Starting phenix.real_space_refine on Sat Mar 23 10:33:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/03_2024/8ane_15540.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/03_2024/8ane_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_15540/03_2024/8ane_15540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/03_2024/8ane_15540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/03_2024/8ane_15540.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ane_15540/03_2024/8ane_15540.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 15.27, per 1000 atoms: 0.42 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: 30.66 Conformation dependent library (CDL) restraints added in 3.5 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: 16.69 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: 14.31 Time building geometry restraints manager: 31.87 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: 16715 35.71 - 71.42: 679 71.42 - 107.14: 46 107.14 - 142.85: 5 142.85 - 178.56: 7 Dihedral angle restraints: 17452 sinusoidal: 10312 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 17449 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.480 Extract box with map and model: 10.510 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 125.180 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.170 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4286 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 : 17.194 178.561 7647 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.93 % Allowed : 8.85 % Favored : 90.22 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 279 HIS 0.006 0.001 HIS G 192 PHE 0.019 0.001 PHE G 208 TYR 0.010 0.001 TYR B 40 ARG 0.004 0.001 ARG A 135 *********************** 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 : 2.536 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 REVERT: A 114 LYS cc_start: 0.1906 (mtmt) cc_final: 0.1384 (mttp) REVERT: B 262 THR cc_start: 0.5108 (t) cc_final: 0.4738 (t) REVERT: C 41 GLU cc_start: 0.5582 (mp0) cc_final: 0.4215 (tt0) REVERT: D 25 THR cc_start: 0.6299 (p) cc_final: 0.6003 (p) REVERT: D 181 ARG cc_start: 0.7008 (mpt-90) cc_final: 0.6600 (mpt180) REVERT: E 1 MET cc_start: 0.1721 (mmm) cc_final: -0.0073 (mpp) REVERT: E 51 VAL cc_start: 0.4340 (t) cc_final: 0.3857 (t) REVERT: E 116 LEU cc_start: 0.7126 (tp) cc_final: 0.6905 (tt) REVERT: F 117 PHE cc_start: 0.5680 (t80) cc_final: 0.5111 (t80) REVERT: F 261 ARG cc_start: 0.4407 (ttm110) cc_final: 0.3505 (mtm-85) REVERT: F 314 TYR cc_start: 0.3125 (t80) cc_final: 0.2318 (t80) REVERT: G 159 GLU cc_start: 0.5774 (mp0) cc_final: 0.5565 (mt-10) REVERT: G 269 GLN cc_start: 0.3818 (mt0) cc_final: 0.3202 (tm-30) outliers start: 17 outliers final: 7 residues processed: 429 average time/residue: 0.8680 time to fit residues: 524.3955 Evaluate side-chains 257 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 250 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 303 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.4915 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 19041 Z= 0.269 Angle : 0.721 8.464 26142 Z= 0.366 Chirality : 0.044 0.231 3032 Planarity : 0.006 0.057 3181 Dihedral : 18.081 171.409 3464 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.09 % Allowed : 13.68 % Favored : 84.23 % 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: -1.43 (0.17), residues: 2198 helix: -0.29 (0.19), residues: 690 sheet: 0.18 (0.24), residues: 431 loop : -1.90 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 279 HIS 0.008 0.001 HIS D 126 PHE 0.016 0.002 PHE G 208 TYR 0.015 0.002 TYR D 221 ARG 0.007 0.001 ARG C 272 *********************** 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 314 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 276 time to evaluate : 2.646 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: A 269 GLN cc_start: 0.2879 (mp10) cc_final: 0.2593 (mp10) REVERT: B 48 MET cc_start: 0.5015 (mmt) cc_final: 0.4033 (ptt) REVERT: B 258 LEU cc_start: 0.6234 (mt) cc_final: 0.6030 (mt) REVERT: C 23 GLN cc_start: 0.6376 (OUTLIER) cc_final: 0.5612 (mm110) REVERT: D 154 PHE cc_start: 0.7136 (t80) cc_final: 0.6688 (t80) REVERT: E 1 MET cc_start: 0.1922 (mmm) cc_final: 0.0023 (mpp) REVERT: E 25 THR cc_start: 0.5503 (p) cc_final: 0.5177 (p) REVERT: E 68 LYS cc_start: 0.4023 (tptp) cc_final: 0.3661 (tptm) REVERT: F 74 VAL cc_start: 0.3272 (m) cc_final: 0.1921 (t) REVERT: F 109 LEU cc_start: 0.5770 (tp) cc_final: 0.5457 (tp) REVERT: F 314 TYR cc_start: 0.3423 (t80) cc_final: 0.2695 (t80) REVERT: G 159 GLU cc_start: 0.5951 (mp0) cc_final: 0.5664 (mt-10) REVERT: G 269 GLN cc_start: 0.3946 (mt0) cc_final: 0.3181 (tm-30) outliers start: 38 outliers final: 22 residues processed: 304 average time/residue: 0.7602 time to fit residues: 339.7935 Evaluate side-chains 237 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 34 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 162 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** C 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5315 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19041 Z= 0.228 Angle : 0.643 7.320 26142 Z= 0.329 Chirality : 0.043 0.196 3032 Planarity : 0.005 0.047 3181 Dihedral : 18.011 171.046 3457 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.03 % Allowed : 14.95 % Favored : 83.02 % 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: -1.34 (0.17), residues: 2198 helix: 0.03 (0.20), residues: 690 sheet: 0.11 (0.24), residues: 423 loop : -1.96 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 73 HIS 0.006 0.001 HIS E 101 PHE 0.011 0.001 PHE E 222 TYR 0.026 0.002 TYR A 213 ARG 0.011 0.001 ARG A 303 *********************** 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 267 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 2.668 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: A 114 LYS cc_start: 0.2545 (mtmt) cc_final: 0.2140 (ptpp) REVERT: B 18 ASP cc_start: 0.4867 (p0) cc_final: 0.4628 (p0) REVERT: B 48 MET cc_start: 0.4423 (mmt) cc_final: 0.3746 (ptt) REVERT: B 143 LYS cc_start: 0.3548 (OUTLIER) cc_final: 0.2767 (mmtt) REVERT: C 180 VAL cc_start: 0.6962 (m) cc_final: 0.6708 (m) REVERT: D 154 PHE cc_start: 0.7477 (t80) cc_final: 0.7211 (t80) REVERT: E 1 MET cc_start: 0.1738 (mmm) cc_final: 0.0032 (mpp) REVERT: E 117 PHE cc_start: 0.7445 (t80) cc_final: 0.7196 (t80) REVERT: F 15 MET cc_start: 0.4697 (mmm) cc_final: 0.4424 (mmm) REVERT: F 314 TYR cc_start: 0.3514 (t80) cc_final: 0.2689 (t80) REVERT: G 85 VAL cc_start: 0.5961 (t) cc_final: 0.5598 (m) REVERT: G 135 ARG cc_start: 0.4781 (mtt-85) cc_final: 0.4468 (mtm180) REVERT: G 159 GLU cc_start: 0.5968 (mp0) cc_final: 0.5687 (mt-10) outliers start: 37 outliers final: 28 residues processed: 261 average time/residue: 0.6876 time to fit residues: 269.4872 Evaluate side-chains 224 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN 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: 2.9990 chunk 105 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 0.0570 chunk 136 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 215 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN F 55 GLN F 228 GLN F 237 GLN G 126 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 19041 Z= 0.329 Angle : 0.754 11.605 26142 Z= 0.386 Chirality : 0.046 0.443 3032 Planarity : 0.007 0.073 3181 Dihedral : 17.898 170.920 3457 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.91 % Allowed : 16.43 % Favored : 80.66 % 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: -1.63 (0.17), residues: 2198 helix: -0.16 (0.20), residues: 662 sheet: -0.42 (0.24), residues: 459 loop : -2.00 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 73 HIS 0.012 0.002 HIS D 126 PHE 0.023 0.002 PHE E 154 TYR 0.026 0.003 TYR G 107 ARG 0.009 0.001 ARG B 166 *********************** 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 289 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 236 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: 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: A 1 MET cc_start: 0.0539 (tpt) cc_final: -0.1806 (mmm) REVERT: B 99 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.4528 (tm-30) REVERT: C 298 VAL cc_start: 0.5082 (t) cc_final: 0.4722 (p) REVERT: C 311 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8003 (mt) REVERT: E 1 MET cc_start: 0.1581 (mmm) cc_final: 0.0021 (mpp) REVERT: E 68 LYS cc_start: 0.3105 (tptp) cc_final: 0.2687 (tptm) REVERT: E 101 HIS cc_start: 0.4914 (OUTLIER) cc_final: 0.2814 (t-170) REVERT: E 117 PHE cc_start: 0.7384 (t80) cc_final: 0.7101 (t80) REVERT: F 109 LEU cc_start: 0.6303 (tp) cc_final: 0.6075 (tp) REVERT: F 181 ARG cc_start: 0.4883 (mpp80) cc_final: 0.4381 (mtt-85) REVERT: G 68 LYS cc_start: 0.6669 (pttt) cc_final: 0.5848 (mmmt) REVERT: G 85 VAL cc_start: 0.6444 (t) cc_final: 0.6116 (m) REVERT: G 135 ARG cc_start: 0.5220 (mtt-85) cc_final: 0.4379 (mtm180) outliers start: 53 outliers final: 33 residues processed: 280 average time/residue: 0.7483 time to fit residues: 308.0396 Evaluate side-chains 222 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 118 ASP 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: 0.8980 chunk 3 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS B 104 ASN E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.8092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19041 Z= 0.252 Angle : 0.659 8.186 26142 Z= 0.337 Chirality : 0.043 0.171 3032 Planarity : 0.006 0.055 3181 Dihedral : 18.002 171.418 3457 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.69 % Allowed : 17.69 % Favored : 79.62 % 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: -1.45 (0.17), residues: 2198 helix: -0.04 (0.21), residues: 666 sheet: -0.29 (0.25), residues: 455 loop : -1.88 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 73 HIS 0.011 0.001 HIS E 101 PHE 0.032 0.002 PHE F 232 TYR 0.010 0.002 TYR F 248 ARG 0.008 0.001 ARG A 303 *********************** 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 255 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 206 time to evaluate : 2.658 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: A 1 MET cc_start: 0.1068 (tpt) cc_final: -0.0439 (mmt) REVERT: B 60 ARG cc_start: 0.6345 (mtt-85) cc_final: 0.5702 (mmt90) REVERT: B 277 GLU cc_start: 0.6722 (mp0) cc_final: 0.6366 (mp0) REVERT: C 23 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.4995 (mt0) REVERT: C 145 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6754 (p0) REVERT: C 298 VAL cc_start: 0.5444 (t) cc_final: 0.5201 (p) REVERT: E 1 MET cc_start: 0.1163 (mmm) cc_final: -0.0210 (mmt) REVERT: E 101 HIS cc_start: 0.4845 (OUTLIER) cc_final: 0.3299 (t-170) REVERT: E 117 PHE cc_start: 0.7403 (t80) cc_final: 0.7108 (t80) REVERT: E 145 ASP cc_start: 0.7477 (p0) cc_final: 0.7002 (p0) REVERT: F 181 ARG cc_start: 0.5218 (mpp80) cc_final: 0.4575 (mtt-85) REVERT: G 68 LYS cc_start: 0.6740 (pttt) cc_final: 0.5905 (mmmt) REVERT: G 85 VAL cc_start: 0.6489 (t) cc_final: 0.6104 (m) REVERT: G 135 ARG cc_start: 0.5099 (mtt-85) cc_final: 0.4762 (mtm180) outliers start: 49 outliers final: 26 residues processed: 249 average time/residue: 0.6832 time to fit residues: 257.0097 Evaluate side-chains 216 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 95 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 215 optimal weight: 0.4980 chunk 179 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.8623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19041 Z= 0.213 Angle : 0.620 6.877 26142 Z= 0.317 Chirality : 0.041 0.201 3032 Planarity : 0.006 0.101 3181 Dihedral : 17.875 172.032 3451 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.69 % Allowed : 18.19 % Favored : 79.12 % 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: -1.35 (0.18), residues: 2198 helix: 0.19 (0.21), residues: 648 sheet: -0.33 (0.25), residues: 468 loop : -1.86 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 66 HIS 0.009 0.001 HIS E 101 PHE 0.012 0.002 PHE E 208 TYR 0.008 0.001 TYR D 221 ARG 0.006 0.001 ARG C 272 *********************** 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 236 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 2.696 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: A 1 MET cc_start: 0.1458 (tpt) cc_final: -0.0484 (mmp) REVERT: B 60 ARG cc_start: 0.6434 (mtt-85) cc_final: 0.5787 (mmt90) REVERT: B 98 LEU cc_start: 0.4916 (OUTLIER) cc_final: 0.4541 (mt) REVERT: B 277 GLU cc_start: 0.6768 (mp0) cc_final: 0.6357 (mp0) REVERT: E 1 MET cc_start: 0.1192 (mmm) cc_final: -0.0511 (mmt) REVERT: E 101 HIS cc_start: 0.5008 (OUTLIER) cc_final: 0.3547 (t-170) REVERT: E 117 PHE cc_start: 0.7379 (t80) cc_final: 0.7088 (t80) REVERT: F 181 ARG cc_start: 0.5406 (mpp80) cc_final: 0.4703 (mtt-85) REVERT: G 68 LYS cc_start: 0.6746 (pttt) cc_final: 0.5914 (mmmt) REVERT: G 85 VAL cc_start: 0.6741 (t) cc_final: 0.6414 (m) REVERT: G 135 ARG cc_start: 0.5355 (mtt-85) cc_final: 0.5009 (mtm180) outliers start: 49 outliers final: 32 residues processed: 231 average time/residue: 0.6891 time to fit residues: 241.6250 Evaluate side-chains 204 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN 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: 4.9990 chunk 122 optimal weight: 0.0980 chunk 157 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.8936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19041 Z= 0.170 Angle : 0.573 6.720 26142 Z= 0.291 Chirality : 0.040 0.184 3032 Planarity : 0.005 0.073 3181 Dihedral : 17.764 172.566 3449 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.36 % Allowed : 18.52 % Favored : 79.12 % 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: -1.12 (0.18), residues: 2198 helix: 0.36 (0.21), residues: 654 sheet: -0.19 (0.25), residues: 468 loop : -1.72 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 73 HIS 0.007 0.001 HIS F 101 PHE 0.013 0.001 PHE C 154 TYR 0.006 0.001 TYR F 248 ARG 0.011 0.001 ARG C 272 *********************** 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 228 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 2.618 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: A 1 MET cc_start: 0.1534 (tpt) cc_final: -0.0489 (mmt) REVERT: B 60 ARG cc_start: 0.6402 (mtt-85) cc_final: 0.5740 (mmt90) REVERT: B 98 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4756 (mt) REVERT: B 112 LYS cc_start: 0.6035 (mmmt) cc_final: 0.5656 (ttmm) REVERT: B 143 LYS cc_start: 0.3689 (OUTLIER) cc_final: 0.2888 (mmtt) REVERT: B 269 GLN cc_start: 0.5452 (mm110) cc_final: 0.5189 (mm110) REVERT: B 277 GLU cc_start: 0.6704 (mp0) cc_final: 0.6339 (mp0) REVERT: C 180 VAL cc_start: 0.7210 (m) cc_final: 0.6984 (m) REVERT: C 298 VAL cc_start: 0.5762 (t) cc_final: 0.5496 (p) REVERT: E 1 MET cc_start: 0.1274 (mmm) cc_final: -0.0493 (mmt) REVERT: E 101 HIS cc_start: 0.4966 (OUTLIER) cc_final: 0.3427 (t-170) REVERT: E 117 PHE cc_start: 0.7423 (t80) cc_final: 0.7158 (t80) REVERT: E 145 ASP cc_start: 0.7340 (p0) cc_final: 0.6912 (p0) REVERT: F 181 ARG cc_start: 0.5438 (mpp80) cc_final: 0.4741 (mtt-85) REVERT: F 212 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5267 (mt-10) REVERT: G 68 LYS cc_start: 0.6722 (pttt) cc_final: 0.5897 (mmmt) REVERT: G 85 VAL cc_start: 0.6699 (t) cc_final: 0.6323 (m) REVERT: G 135 ARG cc_start: 0.5496 (mtt-85) cc_final: 0.5120 (mtm180) outliers start: 43 outliers final: 31 residues processed: 222 average time/residue: 0.7111 time to fit residues: 241.1351 Evaluate side-chains 205 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 0.0030 chunk 128 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 195 optimal weight: 0.0980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 55 GLN B 104 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.9306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19041 Z= 0.179 Angle : 0.573 6.615 26142 Z= 0.291 Chirality : 0.040 0.180 3032 Planarity : 0.005 0.063 3181 Dihedral : 17.686 172.903 3449 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.98 % Allowed : 19.23 % Favored : 78.79 % 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: -0.99 (0.18), residues: 2198 helix: 0.46 (0.21), residues: 654 sheet: 0.02 (0.25), residues: 456 loop : -1.70 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 279 HIS 0.007 0.001 HIS E 101 PHE 0.041 0.001 PHE F 232 TYR 0.016 0.001 TYR B 314 ARG 0.008 0.000 ARG F 169 *********************** 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 222 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 2.700 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: A 1 MET cc_start: 0.1700 (tpt) cc_final: -0.0255 (mmt) REVERT: A 272 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5027 (mtt180) REVERT: B 60 ARG cc_start: 0.6417 (mtt-85) cc_final: 0.5828 (mmt90) REVERT: B 98 LEU cc_start: 0.5106 (OUTLIER) cc_final: 0.4798 (mt) REVERT: B 269 GLN cc_start: 0.5484 (mm110) cc_final: 0.5247 (mm110) REVERT: B 277 GLU cc_start: 0.6683 (mp0) cc_final: 0.6335 (mp0) REVERT: C 180 VAL cc_start: 0.7264 (m) cc_final: 0.7043 (m) REVERT: E 1 MET cc_start: 0.1058 (mmm) cc_final: -0.0417 (mmt) REVERT: E 101 HIS cc_start: 0.5204 (OUTLIER) cc_final: 0.3621 (t-170) REVERT: E 117 PHE cc_start: 0.7438 (t80) cc_final: 0.7213 (t80) REVERT: F 181 ARG cc_start: 0.5479 (mpp80) cc_final: 0.5014 (mtt-85) REVERT: F 212 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5272 (mt-10) REVERT: G 68 LYS cc_start: 0.6669 (pttt) cc_final: 0.5914 (mmmt) REVERT: G 135 ARG cc_start: 0.5511 (mtt-85) cc_final: 0.5206 (mtm180) outliers start: 36 outliers final: 25 residues processed: 218 average time/residue: 0.6777 time to fit residues: 225.9615 Evaluate side-chains 196 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.9696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19041 Z= 0.186 Angle : 0.583 6.664 26142 Z= 0.296 Chirality : 0.040 0.177 3032 Planarity : 0.005 0.059 3181 Dihedral : 17.702 172.758 3449 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 2.47 % Allowed : 18.90 % Favored : 78.63 % 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: -0.94 (0.18), residues: 2198 helix: 0.51 (0.21), residues: 654 sheet: 0.13 (0.25), residues: 452 loop : -1.70 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 279 HIS 0.007 0.001 HIS E 101 PHE 0.013 0.001 PHE F 232 TYR 0.017 0.001 TYR F 314 ARG 0.009 0.000 ARG C 272 *********************** 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 222 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 177 time to evaluate : 2.697 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: A 1 MET cc_start: 0.1466 (tpt) cc_final: -0.0456 (mmt) REVERT: A 176 GLU cc_start: 0.5339 (pp20) cc_final: 0.4810 (mt-10) REVERT: A 208 PHE cc_start: 0.5128 (t80) cc_final: 0.4900 (t80) REVERT: A 272 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.5121 (mtt180) REVERT: B 60 ARG cc_start: 0.6627 (mtt-85) cc_final: 0.6038 (mmt90) REVERT: B 98 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.5170 (mt) REVERT: B 269 GLN cc_start: 0.5629 (mm110) cc_final: 0.5426 (mm110) REVERT: B 277 GLU cc_start: 0.6719 (mp0) cc_final: 0.6390 (mp0) REVERT: C 180 VAL cc_start: 0.7275 (m) cc_final: 0.7055 (m) REVERT: D 83 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.7143 (p) REVERT: E 1 MET cc_start: 0.1006 (mmm) cc_final: -0.0466 (mmt) REVERT: E 101 HIS cc_start: 0.5025 (OUTLIER) cc_final: 0.3421 (t-170) REVERT: E 117 PHE cc_start: 0.7431 (t80) cc_final: 0.7214 (t80) REVERT: F 181 ARG cc_start: 0.5519 (mpp80) cc_final: 0.5073 (mtt-85) REVERT: F 212 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5289 (mt-10) REVERT: G 68 LYS cc_start: 0.6604 (pttt) cc_final: 0.5874 (mmmt) REVERT: G 135 ARG cc_start: 0.5640 (mtt-85) cc_final: 0.5310 (mtm180) outliers start: 45 outliers final: 36 residues processed: 218 average time/residue: 0.6513 time to fit residues: 218.3010 Evaluate side-chains 209 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 D 190 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 1.0170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19041 Z= 0.237 Angle : 0.629 7.788 26142 Z= 0.323 Chirality : 0.042 0.266 3032 Planarity : 0.006 0.056 3181 Dihedral : 17.826 172.536 3449 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.47 % Allowed : 19.23 % Favored : 78.30 % 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: -1.16 (0.18), residues: 2198 helix: 0.28 (0.21), residues: 659 sheet: 0.01 (0.25), residues: 456 loop : -1.82 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 66 HIS 0.010 0.002 HIS E 101 PHE 0.034 0.002 PHE F 232 TYR 0.015 0.002 TYR B 314 ARG 0.008 0.001 ARG C 272 ********************** 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 217 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 3.175 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: A 1 MET cc_start: 0.1135 (tpt) cc_final: -0.0186 (mmt) REVERT: A 176 GLU cc_start: 0.5512 (pp20) cc_final: 0.5208 (mt-10) REVERT: B 60 ARG cc_start: 0.6685 (mtt-85) cc_final: 0.6133 (mmt90) REVERT: B 98 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5428 (mt) REVERT: B 143 LYS cc_start: 0.3589 (OUTLIER) cc_final: 0.2745 (mmtt) REVERT: C 23 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.4912 (mt0) REVERT: D 83 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7177 (p) REVERT: E 1 MET cc_start: 0.0772 (mmm) cc_final: -0.0535 (mmt) REVERT: E 101 HIS cc_start: 0.5151 (OUTLIER) cc_final: 0.3361 (t-170) REVERT: F 212 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5448 (mt-10) REVERT: G 68 LYS cc_start: 0.6632 (pttt) cc_final: 0.5931 (mmmt) REVERT: G 135 ARG cc_start: 0.5583 (mtt-85) cc_final: 0.5260 (mtm180) REVERT: G 311 ILE cc_start: 0.6806 (mm) cc_final: 0.6386 (mm) outliers start: 45 outliers final: 35 residues processed: 213 average time/residue: 0.6879 time to fit residues: 219.8134 Evaluate side-chains 210 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 169 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.178737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.141174 restraints weight = 77161.762| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.83 r_work: 0.4057 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 1.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19041 Z= 0.309 Angle : 0.737 8.298 26142 Z= 0.383 Chirality : 0.045 0.244 3032 Planarity : 0.008 0.120 3181 Dihedral : 18.213 171.545 3449 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 2.64 % Allowed : 19.23 % Favored : 78.13 % 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: -1.82 (0.18), residues: 2198 helix: -0.25 (0.21), residues: 650 sheet: -0.68 (0.24), residues: 491 loop : -2.10 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 66 HIS 0.039 0.003 HIS F 256 PHE 0.026 0.002 PHE F 232 TYR 0.023 0.002 TYR F 314 ARG 0.010 0.001 ARG G 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8773.05 seconds wall clock time: 154 minutes 18.22 seconds (9258.22 seconds total)