67 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.64 (0.19), residues: 2008 helix: 2.71 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.54 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 169 HIS 0.003 0.001 HIS F 57 PHE 0.010 0.001 PHE B 74 TYR 0.022 0.002 TYR H 223 ARG 0.012 0.001 ARG H 106 ********************** 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 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.617 Fit side-chains REVERT: A 74 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8060 (t80) REVERT: A 244 LYS cc_start: 0.8377 (ptpt) cc_final: 0.7623 (ttpp) REVERT: B 74 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7885 (t80) REVERT: B 244 LYS cc_start: 0.8377 (ptmt) cc_final: 0.7714 (ttpp) REVERT: C 74 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8034 (t80) REVERT: C 244 LYS cc_start: 0.8369 (ptmt) cc_final: 0.7722 (ttpp) REVERT: D 74 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8273 (t80) REVERT: D 244 LYS cc_start: 0.8359 (ptmt) cc_final: 0.7710 (ttpp) REVERT: E 74 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8034 (t80) REVERT: E 244 LYS cc_start: 0.8378 (ptpt) cc_final: 0.7619 (ttpp) REVERT: F 74 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8069 (t80) REVERT: F 244 LYS cc_start: 0.8367 (ptmt) cc_final: 0.7704 (ttpp) REVERT: G 74 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8267 (t80) REVERT: G 244 LYS cc_start: 0.8360 (ptmt) cc_final: 0.7697 (ttpp) REVERT: H 244 LYS cc_start: 0.8356 (ptmt) cc_final: 0.7700 (ttpp) outliers start: 30 outliers final: 23 residues processed: 210 average time/residue: 0.3516 time to fit residues: 104.3503 Evaluate side-chains 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 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 187 PHE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 87 ARG 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 48 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 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 = 0.3798 r_free = 0.3798 target = 0.148731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.124737 restraints weight = 18188.355| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.67 r_work: 0.3391 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16248 Z= 0.155 Angle : 0.501 5.564 22120 Z= 0.269 Chirality : 0.037 0.122 2440 Planarity : 0.005 0.056 2752 Dihedral : 6.141 58.565 2248 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.76 % Allowed : 8.79 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.86 (0.19), residues: 2008 helix: 2.86 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 169 HIS 0.002 0.001 HIS F 57 PHE 0.008 0.001 PHE A 172 TYR 0.015 0.001 TYR D 223 ARG 0.013 0.001 ARG H 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.78 seconds wall clock time: 56 minutes 3.58 seconds (3363.58 seconds total)