Starting phenix.real_space_refine on Wed Nov 20 02:11:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k29_36835/11_2024/8k29_36835.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k29_36835/11_2024/8k29_36835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k29_36835/11_2024/8k29_36835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k29_36835/11_2024/8k29_36835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k29_36835/11_2024/8k29_36835.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k29_36835/11_2024/8k29_36835.cif" } resolution = 3.18 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= 0.007 sd= 0.125 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: 5 Type Number sf(0) Gaussians P 127 5.49 5 S 73 5.16 5 C 12855 2.51 5 N 3587 2.21 5 O 4413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21055 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1260 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 16, 'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna2p': 27, 'rna3p': 32} Chain: "A" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1390 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1903 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1290 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 898 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "R" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 12.37, per 1000 atoms: 0.59 Number of scatterers: 21055 At special positions: 0 Unit cell: (113.3, 140.8, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 127 15.00 O 4413 8.00 N 3587 7.00 C 12855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 19760 O5' DA Q 22 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.21 Conformation dependent library (CDL) restraints added in 2.7 seconds 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 44 sheets defined 26.6% alpha, 22.1% beta 15 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 7.27 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.573A pdb=" N VAL A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.937A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.532A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.533A pdb=" N ASN B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.507A pdb=" N LEU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 149' Processing helix chain 'B' and resid 150 through 155 removed outlier: 4.493A pdb=" N ASN B 153 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.806A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.510A pdb=" N ASN C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 165 through 179 removed outlier: 3.524A pdb=" N ILE C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 284 through 298 removed outlier: 3.593A pdb=" N VAL C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.507A pdb=" N TRP D 130 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ARG D 131 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 133 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 134 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 178 removed outlier: 4.070A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 Processing helix chain 'D' and resid 269 through 279 removed outlier: 3.558A pdb=" N LEU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 298 Processing helix chain 'E' and resid 99 through 107 Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.841A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 removed outlier: 3.510A pdb=" N LEU E 129 " --> pdb=" O GLY E 126 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG E 131 " --> pdb=" O THR E 128 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 134 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.615A pdb=" N ASP E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL E 176 " --> pdb=" O MET E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.653A pdb=" N ALA E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 284 through 298 removed outlier: 3.567A pdb=" N PHE E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 111 through 122 Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.685A pdb=" N TRP F 130 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG F 131 " --> pdb=" O THR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 178 removed outlier: 3.863A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL F 176 " --> pdb=" O MET F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 removed outlier: 3.505A pdb=" N ARG F 234 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 280 removed outlier: 4.090A pdb=" N GLY F 276 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.866A pdb=" N PHE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 102 through 107 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.599A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 178 removed outlier: 3.549A pdb=" N VAL G 176 " --> pdb=" O MET G 172 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.838A pdb=" N ASP G 275 " --> pdb=" O PHE G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 298 removed outlier: 3.703A pdb=" N PHE G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE G 296 " --> pdb=" O THR G 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.654A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE H 123 " --> pdb=" O TYR H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 3.574A pdb=" N LEU H 129 " --> pdb=" O GLY H 126 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG H 131 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG H 133 " --> pdb=" O TRP H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 179 removed outlier: 4.163A pdb=" N MET H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 234 Processing helix chain 'H' and resid 269 through 280 Processing helix chain 'H' and resid 285 through 298 Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 61 through 69 removed outlier: 4.153A pdb=" N LEU I 65 " --> pdb=" O ASP I 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 109 removed outlier: 3.711A pdb=" N ARG I 103 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS I 107 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 120 removed outlier: 3.500A pdb=" N TYR I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 removed outlier: 8.774A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 107 removed outlier: 8.774A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA B 205 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU B 190 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 207 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS B 188 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 209 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR B 186 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 211 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN B 180 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 142 Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.745A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.745A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA B 94 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 14 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.725A pdb=" N TYR C 12 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 21 through 26 current: chain 'C' and resid 139 through 145 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 76 through 85 current: chain 'C' and resid 217 through 218 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 45 removed outlier: 4.555A pdb=" N ALA C 68 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 235 through 237 Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.575A pdb=" N VAL C 260 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'D' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 26 current: chain 'D' and resid 139 through 144 Processing sheet with id=AB8, first strand: chain 'D' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 76 through 86 current: chain 'D' and resid 217 through 218 Processing sheet with id=AB9, first strand: chain 'D' and resid 40 through 45 Processing sheet with id=AC1, first strand: chain 'D' and resid 254 through 255 Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AC3, first strand: chain 'E' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 26 current: chain 'E' and resid 139 through 145 Processing sheet with id=AC4, first strand: chain 'E' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 76 through 86 current: chain 'E' and resid 217 through 218 Processing sheet with id=AC5, first strand: chain 'E' and resid 40 through 45 Processing sheet with id=AC6, first strand: chain 'E' and resid 235 through 237 Processing sheet with id=AC7, first strand: chain 'E' and resid 254 through 255 removed outlier: 3.515A pdb=" N VAL E 255 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AC9, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD1, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD2, first strand: chain 'F' and resid 39 through 46 Processing sheet with id=AD3, first strand: chain 'F' and resid 203 through 204 removed outlier: 4.651A pdb=" N GLN F 214 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 217 through 218 Processing sheet with id=AD5, first strand: chain 'F' and resid 235 through 237 Processing sheet with id=AD6, first strand: chain 'F' and resid 254 through 255 removed outlier: 3.642A pdb=" N VAL F 260 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.024A pdb=" N GLY G 299 " --> pdb=" O TYR G 12 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 26 current: chain 'G' and resid 139 through 144 Processing sheet with id=AD9, first strand: chain 'G' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 76 through 86 current: chain 'G' and resid 217 through 218 Processing sheet with id=AE1, first strand: chain 'G' and resid 39 through 44 removed outlier: 4.462A pdb=" N ALA G 68 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 254 through 255 removed outlier: 3.582A pdb=" N VAL G 260 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE4, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.568A pdb=" N MET H 191 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 145 " --> pdb=" O GLN H 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.580A pdb=" N MET H 224 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA H 222 " --> pdb=" O MET H 23 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 40 through 44 removed outlier: 3.867A pdb=" N GLY H 40 " --> pdb=" O PHE H 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 39 through 40 removed outlier: 5.999A pdb=" N THR I 3 " --> pdb=" O PRO I 81 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER I 5 " --> pdb=" O GLY I 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 90 through 93 removed outlier: 3.837A pdb=" N PHE I 147 " --> pdb=" O VAL I 93 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3338 1.30 - 1.43: 6164 1.43 - 1.56: 11796 1.56 - 1.69: 261 1.69 - 1.82: 131 Bond restraints: 21690 Sorted by residual: bond pdb=" CA LYS G 91 " pdb=" C LYS G 91 " ideal model delta sigma weight residual 1.523 1.414 0.108 1.23e-02 6.61e+03 7.77e+01 bond pdb=" CA ASP G 226 " pdb=" C ASP G 226 " ideal model delta sigma weight residual 1.522 1.419 0.104 1.37e-02 5.33e+03 5.71e+01 bond pdb=" CA THR A 99 " pdb=" C THR A 99 " ideal model delta sigma weight residual 1.525 1.442 0.083 1.32e-02 5.74e+03 3.96e+01 bond pdb=" CA LYS G 228 " pdb=" C LYS G 228 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.29e-02 6.01e+03 3.56e+01 bond pdb=" CA HIS G 225 " pdb=" C HIS G 225 " ideal model delta sigma weight residual 1.527 1.452 0.075 1.34e-02 5.57e+03 3.10e+01 ... (remaining 21685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 29383 3.36 - 6.72: 493 6.72 - 10.09: 80 10.09 - 13.45: 11 13.45 - 16.81: 3 Bond angle restraints: 29970 Sorted by residual: angle pdb=" N SER B 150 " pdb=" CA SER B 150 " pdb=" C SER B 150 " ideal model delta sigma weight residual 113.61 96.80 16.81 1.50e+00 4.44e-01 1.26e+02 angle pdb=" N TRP H 239 " pdb=" CA TRP H 239 " pdb=" C TRP H 239 " ideal model delta sigma weight residual 112.92 99.43 13.49 1.23e+00 6.61e-01 1.20e+02 angle pdb=" N LYS B 116 " pdb=" CA LYS B 116 " pdb=" C LYS B 116 " ideal model delta sigma weight residual 113.02 99.94 13.08 1.20e+00 6.94e-01 1.19e+02 angle pdb=" O3' A P 36 " pdb=" C3' A P 36 " pdb=" C2' A P 36 " ideal model delta sigma weight residual 109.50 122.55 -13.05 1.50e+00 4.44e-01 7.57e+01 angle pdb=" C4' DA Q 52 " pdb=" C3' DA Q 52 " pdb=" O3' DA Q 52 " ideal model delta sigma weight residual 110.00 122.78 -12.78 1.50e+00 4.44e-01 7.26e+01 ... (remaining 29965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 11727 34.35 - 68.69: 938 68.69 - 103.04: 68 103.04 - 137.38: 3 137.38 - 171.73: 9 Dihedral angle restraints: 12745 sinusoidal: 5899 harmonic: 6846 Sorted by residual: dihedral pdb=" C MET B 156 " pdb=" N MET B 156 " pdb=" CA MET B 156 " pdb=" CB MET B 156 " ideal model delta harmonic sigma weight residual -122.60 -154.82 32.22 0 2.50e+00 1.60e-01 1.66e+02 dihedral pdb=" N MET B 156 " pdb=" C MET B 156 " pdb=" CA MET B 156 " pdb=" CB MET B 156 " ideal model delta harmonic sigma weight residual 122.80 152.44 -29.64 0 2.50e+00 1.60e-01 1.41e+02 dihedral pdb=" O4' C P 44 " pdb=" C1' C P 44 " pdb=" N1 C P 44 " pdb=" C2 C P 44 " ideal model delta sinusoidal sigma weight residual 200.00 38.95 161.05 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 12742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 3452 0.282 - 0.564: 17 0.564 - 0.847: 4 0.847 - 1.129: 0 1.129 - 1.411: 1 Chirality restraints: 3474 Sorted by residual: chirality pdb=" CA MET B 156 " pdb=" N MET B 156 " pdb=" C MET B 156 " pdb=" CB MET B 156 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 4.98e+01 chirality pdb=" CB VAL C 183 " pdb=" CA VAL C 183 " pdb=" CG1 VAL C 183 " pdb=" CG2 VAL C 183 " both_signs ideal model delta sigma weight residual False -2.63 -1.95 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C3' A P 36 " pdb=" C4' A P 36 " pdb=" O3' A P 36 " pdb=" C2' A P 36 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 3471 not shown) Planarity restraints: 3433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 156 " 0.095 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO B 157 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 154 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C ALA B 154 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA B 154 " 0.029 2.00e-02 2.50e+03 pdb=" N MET B 155 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 196 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C LYS B 196 " 0.066 2.00e-02 2.50e+03 pdb=" O LYS B 196 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS B 197 " -0.022 2.00e-02 2.50e+03 ... (remaining 3430 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 25 1.89 - 2.65: 539 2.65 - 3.40: 27604 3.40 - 4.15: 58262 4.15 - 4.90: 98954 Nonbonded interactions: 185384 Sorted by model distance: nonbonded pdb=" ND2 ASN G 61 " pdb=" C5' DA Q 22 " model vdw 1.142 3.520 nonbonded pdb=" OD1 ASN B 222 " pdb=" OP1 DA R 37 " model vdw 1.181 3.040 nonbonded pdb=" C2 A P 31 " pdb=" C5 DC Q 20 " model vdw 1.244 3.640 nonbonded pdb=" N1 A P 31 " pdb=" N4 DC Q 20 " model vdw 1.246 3.200 nonbonded pdb=" N1 A P 31 " pdb=" C4 DC Q 20 " model vdw 1.355 3.340 ... (remaining 185379 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 '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: 0.730 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: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 51.010 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.007 0.108 21690 Z= 0.429 Angle : 1.120 16.808 29970 Z= 0.680 Chirality : 0.071 1.411 3474 Planarity : 0.007 0.142 3433 Dihedral : 22.140 171.731 8368 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.68 % Favored : 92.77 % Rotamer: Outliers : 2.60 % Allowed : 27.83 % Favored : 69.57 % Cbeta Deviations : 0.14 % 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: -3.09 (0.15), residues: 2379 helix: -2.54 (0.16), residues: 658 sheet: -0.82 (0.24), residues: 438 loop : -2.24 (0.15), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 28 HIS 0.020 0.002 HIS G 225 PHE 0.044 0.002 PHE G 150 TYR 0.045 0.003 TYR H 81 ARG 0.012 0.001 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 395 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.7018 (mm) cc_final: 0.6737 (mm) REVERT: A 137 TYR cc_start: 0.8286 (m-10) cc_final: 0.8048 (m-10) REVERT: A 158 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7701 (mmmt) REVERT: A 159 MET cc_start: 0.8573 (mtp) cc_final: 0.8245 (mtp) REVERT: B 26 MET cc_start: 0.8717 (tpt) cc_final: 0.8184 (tpt) REVERT: B 108 ASP cc_start: 0.8457 (m-30) cc_final: 0.8248 (m-30) REVERT: B 146 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: B 155 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8274 (ptm) REVERT: B 172 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: B 197 HIS cc_start: 0.7781 (m170) cc_final: 0.7474 (m90) REVERT: B 214 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7765 (mtm) REVERT: C 38 MET cc_start: 0.7775 (mmm) cc_final: 0.7412 (mmp) REVERT: C 191 MET cc_start: 0.8220 (mtm) cc_final: 0.8009 (mtm) REVERT: C 224 MET cc_start: 0.8468 (mtp) cc_final: 0.8264 (mtp) REVERT: D 5 LYS cc_start: 0.7848 (mppt) cc_final: 0.7556 (mmtm) REVERT: D 217 ASP cc_start: 0.7005 (p0) cc_final: 0.6750 (p0) REVERT: E 204 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7389 (mt-10) REVERT: E 289 MET cc_start: 0.8424 (mtm) cc_final: 0.8219 (mtm) REVERT: F 117 TYR cc_start: 0.6839 (t80) cc_final: 0.6223 (t80) REVERT: F 148 GLN cc_start: 0.7991 (pt0) cc_final: 0.7658 (pt0) REVERT: F 172 MET cc_start: 0.8561 (mtt) cc_final: 0.8361 (mtt) REVERT: G 63 GLN cc_start: 0.5462 (pm20) cc_final: 0.5077 (pm20) REVERT: G 200 PHE cc_start: 0.7796 (m-80) cc_final: 0.7536 (m-80) REVERT: H 156 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.6539 (tt) outliers start: 51 outliers final: 10 residues processed: 423 average time/residue: 0.3452 time to fit residues: 229.8518 Evaluate side-chains 281 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 265 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 226 optimal weight: 0.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 63 GLN D 109 ASN D 227 GLN E 61 ASN E 63 GLN E 146 ASN F 61 ASN F 63 GLN G 258 ASN H 189 HIS H 214 GLN I 47 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21690 Z= 0.223 Angle : 0.643 7.921 29970 Z= 0.357 Chirality : 0.044 0.277 3474 Planarity : 0.006 0.133 3433 Dihedral : 21.568 179.931 4261 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.25 % Favored : 94.49 % Rotamer: Outliers : 3.47 % Allowed : 25.43 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -2.58 (0.16), residues: 2379 helix: -1.84 (0.17), residues: 682 sheet: -0.87 (0.24), residues: 475 loop : -1.96 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 239 HIS 0.006 0.001 HIS A 134 PHE 0.022 0.001 PHE B 64 TYR 0.021 0.001 TYR H 117 ARG 0.005 0.001 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 301 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.8611 (m-10) cc_final: 0.8312 (m-10) REVERT: A 142 GLN cc_start: 0.8685 (tp40) cc_final: 0.8456 (tp40) REVERT: A 158 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7911 (mmmt) REVERT: B 26 MET cc_start: 0.8668 (tpt) cc_final: 0.8267 (tpt) REVERT: B 213 THR cc_start: 0.8741 (t) cc_final: 0.8459 (t) REVERT: B 214 MET cc_start: 0.8535 (mmm) cc_final: 0.8031 (mmm) REVERT: C 191 MET cc_start: 0.8320 (mtm) cc_final: 0.8044 (mtm) REVERT: C 275 ASP cc_start: 0.8006 (m-30) cc_final: 0.7223 (m-30) REVERT: D 5 LYS cc_start: 0.7802 (mppt) cc_final: 0.7532 (mmtm) REVERT: D 217 ASP cc_start: 0.7340 (p0) cc_final: 0.7050 (p0) REVERT: E 204 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7307 (mt-10) REVERT: E 245 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7527 (t) REVERT: F 5 LYS cc_start: 0.7888 (tttp) cc_final: 0.7647 (mtpp) REVERT: F 99 TYR cc_start: 0.8775 (t80) cc_final: 0.8567 (t80) REVERT: H 78 LEU cc_start: 0.7532 (tp) cc_final: 0.7185 (tp) outliers start: 68 outliers final: 27 residues processed: 347 average time/residue: 0.3238 time to fit residues: 179.1178 Evaluate side-chains 280 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 239 TRP Chi-restraints excluded: chain I residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 226 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 151 ASN B 180 GLN E 17 ASN E 33 ASN F 63 GLN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 21690 Z= 0.402 Angle : 0.678 9.057 29970 Z= 0.370 Chirality : 0.046 0.252 3474 Planarity : 0.005 0.137 3433 Dihedral : 21.328 178.194 4233 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.80 % Favored : 93.99 % Rotamer: Outliers : 4.28 % Allowed : 24.72 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -2.21 (0.16), residues: 2379 helix: -1.25 (0.19), residues: 652 sheet: -0.89 (0.24), residues: 443 loop : -1.80 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 239 HIS 0.007 0.002 HIS B 197 PHE 0.018 0.002 PHE B 64 TYR 0.020 0.002 TYR E 190 ARG 0.006 0.001 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 248 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.8798 (m-10) cc_final: 0.8522 (m-10) REVERT: B 26 MET cc_start: 0.8905 (tpt) cc_final: 0.8389 (tpt) REVERT: B 62 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8147 (p) REVERT: B 182 MET cc_start: 0.8753 (ttp) cc_final: 0.8199 (ttp) REVERT: C 5 LYS cc_start: 0.6193 (tmtt) cc_final: 0.5954 (tmtt) REVERT: C 121 TYR cc_start: 0.8814 (t80) cc_final: 0.7980 (t80) REVERT: D 5 LYS cc_start: 0.7998 (mppt) cc_final: 0.7683 (mmtm) REVERT: D 133 ARG cc_start: 0.8674 (mtp85) cc_final: 0.8390 (mtp85) REVERT: E 61 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8850 (p0) REVERT: E 204 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7678 (mm-30) REVERT: F 5 LYS cc_start: 0.8152 (tttp) cc_final: 0.7930 (mtpp) REVERT: F 99 TYR cc_start: 0.8817 (t80) cc_final: 0.8487 (t80) REVERT: G 235 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7863 (p) REVERT: G 262 TYR cc_start: 0.8653 (m-80) cc_final: 0.8334 (m-80) REVERT: H 224 MET cc_start: 0.7759 (tpt) cc_final: 0.7429 (tpp) REVERT: I 135 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.4995 (t) outliers start: 84 outliers final: 48 residues processed: 308 average time/residue: 0.3248 time to fit residues: 159.0540 Evaluate side-chains 274 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 227 optimal weight: 30.0000 chunk 240 optimal weight: 30.0000 chunk 118 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN B 180 GLN D 63 GLN D 158 ASN E 61 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN G 203 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21690 Z= 0.261 Angle : 0.607 8.909 29970 Z= 0.332 Chirality : 0.043 0.284 3474 Planarity : 0.005 0.137 3433 Dihedral : 21.307 178.957 4226 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.46 % Favored : 94.33 % Rotamer: Outliers : 3.72 % Allowed : 25.48 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -2.02 (0.16), residues: 2379 helix: -0.96 (0.19), residues: 648 sheet: -0.88 (0.24), residues: 454 loop : -1.71 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 239 HIS 0.006 0.001 HIS B 197 PHE 0.012 0.001 PHE B 64 TYR 0.014 0.001 TYR H 117 ARG 0.003 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 137 TYR cc_start: 0.8814 (m-10) cc_final: 0.8443 (m-10) REVERT: B 26 MET cc_start: 0.8917 (tpt) cc_final: 0.8309 (tpt) REVERT: B 62 SER cc_start: 0.8531 (t) cc_final: 0.8172 (p) REVERT: B 214 MET cc_start: 0.8261 (mmm) cc_final: 0.8030 (mmm) REVERT: C 5 LYS cc_start: 0.6343 (tmtt) cc_final: 0.6050 (tmtt) REVERT: C 121 TYR cc_start: 0.8769 (t80) cc_final: 0.7951 (t80) REVERT: C 275 ASP cc_start: 0.7871 (m-30) cc_final: 0.7439 (m-30) REVERT: D 5 LYS cc_start: 0.7963 (mppt) cc_final: 0.7683 (mmtm) REVERT: D 38 MET cc_start: 0.8608 (mmt) cc_final: 0.7998 (mmt) REVERT: E 204 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7640 (mm-30) REVERT: F 5 LYS cc_start: 0.8023 (tttp) cc_final: 0.7811 (mtpp) REVERT: F 99 TYR cc_start: 0.8847 (t80) cc_final: 0.8563 (t80) REVERT: G 235 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7852 (p) REVERT: G 262 TYR cc_start: 0.8620 (m-80) cc_final: 0.8332 (m-80) REVERT: H 38 MET cc_start: 0.7508 (mmm) cc_final: 0.7022 (mmm) REVERT: H 118 ARG cc_start: 0.6995 (ttm-80) cc_final: 0.6784 (ttm170) REVERT: H 224 MET cc_start: 0.7834 (tpt) cc_final: 0.7614 (tpp) outliers start: 73 outliers final: 42 residues processed: 289 average time/residue: 0.3297 time to fit residues: 150.5362 Evaluate side-chains 269 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN D 63 GLN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21690 Z= 0.278 Angle : 0.603 9.385 29970 Z= 0.328 Chirality : 0.043 0.250 3474 Planarity : 0.005 0.135 3433 Dihedral : 21.258 179.023 4225 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.55 % Favored : 94.24 % Rotamer: Outliers : 3.57 % Allowed : 25.38 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.81 (0.16), residues: 2379 helix: -0.72 (0.19), residues: 645 sheet: -0.61 (0.26), residues: 411 loop : -1.66 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 239 HIS 0.006 0.001 HIS B 197 PHE 0.023 0.001 PHE B 202 TYR 0.014 0.001 TYR H 117 ARG 0.007 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 236 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7981 (tp) REVERT: A 137 TYR cc_start: 0.8778 (m-10) cc_final: 0.8425 (m-10) REVERT: B 26 MET cc_start: 0.8925 (tpt) cc_final: 0.8345 (tpt) REVERT: B 62 SER cc_start: 0.8520 (t) cc_final: 0.8167 (p) REVERT: B 108 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8163 (m-30) REVERT: B 182 MET cc_start: 0.8838 (ttp) cc_final: 0.8622 (ttp) REVERT: C 5 LYS cc_start: 0.6366 (tmtt) cc_final: 0.6078 (tmtt) REVERT: C 121 TYR cc_start: 0.8815 (t80) cc_final: 0.7955 (t80) REVERT: C 183 VAL cc_start: 0.8792 (m) cc_final: 0.8548 (p) REVERT: C 214 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: C 275 ASP cc_start: 0.7920 (m-30) cc_final: 0.7496 (m-30) REVERT: D 5 LYS cc_start: 0.7983 (mppt) cc_final: 0.7758 (mmtm) REVERT: D 227 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8241 (pt0) REVERT: E 204 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7617 (mm-30) REVERT: F 5 LYS cc_start: 0.8007 (tttp) cc_final: 0.7798 (mtpp) REVERT: F 99 TYR cc_start: 0.8830 (t80) cc_final: 0.8595 (t80) REVERT: G 235 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7859 (p) REVERT: G 262 TYR cc_start: 0.8664 (m-80) cc_final: 0.8434 (m-80) REVERT: H 38 MET cc_start: 0.7517 (mmm) cc_final: 0.7016 (mmm) REVERT: H 118 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6875 (ttm170) outliers start: 70 outliers final: 46 residues processed: 287 average time/residue: 0.3165 time to fit residues: 146.0550 Evaluate side-chains 280 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 240 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN D 63 GLN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN G 221 GLN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21690 Z= 0.199 Angle : 0.573 9.113 29970 Z= 0.313 Chirality : 0.042 0.239 3474 Planarity : 0.005 0.133 3433 Dihedral : 21.220 179.558 4225 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.46 % Favored : 94.33 % Rotamer: Outliers : 3.36 % Allowed : 25.79 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.64 (0.16), residues: 2379 helix: -0.53 (0.20), residues: 645 sheet: -0.58 (0.26), residues: 401 loop : -1.54 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 239 HIS 0.006 0.001 HIS B 197 PHE 0.024 0.001 PHE B 202 TYR 0.015 0.001 TYR H 117 ARG 0.005 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7712 (t0) cc_final: 0.7314 (t0) REVERT: A 137 TYR cc_start: 0.8748 (m-10) cc_final: 0.8343 (m-10) REVERT: B 26 MET cc_start: 0.8865 (tpt) cc_final: 0.8262 (tpt) REVERT: B 52 TYR cc_start: 0.8820 (p90) cc_final: 0.8585 (p90) REVERT: B 62 SER cc_start: 0.8432 (t) cc_final: 0.8041 (p) REVERT: B 108 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: B 182 MET cc_start: 0.8955 (ttp) cc_final: 0.8293 (ttp) REVERT: C 5 LYS cc_start: 0.6424 (tmtt) cc_final: 0.6078 (tmtt) REVERT: C 121 TYR cc_start: 0.8759 (t80) cc_final: 0.7906 (t80) REVERT: C 183 VAL cc_start: 0.8528 (m) cc_final: 0.8281 (p) REVERT: C 214 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: C 275 ASP cc_start: 0.7938 (m-30) cc_final: 0.7595 (m-30) REVERT: D 5 LYS cc_start: 0.7925 (mppt) cc_final: 0.7673 (mmtm) REVERT: D 227 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: E 61 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8458 (p0) REVERT: E 202 SER cc_start: 0.8839 (p) cc_final: 0.8553 (p) REVERT: E 204 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7593 (mm-30) REVERT: F 5 LYS cc_start: 0.7952 (tttp) cc_final: 0.7743 (mtpp) REVERT: F 99 TYR cc_start: 0.8791 (t80) cc_final: 0.8535 (t80) REVERT: F 148 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: G 235 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7857 (p) REVERT: G 262 TYR cc_start: 0.8621 (m-80) cc_final: 0.8406 (m-80) REVERT: H 38 MET cc_start: 0.7494 (mmm) cc_final: 0.6987 (mmm) REVERT: H 169 ILE cc_start: 0.6774 (tt) cc_final: 0.6524 (tp) outliers start: 66 outliers final: 47 residues processed: 301 average time/residue: 0.3280 time to fit residues: 160.0195 Evaluate side-chains 293 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 137 optimal weight: 0.0010 chunk 175 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 239 optimal weight: 0.0050 chunk 150 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN F 33 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21690 Z= 0.196 Angle : 0.570 9.221 29970 Z= 0.310 Chirality : 0.042 0.227 3474 Planarity : 0.005 0.132 3433 Dihedral : 21.171 179.903 4225 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.96 % Favored : 94.83 % Rotamer: Outliers : 3.31 % Allowed : 26.30 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.50 (0.17), residues: 2379 helix: -0.38 (0.20), residues: 645 sheet: -0.50 (0.26), residues: 401 loop : -1.48 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 PHE 0.026 0.001 PHE B 202 TYR 0.015 0.001 TYR H 117 ARG 0.005 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 242 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7660 (t0) cc_final: 0.7316 (t0) REVERT: A 137 TYR cc_start: 0.8691 (m-10) cc_final: 0.8249 (m-10) REVERT: B 26 MET cc_start: 0.8880 (tpt) cc_final: 0.8266 (tpt) REVERT: B 62 SER cc_start: 0.8415 (t) cc_final: 0.8044 (p) REVERT: B 108 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: B 182 MET cc_start: 0.8861 (ttp) cc_final: 0.8204 (ttp) REVERT: C 5 LYS cc_start: 0.6435 (tmtt) cc_final: 0.6059 (tmtt) REVERT: C 121 TYR cc_start: 0.8757 (t80) cc_final: 0.7894 (t80) REVERT: C 183 VAL cc_start: 0.8467 (m) cc_final: 0.8254 (p) REVERT: C 214 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: C 275 ASP cc_start: 0.7933 (m-30) cc_final: 0.7614 (m-30) REVERT: C 301 PHE cc_start: 0.7921 (m-10) cc_final: 0.7647 (m-10) REVERT: D 5 LYS cc_start: 0.7918 (mppt) cc_final: 0.7672 (mmtm) REVERT: D 131 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8181 (ttt90) REVERT: D 227 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: E 202 SER cc_start: 0.8824 (p) cc_final: 0.8542 (p) REVERT: E 204 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7605 (mm-30) REVERT: F 5 LYS cc_start: 0.7752 (tttp) cc_final: 0.7521 (mtpp) REVERT: F 148 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: G 235 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7771 (p) REVERT: H 38 MET cc_start: 0.7530 (mmm) cc_final: 0.7018 (mmm) REVERT: H 78 LEU cc_start: 0.7832 (tp) cc_final: 0.7575 (tp) REVERT: H 169 ILE cc_start: 0.6639 (tt) cc_final: 0.6331 (tp) outliers start: 65 outliers final: 51 residues processed: 288 average time/residue: 0.3166 time to fit residues: 145.6709 Evaluate side-chains 293 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN E 61 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21690 Z= 0.234 Angle : 0.578 9.269 29970 Z= 0.314 Chirality : 0.042 0.225 3474 Planarity : 0.005 0.131 3433 Dihedral : 21.159 179.878 4225 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.46 % Favored : 94.37 % Rotamer: Outliers : 3.41 % Allowed : 26.35 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.46 (0.17), residues: 2379 helix: -0.26 (0.20), residues: 633 sheet: -0.65 (0.26), residues: 425 loop : -1.43 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 PHE 0.026 0.001 PHE B 202 TYR 0.015 0.001 TYR H 117 ARG 0.005 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 245 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7691 (t0) cc_final: 0.7348 (t0) REVERT: A 137 TYR cc_start: 0.8660 (m-10) cc_final: 0.8215 (m-10) REVERT: B 26 MET cc_start: 0.8868 (tpt) cc_final: 0.8314 (tpt) REVERT: B 62 SER cc_start: 0.8426 (t) cc_final: 0.8058 (p) REVERT: B 108 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8263 (m-30) REVERT: B 182 MET cc_start: 0.8851 (ttp) cc_final: 0.8645 (ttp) REVERT: B 214 MET cc_start: 0.8129 (mmm) cc_final: 0.7874 (mmm) REVERT: C 121 TYR cc_start: 0.8762 (t80) cc_final: 0.7881 (t80) REVERT: C 183 VAL cc_start: 0.8575 (m) cc_final: 0.8363 (p) REVERT: C 214 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: C 275 ASP cc_start: 0.7866 (m-30) cc_final: 0.7489 (m-30) REVERT: C 301 PHE cc_start: 0.7972 (m-10) cc_final: 0.7719 (m-10) REVERT: D 5 LYS cc_start: 0.7930 (mppt) cc_final: 0.7658 (mmtm) REVERT: D 38 MET cc_start: 0.8514 (mmt) cc_final: 0.7997 (mmp) REVERT: D 131 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8204 (ttt90) REVERT: D 227 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8134 (pt0) REVERT: E 202 SER cc_start: 0.8856 (p) cc_final: 0.8589 (p) REVERT: E 204 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7611 (mm-30) REVERT: F 5 LYS cc_start: 0.7901 (tttp) cc_final: 0.7673 (mtpp) REVERT: G 235 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7865 (p) REVERT: H 38 MET cc_start: 0.7499 (mmm) cc_final: 0.6974 (mmm) REVERT: H 78 LEU cc_start: 0.7797 (tp) cc_final: 0.7555 (tp) REVERT: H 169 ILE cc_start: 0.6613 (tt) cc_final: 0.5743 (mt) outliers start: 67 outliers final: 55 residues processed: 290 average time/residue: 0.3202 time to fit residues: 149.8210 Evaluate side-chains 299 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 239 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 7.9990 chunk 229 optimal weight: 20.0000 chunk 209 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 0.2980 chunk 211 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN F 33 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21690 Z= 0.214 Angle : 0.575 9.398 29970 Z= 0.310 Chirality : 0.042 0.223 3474 Planarity : 0.005 0.130 3433 Dihedral : 21.154 179.524 4225 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.17 % Favored : 94.66 % Rotamer: Outliers : 3.47 % Allowed : 26.20 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.39 (0.17), residues: 2379 helix: -0.21 (0.20), residues: 633 sheet: -0.62 (0.26), residues: 425 loop : -1.39 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 PHE 0.027 0.001 PHE B 202 TYR 0.016 0.001 TYR H 117 ARG 0.005 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 242 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7696 (t0) cc_final: 0.7335 (t0) REVERT: A 137 TYR cc_start: 0.8643 (m-10) cc_final: 0.8214 (m-10) REVERT: B 26 MET cc_start: 0.8818 (tpt) cc_final: 0.8313 (tpt) REVERT: B 62 SER cc_start: 0.8422 (t) cc_final: 0.8056 (p) REVERT: B 108 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: B 182 MET cc_start: 0.8853 (ttp) cc_final: 0.8171 (ttp) REVERT: B 198 MET cc_start: 0.8371 (mmm) cc_final: 0.8145 (tpt) REVERT: B 214 MET cc_start: 0.8131 (mmm) cc_final: 0.7910 (mmm) REVERT: C 5 LYS cc_start: 0.6217 (tmtt) cc_final: 0.5804 (tmtt) REVERT: C 121 TYR cc_start: 0.8743 (t80) cc_final: 0.7866 (t80) REVERT: C 183 VAL cc_start: 0.8563 (m) cc_final: 0.8347 (p) REVERT: C 214 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: C 275 ASP cc_start: 0.7908 (m-30) cc_final: 0.7597 (m-30) REVERT: C 301 PHE cc_start: 0.7990 (m-10) cc_final: 0.7747 (m-10) REVERT: D 5 LYS cc_start: 0.7924 (mppt) cc_final: 0.7660 (mmtm) REVERT: D 38 MET cc_start: 0.8468 (mmt) cc_final: 0.7858 (mmp) REVERT: D 131 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8227 (ttt90) REVERT: D 227 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: D 257 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7880 (mtt90) REVERT: E 202 SER cc_start: 0.8834 (p) cc_final: 0.8566 (p) REVERT: E 204 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7618 (mm-30) REVERT: F 5 LYS cc_start: 0.7871 (tttp) cc_final: 0.7639 (mtpp) REVERT: G 235 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7855 (p) REVERT: G 262 TYR cc_start: 0.8713 (m-80) cc_final: 0.8396 (m-80) REVERT: H 38 MET cc_start: 0.7384 (mmm) cc_final: 0.6897 (mmm) REVERT: H 169 ILE cc_start: 0.6679 (tt) cc_final: 0.6414 (tp) REVERT: H 221 GLN cc_start: 0.8467 (tt0) cc_final: 0.8252 (tt0) REVERT: H 263 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7806 (mtp85) outliers start: 68 outliers final: 58 residues processed: 288 average time/residue: 0.3098 time to fit residues: 144.2110 Evaluate side-chains 305 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 144 optimal weight: 0.3980 chunk 112 optimal weight: 0.5980 chunk 164 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 180 GLN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21690 Z= 0.210 Angle : 0.572 9.533 29970 Z= 0.309 Chirality : 0.042 0.221 3474 Planarity : 0.005 0.129 3433 Dihedral : 21.138 179.216 4225 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 3.41 % Allowed : 26.20 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.35 (0.17), residues: 2379 helix: -0.18 (0.20), residues: 633 sheet: -0.60 (0.26), residues: 425 loop : -1.35 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 PHE 0.028 0.001 PHE B 202 TYR 0.023 0.001 TYR H 81 ARG 0.005 0.000 ARG D 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 244 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7697 (t0) cc_final: 0.7480 (t0) REVERT: A 137 TYR cc_start: 0.8590 (m-10) cc_final: 0.8095 (m-10) REVERT: B 26 MET cc_start: 0.8824 (tpt) cc_final: 0.8334 (tpt) REVERT: B 62 SER cc_start: 0.8424 (t) cc_final: 0.8062 (p) REVERT: B 108 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: B 182 MET cc_start: 0.8821 (ttp) cc_final: 0.8122 (ttp) REVERT: B 214 MET cc_start: 0.8122 (mmm) cc_final: 0.7912 (mmm) REVERT: C 5 LYS cc_start: 0.6228 (tmtt) cc_final: 0.5819 (tmtt) REVERT: C 121 TYR cc_start: 0.8736 (t80) cc_final: 0.7854 (t80) REVERT: C 183 VAL cc_start: 0.8536 (m) cc_final: 0.8318 (p) REVERT: C 214 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: C 275 ASP cc_start: 0.7917 (m-30) cc_final: 0.7604 (m-30) REVERT: C 301 PHE cc_start: 0.8001 (m-10) cc_final: 0.7768 (m-10) REVERT: D 5 LYS cc_start: 0.7912 (mppt) cc_final: 0.7686 (mmtm) REVERT: D 38 MET cc_start: 0.8449 (mmt) cc_final: 0.7844 (mmp) REVERT: D 131 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8215 (ttt90) REVERT: D 227 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8137 (pt0) REVERT: D 257 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7890 (mtt90) REVERT: E 202 SER cc_start: 0.8825 (p) cc_final: 0.8545 (p) REVERT: E 204 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7610 (mm-30) REVERT: F 5 LYS cc_start: 0.7882 (tttp) cc_final: 0.7619 (mtpp) REVERT: F 148 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7945 (pt0) REVERT: G 235 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7853 (p) REVERT: G 262 TYR cc_start: 0.8710 (m-80) cc_final: 0.8395 (m-80) REVERT: H 38 MET cc_start: 0.7344 (mmm) cc_final: 0.6861 (mmm) REVERT: H 169 ILE cc_start: 0.6617 (tt) cc_final: 0.6327 (tp) REVERT: H 263 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7803 (mtp85) outliers start: 67 outliers final: 58 residues processed: 290 average time/residue: 0.3084 time to fit residues: 143.3668 Evaluate side-chains 304 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 240 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 0.0030 chunk 210 optimal weight: 20.0000 chunk 60 optimal weight: 0.0040 chunk 182 optimal weight: 7.9990 chunk 29 optimal weight: 0.0060 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 chunk 82 optimal weight: 0.0570 chunk 203 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.1336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN G 288 GLN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.161797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119504 restraints weight = 29235.864| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.77 r_work: 0.3225 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3360 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: