Starting phenix.real_space_refine (version: dev) on Mon Dec 19 20:18:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/12_2022/8ane_15540.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/12_2022/8ane_15540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/12_2022/8ane_15540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/12_2022/8ane_15540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/12_2022/8ane_15540.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/12_2022/8ane_15540.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 41": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 36740 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 295} Chain: "B" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "C" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "D" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "E" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "F" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "G" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "R" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 2104 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 18, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 26, 'rna3p': 39} Time building chain proxies: 16.47, per 1000 atoms: 0.45 Number of scatterers: 36740 At special positions: 0 Unit cell: (117.936, 156.24, 168.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 66 15.00 O 3624 8.00 N 3263 7.00 C 11536 6.00 H 18195 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.65 Conformation dependent library (CDL) restraints added in 2.8 seconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4088 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 36 sheets defined 36.5% alpha, 20.1% beta 2 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 15.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.667A pdb=" N LEU A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.523A pdb=" N GLU A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 removed outlier: 4.007A pdb=" N ASP A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 157 through 164 removed outlier: 5.816A pdb=" N GLY A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A 163 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.960A pdb=" N ALA A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'B' and resid 3 through 9 Processing helix chain 'B' and resid 53 through 65 removed outlier: 3.688A pdb=" N ASN B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 removed outlier: 3.866A pdb=" N ASP B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N MET B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.522A pdb=" N VAL B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 removed outlier: 3.540A pdb=" N VAL B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.957A pdb=" N ILE B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 257 removed outlier: 3.963A pdb=" N VAL B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 301 removed outlier: 3.524A pdb=" N ALA B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 53 through 64 removed outlier: 3.568A pdb=" N THR C 63 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.828A pdb=" N ASP C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 128 removed outlier: 3.708A pdb=" N GLU C 128 " --> pdb=" O ALA C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 128' Processing helix chain 'C' and resid 133 through 145 removed outlier: 3.513A pdb=" N VAL C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.508A pdb=" N ARG C 164 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.855A pdb=" N GLY C 233 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 257 Processing helix chain 'C' and resid 283 through 301 Proline residue: C 292 - end of helix Processing helix chain 'D' and resid 3 through 10 removed outlier: 3.573A pdb=" N ASP D 9 " --> pdb=" O PRO D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 65 removed outlier: 4.256A pdb=" N CYS D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 114 through 125 removed outlier: 4.373A pdb=" N ASP D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.581A pdb=" N HIS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.672A pdb=" N ILE D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 254 Processing helix chain 'D' and resid 283 through 301 Proline residue: D 292 - end of helix Processing helix chain 'E' and resid 3 through 10 removed outlier: 3.551A pdb=" N LEU E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 Processing helix chain 'E' and resid 75 through 78 Processing helix chain 'E' and resid 101 through 105 Processing helix chain 'E' and resid 114 through 128 removed outlier: 5.164A pdb=" N GLU E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N HIS E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 145 through 152 removed outlier: 4.051A pdb=" N VAL E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 150 " --> pdb=" O ALA E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 198 through 202 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 236 through 254 Processing helix chain 'E' and resid 283 through 301 Proline residue: E 292 - end of helix Processing helix chain 'F' and resid 3 through 8 removed outlier: 3.516A pdb=" N SER F 8 " --> pdb=" O PRO F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 64 Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 114 through 125 removed outlier: 3.763A pdb=" N ASP F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'F' and resid 133 through 145 removed outlier: 3.771A pdb=" N VAL F 144 " --> pdb=" O THR F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 198 through 202 removed outlier: 3.768A pdb=" N ARG F 201 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 233 removed outlier: 3.546A pdb=" N GLY F 233 " --> pdb=" O ILE F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 257 Processing helix chain 'F' and resid 283 through 301 Proline residue: F 292 - end of helix Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 53 through 64 removed outlier: 3.782A pdb=" N GLU G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 78 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'G' and resid 117 through 129 removed outlier: 3.759A pdb=" N HIS G 126 " --> pdb=" O GLN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 145 removed outlier: 3.518A pdb=" N LEU G 137 " --> pdb=" O ASP G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 152 removed outlier: 3.731A pdb=" N VAL G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 164 Processing helix chain 'G' and resid 225 through 233 Processing helix chain 'G' and resid 235 through 257 removed outlier: 4.116A pdb=" N VAL G 255 " --> pdb=" O ARG G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 301 Proline residue: G 292 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 52 removed outlier: 6.431A pdb=" N ILE A 175 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG A 217 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 218 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 270 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 20 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N CYS A 268 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.622A pdb=" N ASP A 72 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 4.132A pdb=" N THR A 94 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 310 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 188 Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 41 removed outlier: 4.740A pdb=" N ALA B 38 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE B 175 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG B 217 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 218 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B 14 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 270 " --> pdb=" O ASP B 18 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 20 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N CYS B 268 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB2, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 189 removed outlier: 3.622A pdb=" N VAL B 206 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.601A pdb=" N ALA C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 178 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG C 217 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE C 218 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C 14 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 270 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL C 20 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N CYS C 268 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AB6, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AB7, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 189 removed outlier: 3.742A pdb=" N VAL C 206 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.630A pdb=" N ILE D 175 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG D 217 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D 218 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 14 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP D 18 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA D 270 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL D 20 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N CYS D 268 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.638A pdb=" N VAL D 82 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL D 312 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS D 84 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC3, first strand: chain 'D' and resid 181 through 189 Processing sheet with id=AC4, first strand: chain 'E' and resid 39 through 41 removed outlier: 7.137A pdb=" N ILE E 175 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG E 217 " --> pdb=" O GLU E 178 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE E 218 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU E 14 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA E 270 " --> pdb=" O ASP E 18 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL E 20 " --> pdb=" O CYS E 268 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N CYS E 268 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 261 " --> pdb=" O CYS E 264 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU E 266 " --> pdb=" O ARG E 259 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG E 259 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=AC6, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=AC7, first strand: chain 'E' and resid 92 through 95 Processing sheet with id=AC8, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC9, first strand: chain 'E' and resid 187 through 188 Processing sheet with id=AD1, first strand: chain 'F' and resid 39 through 41 removed outlier: 7.158A pdb=" N ILE F 175 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG F 217 " --> pdb=" O GLU F 178 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE F 218 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU F 14 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL F 273 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU F 16 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU F 271 " --> pdb=" O GLU F 16 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP F 18 " --> pdb=" O GLN F 269 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 92 through 95 removed outlier: 3.517A pdb=" N THR F 94 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AD4, first strand: chain 'F' and resid 181 through 188 Processing sheet with id=AD5, first strand: chain 'G' and resid 39 through 41 removed outlier: 6.636A pdb=" N ILE G 175 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 178 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG G 217 " --> pdb=" O GLU G 178 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE G 218 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU G 14 " --> pdb=" O THR G 274 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA G 270 " --> pdb=" O ASP G 18 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL G 20 " --> pdb=" O CYS G 268 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N CYS G 268 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU G 266 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 259 " --> pdb=" O LEU G 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 26 through 27 removed outlier: 3.600A pdb=" N PHE G 27 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR G 213 " --> pdb=" O PHE G 27 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 66 through 67 removed outlier: 3.693A pdb=" N ASP G 72 " --> pdb=" O ASP G 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 94 through 95 Processing sheet with id=AD9, first strand: chain 'G' and resid 153 through 154 720 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 15.01 Time building geometry restraints manager: 31.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 5982 1.05 - 1.24: 14392 1.24 - 1.43: 5683 1.43 - 1.62: 11088 1.62 - 1.81: 91 Bond restraints: 37236 Sorted by residual: bond pdb=" NE1 TRP C 279 " pdb=" HE1 TRP C 279 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP F 66 " pdb=" HE1 TRP F 66 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP F 73 " pdb=" HE1 TRP F 73 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP G 279 " pdb=" HE1 TRP G 279 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 66 " pdb=" HE1 TRP D 66 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 ... (remaining 37231 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.41: 1055 105.41 - 112.56: 43359 112.56 - 119.71: 9788 119.71 - 126.86: 13109 126.86 - 134.01: 385 Bond angle restraints: 67696 Sorted by residual: angle pdb=" O4' U R 58 " pdb=" C1' U R 58 " pdb=" C2' U R 58 " ideal model delta sigma weight residual 107.60 102.44 5.16 1.00e+00 1.00e+00 2.66e+01 angle pdb=" N TYR B 40 " pdb=" CA TYR B 40 " pdb=" C TYR B 40 " ideal model delta sigma weight residual 107.88 115.12 -7.24 1.41e+00 5.03e-01 2.64e+01 angle pdb=" C2' U R 58 " pdb=" C1' U R 58 " pdb=" N1 U R 58 " ideal model delta sigma weight residual 112.00 119.68 -7.68 1.50e+00 4.44e-01 2.62e+01 angle pdb=" N THR B 140 " pdb=" CA THR B 140 " pdb=" C THR B 140 " ideal model delta sigma weight residual 111.28 105.93 5.35 1.09e+00 8.42e-01 2.41e+01 angle pdb=" O3' G R 38 " pdb=" C3' G R 38 " pdb=" H3' G R 38 " ideal model delta sigma weight residual 109.00 98.26 10.74 3.00e+00 1.11e-01 1.28e+01 ... (remaining 67691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 14300 35.71 - 71.42: 334 71.42 - 107.14: 27 107.14 - 142.85: 5 142.85 - 178.56: 7 Dihedral angle restraints: 14673 sinusoidal: 7533 harmonic: 7140 Sorted by residual: dihedral pdb=" O4' C R 51 " pdb=" C1' C R 51 " pdb=" N1 C R 51 " pdb=" C2 C R 51 " ideal model delta sinusoidal sigma weight residual 200.00 54.20 145.80 1 1.50e+01 4.44e-03 7.80e+01 dihedral pdb=" O4' U R 33 " pdb=" C1' U R 33 " pdb=" N1 U R 33 " pdb=" C2 U R 33 " ideal model delta sinusoidal sigma weight residual 200.00 59.86 140.14 1 1.50e+01 4.44e-03 7.54e+01 dihedral pdb=" O4' C R 32 " pdb=" C1' C R 32 " pdb=" N1 C R 32 " pdb=" C2 C R 32 " ideal model delta sinusoidal sigma weight residual 200.00 70.42 129.58 1 1.50e+01 4.44e-03 6.99e+01 ... (remaining 14670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2230 0.039 - 0.078: 580 0.078 - 0.118: 163 0.118 - 0.157: 57 0.157 - 0.196: 2 Chirality restraints: 3032 Sorted by residual: chirality pdb=" C3' G R 42 " pdb=" C4' G R 42 " pdb=" O3' G R 42 " pdb=" C2' G R 42 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" C1' C R 29 " pdb=" O4' C R 29 " pdb=" C2' C R 29 " pdb=" N1 C R 29 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 3029 not shown) Planarity restraints: 5295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 136 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C LYS F 136 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS F 136 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU F 137 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 41 " -0.031 2.00e-02 2.50e+03 1.49e-02 6.66e+00 pdb=" N1 U R 41 " 0.033 2.00e-02 2.50e+03 pdb=" C2 U R 41 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U R 41 " 0.006 2.00e-02 2.50e+03 pdb=" N3 U R 41 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U R 41 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U R 41 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U R 41 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U R 41 " 0.008 2.00e-02 2.50e+03 pdb=" H5 U R 41 " 0.002 2.00e-02 2.50e+03 pdb=" H3 U R 41 " -0.013 2.00e-02 2.50e+03 pdb=" H6 U R 41 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 292 " 0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C PRO F 292 " -0.042 2.00e-02 2.50e+03 pdb=" O PRO F 292 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY F 293 " 0.014 2.00e-02 2.50e+03 ... (remaining 5292 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 969 2.05 - 2.69: 52385 2.69 - 3.33: 104952 3.33 - 3.96: 136853 3.96 - 4.60: 207960 Nonbonded interactions: 503119 Sorted by model distance: nonbonded pdb=" HG1 THR E 25 " pdb=" HH TYR F 40 " model vdw 1.419 2.100 nonbonded pdb=" O2 C R 40 " pdb="HO2' C R 40 " model vdw 1.487 1.850 nonbonded pdb="HO2' U R 59 " pdb=" H61 A R 61 " model vdw 1.504 2.100 nonbonded pdb="HD13 LEU E 150 " pdb=" HZ2 LYS E 249 " model vdw 1.542 2.270 nonbonded pdb=" O2 U R 46 " pdb="HO2' U R 46 " model vdw 1.549 1.850 ... (remaining 503114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 66 5.49 5 S 56 5.16 5 C 11536 2.51 5 N 3263 2.21 5 O 3624 1.98 5 H 18195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 1.010 Extract box with map and model: 11.400 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.310 Process input model: 123.990 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4309 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 : 0.003 0.070 19041 Z= 0.183 Angle : 0.645 7.681 26142 Z= 0.342 Chirality : 0.042 0.196 3032 Planarity : 0.006 0.066 3181 Dihedral : 15.689 178.561 7397 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.93 (0.16), residues: 2198 helix: -1.60 (0.17), residues: 675 sheet: 0.71 (0.25), residues: 414 loop : -1.88 (0.17), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 419 time to evaluate : 2.727 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash outliers start: 17 outliers final: 7 residues processed: 429 average time/residue: 0.8410 time to fit residues: 521.3629 Evaluate side-chains 252 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 245 time to evaluate : 3.008 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.6941 time to fit residues: 11.1800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4865 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 19041 Z= 0.265 Angle : 0.691 8.274 26142 Z= 0.351 Chirality : 0.043 0.225 3032 Planarity : 0.006 0.051 3181 Dihedral : 14.540 173.124 3197 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.39 (0.17), residues: 2198 helix: -0.32 (0.19), residues: 692 sheet: 0.31 (0.24), residues: 431 loop : -1.89 (0.18), residues: 1075 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 270 time to evaluate : 2.770 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash outliers start: 34 outliers final: 19 residues processed: 294 average time/residue: 0.7452 time to fit residues: 330.2156 Evaluate side-chains 230 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 211 time to evaluate : 2.753 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.5011 time to fit residues: 20.2285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 269 GLN C 147 ASN C 256 HIS F 55 GLN F 228 GLN F 237 GLN G 101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.112 19041 Z= 0.384 Angle : 0.911 16.942 26142 Z= 0.469 Chirality : 0.052 0.542 3032 Planarity : 0.008 0.082 3181 Dihedral : 15.119 169.905 3197 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.01 % Favored : 92.95 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.27 (0.17), residues: 2198 helix: -0.80 (0.20), residues: 649 sheet: -0.87 (0.23), residues: 476 loop : -2.27 (0.17), residues: 1073 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 266 time to evaluate : 3.006 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 31 residues processed: 318 average time/residue: 0.7577 time to fit residues: 358.2934 Evaluate side-chains 230 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 2.862 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 31 outliers final: 1 residues processed: 31 average time/residue: 0.4631 time to fit residues: 28.9742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 269 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.8046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 19041 Z= 0.272 Angle : 0.701 6.783 26142 Z= 0.361 Chirality : 0.044 0.194 3032 Planarity : 0.006 0.075 3181 Dihedral : 14.725 170.830 3197 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.97 (0.17), residues: 2198 helix: -0.56 (0.20), residues: 663 sheet: -0.48 (0.24), residues: 456 loop : -2.19 (0.17), residues: 1079 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 3.091 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 228 average time/residue: 0.6327 time to fit residues: 230.2490 Evaluate side-chains 197 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 2.719 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4320 time to fit residues: 15.9352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN C 126 HIS ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.9602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 19041 Z= 0.355 Angle : 0.817 8.058 26142 Z= 0.425 Chirality : 0.048 0.308 3032 Planarity : 0.008 0.082 3181 Dihedral : 15.089 171.877 3197 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.28 % Favored : 91.67 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.39 (0.17), residues: 2198 helix: -0.81 (0.20), residues: 656 sheet: -1.02 (0.23), residues: 496 loop : -2.39 (0.17), residues: 1046 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 219 time to evaluate : 2.907 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 29 residues processed: 265 average time/residue: 0.6384 time to fit residues: 265.8153 Evaluate side-chains 206 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 2.759 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.4369 time to fit residues: 25.9812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN E 59 ASN E 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.9867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19041 Z= 0.191 Angle : 0.632 6.544 26142 Z= 0.323 Chirality : 0.041 0.204 3032 Planarity : 0.005 0.061 3181 Dihedral : 14.847 171.980 3197 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.85 (0.18), residues: 2198 helix: -0.21 (0.21), residues: 640 sheet: -0.64 (0.24), residues: 468 loop : -2.16 (0.17), residues: 1090 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 2.813 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 210 average time/residue: 0.6782 time to fit residues: 218.9218 Evaluate side-chains 194 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 2.646 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.5298 time to fit residues: 15.7532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 1.0426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 19041 Z= 0.253 Angle : 0.667 6.576 26142 Z= 0.343 Chirality : 0.042 0.209 3032 Planarity : 0.006 0.057 3181 Dihedral : 14.722 172.794 3197 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.83 (0.18), residues: 2198 helix: -0.26 (0.21), residues: 659 sheet: -0.53 (0.25), residues: 462 loop : -2.17 (0.18), residues: 1077 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 2.793 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 199 average time/residue: 0.6700 time to fit residues: 205.5967 Evaluate side-chains 180 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 2.782 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5074 time to fit residues: 12.5213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 64 optimal weight: 0.0570 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 1.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19041 Z= 0.224 Angle : 0.632 6.868 26142 Z= 0.323 Chirality : 0.041 0.206 3032 Planarity : 0.006 0.064 3181 Dihedral : 14.759 172.581 3197 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.65 (0.18), residues: 2198 helix: 0.01 (0.21), residues: 641 sheet: -0.40 (0.24), residues: 468 loop : -2.14 (0.18), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 2.868 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 191 average time/residue: 0.6598 time to fit residues: 195.8668 Evaluate side-chains 169 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 2.954 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4071 time to fit residues: 9.6572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN D 190 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 1.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 19041 Z= 0.248 Angle : 0.648 6.473 26142 Z= 0.333 Chirality : 0.042 0.198 3032 Planarity : 0.006 0.052 3181 Dihedral : 14.718 172.962 3197 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.37 % Favored : 92.58 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.70 (0.18), residues: 2198 helix: -0.15 (0.21), residues: 656 sheet: -0.40 (0.24), residues: 475 loop : -2.14 (0.18), residues: 1067 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 2.853 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 180 average time/residue: 0.6439 time to fit residues: 183.9895 Evaluate side-chains 164 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 3.007 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4557 time to fit residues: 9.2889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 147 optimal weight: 0.6980 chunk 222 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 1.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 19041 Z= 0.180 Angle : 0.599 6.393 26142 Z= 0.303 Chirality : 0.040 0.190 3032 Planarity : 0.005 0.061 3181 Dihedral : 14.653 172.858 3197 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.48 (0.18), residues: 2198 helix: 0.16 (0.21), residues: 644 sheet: -0.25 (0.25), residues: 467 loop : -2.07 (0.18), residues: 1087 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 2.776 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 167 average time/residue: 0.6114 time to fit residues: 162.3670 Evaluate side-chains 157 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.822 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3838 time to fit residues: 4.2790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.176372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.136805 restraints weight = 78002.249| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.57 r_work: 0.4044 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 1.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 19041 Z= 0.291 Angle : 0.705 7.134 26142 Z= 0.362 Chirality : 0.044 0.178 3032 Planarity : 0.007 0.064 3181 Dihedral : 14.845 172.253 3197 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.96 (0.17), residues: 2198 helix: -0.33 (0.20), residues: 653 sheet: -0.68 (0.24), residues: 496 loop : -2.27 (0.18), residues: 1049 =============================================================================== Job complete usr+sys time: 8435.91 seconds wall clock time: 148 minutes 39.07 seconds (8919.07 seconds total)