Starting phenix.real_space_refine on Fri Feb 16 06:14:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/02_2024/8fyc_29564.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/02_2024/8fyc_29564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/02_2024/8fyc_29564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/02_2024/8fyc_29564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/02_2024/8fyc_29564.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/02_2024/8fyc_29564.pdb" } resolution = 4.1 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= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 34 5.16 5 C 8774 2.51 5 N 2623 2.21 5 O 3001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14575 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1314 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 3, 'TRANS': 160} Chain: "J" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2423 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "E" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "F" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1770 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Chain: "G" Number of atoms: 1187 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 57, 1165 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Conformer: "B" Number of residues, atoms: 57, 1165 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} bond proxies already assigned to first conformer: 1279 Chain: "H" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 632 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DG G 29 " occ=0.74 ... (42 atoms not shown) pdb=" C4 B DG G 29 " occ=0.26 Time building chain proxies: 8.30, per 1000 atoms: 0.57 Number of scatterers: 14575 At special positions: 0 Unit cell: (107.04, 95.89, 157.215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 143 15.00 O 3001 8.00 N 2623 7.00 C 8774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.41 Conformation dependent library (CDL) restraints added in 2.2 seconds 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 50.2% alpha, 13.7% beta 44 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'K' and resid 171 through 178 Processing helix chain 'K' and resid 181 through 189 Processing helix chain 'K' and resid 191 through 203 Processing helix chain 'K' and resid 212 through 228 removed outlier: 3.929A pdb=" N ASP K 216 " --> pdb=" O HIS K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 246 removed outlier: 3.922A pdb=" N ILE K 242 " --> pdb=" O ASP K 238 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU K 246 " --> pdb=" O ILE K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 262 Processing helix chain 'K' and resid 271 through 287 Processing helix chain 'D' and resid 12 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 51 removed outlier: 4.057A pdb=" N GLU D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.577A pdb=" N GLU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 removed outlier: 3.755A pdb=" N THR B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 114 through 129 removed outlier: 3.532A pdb=" N ARG B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 163 removed outlier: 3.533A pdb=" N ARG B 144 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 removed outlier: 3.938A pdb=" N LEU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.337A pdb=" N ASP B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 removed outlier: 4.380A pdb=" N GLN B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.642A pdb=" N VAL B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.883A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 Processing helix chain 'C' and resid 68 through 77 removed outlier: 3.897A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.910A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 removed outlier: 3.572A pdb=" N ARG C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 142 through 163 Processing helix chain 'C' and resid 180 through 205 removed outlier: 3.693A pdb=" N GLN C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 202 " --> pdb=" O HIS C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.748A pdb=" N TYR C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 250 through 266 removed outlier: 3.722A pdb=" N ARG C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'E' and resid 68 through 77 removed outlier: 4.483A pdb=" N LEU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.799A pdb=" N ARG E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.954A pdb=" N LYS E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL E 112 " --> pdb=" O GLN E 108 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 Processing helix chain 'E' and resid 139 through 162 removed outlier: 3.761A pdb=" N LYS E 160 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 205 removed outlier: 4.077A pdb=" N GLN E 184 " --> pdb=" O ASP E 180 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 226 through 231 removed outlier: 4.625A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.199A pdb=" N ASP E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 68 through 78 removed outlier: 3.560A pdb=" N THR F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.704A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 removed outlier: 3.753A pdb=" N GLN F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 204 Processing helix chain 'F' and resid 219 through 226 Processing helix chain 'F' and resid 226 through 231 removed outlier: 4.306A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 250 through 267 removed outlier: 3.534A pdb=" N ARG F 256 " --> pdb=" O GLY F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 280 removed outlier: 4.024A pdb=" N VAL F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS F 274 " --> pdb=" O LYS F 270 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 161 through 164 removed outlier: 3.655A pdb=" N PHE K 161 " --> pdb=" O ALA K 150 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU K 147 " --> pdb=" O GLU K 134 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU K 134 " --> pdb=" O GLU K 147 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR K 128 " --> pdb=" O CYS K 153 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL K 129 " --> pdb=" O VAL K 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 24 through 25 removed outlier: 4.485A pdb=" N ALA D 56 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 73 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 60 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP D 69 " --> pdb=" O PHE D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 78 through 81 removed outlier: 5.591A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 67 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER B 67 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE B 32 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.679A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 56 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 82 removed outlier: 6.773A pdb=" N ARG F 34 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE E 32 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 289 through 291 removed outlier: 7.773A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 82 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU B 81 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C 88 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 85 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP C 83 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR C 92 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU C 81 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 58 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL C 84 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU C 60 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA8, first strand: chain 'E' and resid 289 through 292 removed outlier: 6.293A pdb=" N ALA E 22 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL E 84 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU E 60 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU E 81 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR F 91 " --> pdb=" O TRP F 83 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 81 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL F 82 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 48 568 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 7.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2152 1.32 - 1.44: 4712 1.44 - 1.57: 7932 1.57 - 1.69: 286 1.69 - 1.82: 64 Bond restraints: 15146 Sorted by residual: bond pdb=" C ASP E 250 " pdb=" O ASP E 250 " ideal model delta sigma weight residual 1.234 1.311 -0.077 1.14e-02 7.69e+03 4.55e+01 bond pdb=" C SER C 159 " pdb=" O SER C 159 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.15e-02 7.56e+03 1.47e+01 bond pdb=" N THR B 102 " pdb=" CA THR B 102 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.06e-02 8.90e+03 1.30e+01 bond pdb=" N ILE K 133 " pdb=" CA ILE K 133 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.10e+01 bond pdb=" N VAL E 264 " pdb=" CA VAL E 264 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 8.94e+00 ... (remaining 15141 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.79: 918 105.79 - 112.91: 8167 112.91 - 120.03: 5530 120.03 - 127.14: 6123 127.14 - 134.26: 372 Bond angle restraints: 21110 Sorted by residual: angle pdb=" C ARG E 260 " pdb=" CA ARG E 260 " pdb=" CB ARG E 260 " ideal model delta sigma weight residual 110.79 102.68 8.11 1.66e+00 3.63e-01 2.39e+01 angle pdb=" N GLU C 147 " pdb=" CA GLU C 147 " pdb=" C GLU C 147 " ideal model delta sigma weight residual 111.28 105.98 5.30 1.09e+00 8.42e-01 2.36e+01 angle pdb=" N SER C 159 " pdb=" CA SER C 159 " pdb=" C SER C 159 " ideal model delta sigma weight residual 111.07 106.33 4.74 1.07e+00 8.73e-01 1.96e+01 angle pdb=" N TYR C 155 " pdb=" CA TYR C 155 " pdb=" C TYR C 155 " ideal model delta sigma weight residual 111.07 106.47 4.60 1.07e+00 8.73e-01 1.85e+01 angle pdb=" CA LYS C 160 " pdb=" C LYS C 160 " pdb=" O LYS C 160 " ideal model delta sigma weight residual 120.82 116.37 4.45 1.05e+00 9.07e-01 1.79e+01 ... (remaining 21105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 8083 35.72 - 71.45: 594 71.45 - 107.17: 21 107.17 - 142.90: 4 142.90 - 178.62: 4 Dihedral angle restraints: 8706 sinusoidal: 4458 harmonic: 4248 Sorted by residual: dihedral pdb=" C ARG E 260 " pdb=" N ARG E 260 " pdb=" CA ARG E 260 " pdb=" CB ARG E 260 " ideal model delta harmonic sigma weight residual -122.60 -111.60 -11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" CA THR C 139 " pdb=" C THR C 139 " pdb=" N MET C 140 " pdb=" CA MET C 140 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DA J 31 " pdb=" C3' DA J 31 " pdb=" O3' DA J 31 " pdb=" P DA J 32 " ideal model delta sinusoidal sigma weight residual 220.00 41.38 178.62 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2108 0.066 - 0.132: 228 0.132 - 0.199: 32 0.199 - 0.265: 10 0.265 - 0.331: 1 Chirality restraints: 2379 Sorted by residual: chirality pdb=" CA ARG E 260 " pdb=" N ARG E 260 " pdb=" C ARG E 260 " pdb=" CB ARG E 260 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA TYR C 155 " pdb=" N TYR C 155 " pdb=" C TYR C 155 " pdb=" CB TYR C 155 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA LYS F 9 " pdb=" N LYS F 9 " pdb=" C LYS F 9 " pdb=" CB LYS F 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2376 not shown) Planarity restraints: 2203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 159 " -0.025 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C SER C 159 " 0.087 2.00e-02 2.50e+03 pdb=" O SER C 159 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS C 160 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 249 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C GLN E 249 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN E 249 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP E 250 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 250 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C ASP E 250 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP E 250 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE E 251 " 0.017 2.00e-02 2.50e+03 ... (remaining 2200 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1245 2.74 - 3.28: 15722 3.28 - 3.82: 27656 3.82 - 4.36: 31538 4.36 - 4.90: 48790 Nonbonded interactions: 124951 Sorted by model distance: nonbonded pdb=" O GLY D 17 " pdb=" OG1 THR D 20 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR E 223 " pdb=" N2 DG G 27 " model vdw 2.229 2.520 nonbonded pdb=" NH1 ARG E 34 " pdb=" O ARG E 69 " model vdw 2.229 2.520 nonbonded pdb=" OH TYR C 229 " pdb=" OD2 ASP C 275 " model vdw 2.231 2.440 nonbonded pdb=" O ARG C 256 " pdb=" OG1 THR C 259 " model vdw 2.233 2.440 ... (remaining 124946 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 'D' } ncs_group { reference = chain 'B' selection = (chain 'C' and resid 20 through 311) selection = chain 'E' } 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=0.26 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.010 Extract box with map and model: 3.700 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 44.660 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.004 0.077 15146 Z= 0.246 Angle : 0.684 8.108 21110 Z= 0.429 Chirality : 0.046 0.331 2379 Planarity : 0.004 0.051 2203 Dihedral : 20.674 178.623 5982 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.71 % Rotamer: Outliers : 0.25 % Allowed : 1.16 % Favored : 98.60 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1459 helix: 0.48 (0.21), residues: 624 sheet: -0.95 (0.34), residues: 211 loop : -1.00 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 44 HIS 0.005 0.001 HIS E 29 PHE 0.019 0.001 PHE K 224 TYR 0.012 0.001 TYR F 91 ARG 0.006 0.000 ARG F 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 301 time to evaluate : 1.411 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: K 271 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7533 (mmt180) REVERT: D 69 ASP cc_start: 0.8191 (t70) cc_final: 0.7957 (t70) REVERT: A 49 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8269 (mt-10) REVERT: B 81 LEU cc_start: 0.8752 (tt) cc_final: 0.8506 (tt) REVERT: B 86 GLU cc_start: 0.8038 (tp30) cc_final: 0.7831 (tp30) REVERT: B 141 GLN cc_start: 0.9381 (tm-30) cc_final: 0.8875 (tm-30) REVERT: B 163 ASN cc_start: 0.8846 (m-40) cc_final: 0.8543 (m-40) REVERT: B 217 HIS cc_start: 0.9200 (t-90) cc_final: 0.8844 (t70) REVERT: C 156 ARG cc_start: 0.9251 (mtt180) cc_final: 0.8567 (tpp80) REVERT: C 197 VAL cc_start: 0.8996 (t) cc_final: 0.8762 (p) REVERT: C 253 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7148 (tp40) REVERT: C 282 ILE cc_start: 0.9182 (mm) cc_final: 0.8981 (mm) REVERT: C 295 LEU cc_start: 0.9372 (mm) cc_final: 0.9144 (mm) REVERT: E 69 ARG cc_start: 0.7745 (tpm170) cc_final: 0.7099 (tpm170) REVERT: E 272 MET cc_start: 0.9143 (mpp) cc_final: 0.8934 (mpp) REVERT: F 114 ASN cc_start: 0.9107 (m110) cc_final: 0.8903 (t0) REVERT: F 125 MET cc_start: 0.8866 (ttt) cc_final: 0.8263 (tmm) REVERT: F 190 HIS cc_start: 0.7674 (m170) cc_final: 0.7453 (m-70) outliers start: 3 outliers final: 0 residues processed: 301 average time/residue: 0.2928 time to fit residues: 124.0418 Evaluate side-chains 223 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15146 Z= 0.244 Angle : 0.624 6.953 21110 Z= 0.352 Chirality : 0.042 0.158 2379 Planarity : 0.004 0.045 2203 Dihedral : 23.960 179.808 3215 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1459 helix: 0.48 (0.19), residues: 670 sheet: -1.21 (0.33), residues: 216 loop : -1.16 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 44 HIS 0.006 0.001 HIS E 29 PHE 0.019 0.002 PHE K 202 TYR 0.019 0.002 TYR B 194 ARG 0.007 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 148 ILE cc_start: 0.9291 (mt) cc_final: 0.9034 (mt) REVERT: K 271 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7629 (mmt180) REVERT: D 69 ASP cc_start: 0.8371 (t70) cc_final: 0.8152 (t70) REVERT: B 83 TRP cc_start: 0.8892 (m100) cc_final: 0.8687 (m100) REVERT: B 86 GLU cc_start: 0.8323 (tp30) cc_final: 0.8063 (tp30) REVERT: B 141 GLN cc_start: 0.9389 (tm-30) cc_final: 0.9097 (tm-30) REVERT: B 182 ILE cc_start: 0.9391 (tp) cc_final: 0.9167 (tp) REVERT: B 217 HIS cc_start: 0.9204 (t-90) cc_final: 0.8853 (t70) REVERT: C 81 LEU cc_start: 0.8806 (mm) cc_final: 0.8596 (mm) REVERT: C 197 VAL cc_start: 0.8969 (t) cc_final: 0.8697 (p) REVERT: C 272 MET cc_start: 0.8117 (tmm) cc_final: 0.7828 (tmm) REVERT: C 282 ILE cc_start: 0.9152 (mm) cc_final: 0.8923 (mm) REVERT: E 69 ARG cc_start: 0.7665 (tpm170) cc_final: 0.7122 (tpm170) REVERT: E 83 TRP cc_start: 0.8411 (m-90) cc_final: 0.7836 (m-90) REVERT: E 140 MET cc_start: 0.9384 (mmt) cc_final: 0.9143 (mmt) REVERT: F 15 LEU cc_start: 0.9305 (mt) cc_final: 0.9090 (mt) REVERT: F 19 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7980 (mm-30) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.2966 time to fit residues: 121.3766 Evaluate side-chains 214 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 128 optimal weight: 0.1980 chunk 143 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 0.0670 overall best weight: 3.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN K 237 HIS ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15146 Z= 0.301 Angle : 0.645 8.300 21110 Z= 0.357 Chirality : 0.042 0.152 2379 Planarity : 0.005 0.066 2203 Dihedral : 24.266 175.789 3215 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.08 % Allowed : 6.53 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1459 helix: 0.28 (0.19), residues: 676 sheet: -1.36 (0.33), residues: 217 loop : -1.30 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 296 HIS 0.007 0.001 HIS E 29 PHE 0.018 0.002 PHE K 224 TYR 0.018 0.002 TYR C 162 ARG 0.013 0.001 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 241 ARG cc_start: 0.4565 (ttm170) cc_final: 0.3776 (ttm170) REVERT: K 271 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7661 (mmt180) REVERT: D 38 ARG cc_start: 0.8614 (tmm-80) cc_final: 0.8239 (tmm-80) REVERT: D 41 GLU cc_start: 0.8490 (mp0) cc_final: 0.7944 (mp0) REVERT: D 69 ASP cc_start: 0.8498 (t70) cc_final: 0.8248 (t70) REVERT: B 83 TRP cc_start: 0.8907 (m100) cc_final: 0.8690 (m100) REVERT: B 210 LEU cc_start: 0.8984 (mm) cc_final: 0.8751 (mm) REVERT: B 217 HIS cc_start: 0.9240 (t-90) cc_final: 0.8878 (t70) REVERT: C 141 GLN cc_start: 0.8911 (mp10) cc_final: 0.8710 (mp10) REVERT: C 197 VAL cc_start: 0.9114 (t) cc_final: 0.8863 (p) REVERT: C 272 MET cc_start: 0.8171 (tmm) cc_final: 0.7947 (tmm) REVERT: C 282 ILE cc_start: 0.9108 (mm) cc_final: 0.8721 (mm) REVERT: E 69 ARG cc_start: 0.7524 (tpm170) cc_final: 0.7082 (tpm170) REVERT: E 128 MET cc_start: 0.8986 (tpp) cc_final: 0.8715 (tpp) REVERT: E 244 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8944 (tm-30) REVERT: F 15 LEU cc_start: 0.9291 (mt) cc_final: 0.9066 (mt) REVERT: F 17 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.7884 (ptp-170) REVERT: F 19 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8094 (mm-30) outliers start: 1 outliers final: 1 residues processed: 273 average time/residue: 0.2618 time to fit residues: 104.3259 Evaluate side-chains 213 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15146 Z= 0.228 Angle : 0.604 6.680 21110 Z= 0.334 Chirality : 0.041 0.149 2379 Planarity : 0.004 0.053 2203 Dihedral : 24.350 178.996 3215 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.21), residues: 1459 helix: 0.46 (0.19), residues: 674 sheet: -1.37 (0.33), residues: 217 loop : -1.23 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 44 HIS 0.006 0.001 HIS E 29 PHE 0.024 0.002 PHE B 24 TYR 0.018 0.001 TYR C 126 ARG 0.006 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 147 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6754 (tm-30) REVERT: K 241 ARG cc_start: 0.4533 (ttm170) cc_final: 0.3868 (ttm170) REVERT: K 271 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7705 (mmt180) REVERT: D 35 PHE cc_start: 0.7707 (m-10) cc_final: 0.7507 (m-10) REVERT: D 38 ARG cc_start: 0.8623 (tmm-80) cc_final: 0.8385 (tmm-80) REVERT: D 41 GLU cc_start: 0.8578 (mp0) cc_final: 0.8180 (mp0) REVERT: D 69 ASP cc_start: 0.8465 (t70) cc_final: 0.8219 (t70) REVERT: B 84 VAL cc_start: 0.8015 (m) cc_final: 0.6777 (m) REVERT: B 217 HIS cc_start: 0.9207 (t-90) cc_final: 0.8859 (t70) REVERT: C 197 VAL cc_start: 0.9048 (t) cc_final: 0.8791 (p) REVERT: C 282 ILE cc_start: 0.9107 (mm) cc_final: 0.8742 (mm) REVERT: F 17 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7822 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2750 time to fit residues: 105.1141 Evaluate side-chains 204 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15146 Z= 0.267 Angle : 0.614 6.634 21110 Z= 0.339 Chirality : 0.041 0.159 2379 Planarity : 0.004 0.055 2203 Dihedral : 24.426 177.128 3215 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1459 helix: 0.50 (0.19), residues: 673 sheet: -1.47 (0.32), residues: 220 loop : -1.26 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 44 HIS 0.008 0.001 HIS E 29 PHE 0.021 0.002 PHE K 224 TYR 0.024 0.002 TYR C 126 ARG 0.004 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 148 ILE cc_start: 0.9322 (mt) cc_final: 0.9042 (mt) REVERT: K 241 ARG cc_start: 0.4724 (ttm170) cc_final: 0.4017 (ttm170) REVERT: K 271 ARG cc_start: 0.8246 (mtt180) cc_final: 0.7782 (mmt180) REVERT: D 38 ARG cc_start: 0.8647 (tmm-80) cc_final: 0.8172 (tmm-80) REVERT: D 41 GLU cc_start: 0.8558 (mp0) cc_final: 0.7814 (mp0) REVERT: D 69 ASP cc_start: 0.8558 (t70) cc_final: 0.8313 (t70) REVERT: B 84 VAL cc_start: 0.7970 (m) cc_final: 0.6971 (m) REVERT: B 206 LEU cc_start: 0.8699 (mt) cc_final: 0.8470 (mt) REVERT: B 217 HIS cc_start: 0.9260 (t-90) cc_final: 0.8944 (t70) REVERT: C 197 VAL cc_start: 0.9052 (t) cc_final: 0.8799 (p) REVERT: C 282 ILE cc_start: 0.9066 (mm) cc_final: 0.8685 (mm) REVERT: E 272 MET cc_start: 0.8870 (mpp) cc_final: 0.8617 (mpp) REVERT: F 15 LEU cc_start: 0.9254 (mt) cc_final: 0.9024 (mt) REVERT: F 19 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7932 (mm-30) REVERT: F 128 MET cc_start: 0.7531 (pmm) cc_final: 0.7317 (pmm) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2691 time to fit residues: 100.0707 Evaluate side-chains 200 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 0.0870 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15146 Z= 0.216 Angle : 0.604 6.599 21110 Z= 0.331 Chirality : 0.041 0.168 2379 Planarity : 0.004 0.055 2203 Dihedral : 24.458 179.177 3215 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1459 helix: 0.58 (0.20), residues: 676 sheet: -1.40 (0.32), residues: 220 loop : -1.19 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 83 HIS 0.008 0.001 HIS E 29 PHE 0.021 0.001 PHE K 224 TYR 0.021 0.001 TYR E 229 ARG 0.004 0.000 ARG F 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 271 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7864 (mmt180) REVERT: D 38 ARG cc_start: 0.8585 (tmm-80) cc_final: 0.8106 (tmm-80) REVERT: D 41 GLU cc_start: 0.8548 (mp0) cc_final: 0.7744 (mp0) REVERT: D 69 ASP cc_start: 0.8467 (t70) cc_final: 0.8210 (t70) REVERT: B 84 VAL cc_start: 0.8001 (m) cc_final: 0.7140 (m) REVERT: B 134 ASP cc_start: 0.9105 (m-30) cc_final: 0.8656 (t0) REVERT: B 163 ASN cc_start: 0.8961 (m-40) cc_final: 0.8706 (m-40) REVERT: B 186 LEU cc_start: 0.9046 (tt) cc_final: 0.8835 (tt) REVERT: B 217 HIS cc_start: 0.9186 (t-90) cc_final: 0.8852 (t70) REVERT: C 197 VAL cc_start: 0.9023 (t) cc_final: 0.8770 (p) REVERT: C 282 ILE cc_start: 0.9096 (mm) cc_final: 0.8726 (mm) REVERT: E 171 TYR cc_start: 0.8242 (p90) cc_final: 0.8035 (p90) REVERT: E 272 MET cc_start: 0.8856 (mpp) cc_final: 0.8630 (mpp) REVERT: E 296 TRP cc_start: 0.6593 (m100) cc_final: 0.6224 (m100) REVERT: F 15 LEU cc_start: 0.9246 (mt) cc_final: 0.9039 (mt) REVERT: F 19 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7776 (mm-30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2760 time to fit residues: 104.2506 Evaluate side-chains 207 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 186 GLN ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15146 Z= 0.221 Angle : 0.606 10.708 21110 Z= 0.330 Chirality : 0.041 0.189 2379 Planarity : 0.004 0.057 2203 Dihedral : 24.469 178.436 3215 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1459 helix: 0.65 (0.20), residues: 681 sheet: -1.40 (0.32), residues: 220 loop : -1.19 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 83 HIS 0.008 0.001 HIS E 29 PHE 0.024 0.002 PHE K 224 TYR 0.022 0.001 TYR E 229 ARG 0.004 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6085 (mtt180) cc_final: 0.4179 (mtm180) REVERT: K 161 PHE cc_start: 0.7984 (t80) cc_final: 0.7562 (t80) REVERT: K 220 LEU cc_start: 0.6377 (tt) cc_final: 0.6163 (tt) REVERT: K 271 ARG cc_start: 0.8402 (mtt180) cc_final: 0.7864 (mmt180) REVERT: D 38 ARG cc_start: 0.8672 (tmm-80) cc_final: 0.8104 (tmm-80) REVERT: D 41 GLU cc_start: 0.8430 (mp0) cc_final: 0.7736 (mp0) REVERT: D 69 ASP cc_start: 0.8473 (t70) cc_final: 0.8225 (t70) REVERT: A 20 THR cc_start: 0.9153 (p) cc_final: 0.8936 (t) REVERT: B 81 LEU cc_start: 0.8597 (tt) cc_final: 0.8351 (tt) REVERT: B 84 VAL cc_start: 0.8151 (m) cc_final: 0.7394 (m) REVERT: B 86 GLU cc_start: 0.8269 (tp30) cc_final: 0.7779 (tp30) REVERT: B 134 ASP cc_start: 0.9075 (m-30) cc_final: 0.8607 (t0) REVERT: B 163 ASN cc_start: 0.8938 (m-40) cc_final: 0.8715 (m-40) REVERT: B 186 LEU cc_start: 0.9027 (tt) cc_final: 0.8689 (tp) REVERT: B 217 HIS cc_start: 0.9201 (t-90) cc_final: 0.8876 (t70) REVERT: C 282 ILE cc_start: 0.9099 (mm) cc_final: 0.8753 (mm) REVERT: E 171 TYR cc_start: 0.8293 (p90) cc_final: 0.8030 (p90) REVERT: E 272 MET cc_start: 0.8815 (mpp) cc_final: 0.8583 (mpp) REVERT: F 15 LEU cc_start: 0.9249 (mt) cc_final: 0.9030 (mt) REVERT: F 19 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7717 (mm-30) REVERT: F 274 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8407 (mmmt) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2644 time to fit residues: 102.3660 Evaluate side-chains 208 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 190 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15146 Z= 0.224 Angle : 0.607 9.166 21110 Z= 0.332 Chirality : 0.041 0.147 2379 Planarity : 0.004 0.056 2203 Dihedral : 24.489 178.362 3215 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1459 helix: 0.70 (0.20), residues: 681 sheet: -1.41 (0.33), residues: 220 loop : -1.22 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 83 HIS 0.008 0.001 HIS E 29 PHE 0.026 0.002 PHE K 224 TYR 0.034 0.002 TYR B 155 ARG 0.004 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6084 (mtt180) cc_final: 0.4237 (mtm180) REVERT: K 161 PHE cc_start: 0.7963 (t80) cc_final: 0.7568 (t80) REVERT: K 220 LEU cc_start: 0.6410 (tt) cc_final: 0.6141 (tt) REVERT: K 271 ARG cc_start: 0.8419 (mtt180) cc_final: 0.7866 (mmt180) REVERT: D 4 THR cc_start: 0.8294 (t) cc_final: 0.8087 (t) REVERT: D 38 ARG cc_start: 0.8646 (tmm-80) cc_final: 0.8039 (tmm-80) REVERT: D 41 GLU cc_start: 0.8435 (mp0) cc_final: 0.7603 (mp0) REVERT: D 69 ASP cc_start: 0.8500 (t70) cc_final: 0.8241 (t70) REVERT: B 86 GLU cc_start: 0.8257 (tp30) cc_final: 0.7952 (tp30) REVERT: B 134 ASP cc_start: 0.9084 (m-30) cc_final: 0.8633 (t0) REVERT: B 163 ASN cc_start: 0.8926 (m-40) cc_final: 0.8697 (m-40) REVERT: B 217 HIS cc_start: 0.9209 (t-90) cc_final: 0.8882 (t70) REVERT: C 282 ILE cc_start: 0.9100 (mm) cc_final: 0.8762 (mm) REVERT: E 171 TYR cc_start: 0.8373 (p90) cc_final: 0.8075 (p90) REVERT: F 15 LEU cc_start: 0.9221 (mt) cc_final: 0.9012 (mt) REVERT: F 19 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7738 (mm-30) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2629 time to fit residues: 100.5331 Evaluate side-chains 214 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 146 optimal weight: 0.0270 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 0.0470 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 ASN B 190 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15146 Z= 0.191 Angle : 0.615 9.218 21110 Z= 0.331 Chirality : 0.041 0.156 2379 Planarity : 0.004 0.055 2203 Dihedral : 24.467 179.660 3215 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1459 helix: 0.77 (0.20), residues: 681 sheet: -1.30 (0.33), residues: 220 loop : -1.14 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 83 HIS 0.009 0.001 HIS C 146 PHE 0.023 0.001 PHE K 224 TYR 0.030 0.001 TYR B 155 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 147 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6876 (tm-30) REVERT: K 154 GLU cc_start: 0.7188 (pp20) cc_final: 0.6973 (mp0) REVERT: K 161 PHE cc_start: 0.8014 (t80) cc_final: 0.7545 (t80) REVERT: K 220 LEU cc_start: 0.6499 (tt) cc_final: 0.6250 (tt) REVERT: K 271 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7877 (mmt180) REVERT: D 38 ARG cc_start: 0.8597 (tmm-80) cc_final: 0.7935 (tmm-80) REVERT: D 41 GLU cc_start: 0.8439 (mp0) cc_final: 0.7619 (mp0) REVERT: D 69 ASP cc_start: 0.8305 (t70) cc_final: 0.8046 (t70) REVERT: B 134 ASP cc_start: 0.9079 (m-30) cc_final: 0.8612 (t0) REVERT: B 163 ASN cc_start: 0.8883 (m-40) cc_final: 0.8662 (m-40) REVERT: B 217 HIS cc_start: 0.9132 (t-90) cc_final: 0.8773 (t70) REVERT: C 162 TYR cc_start: 0.8016 (m-10) cc_final: 0.7660 (m-10) REVERT: C 282 ILE cc_start: 0.9093 (mm) cc_final: 0.8748 (mm) REVERT: E 69 ARG cc_start: 0.7385 (tpm170) cc_final: 0.7131 (tpm170) REVERT: E 171 TYR cc_start: 0.8283 (p90) cc_final: 0.7840 (p90) REVERT: F 15 LEU cc_start: 0.9135 (mt) cc_final: 0.8899 (mt) REVERT: F 19 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7443 (mm-30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2686 time to fit residues: 108.2734 Evaluate side-chains 217 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15146 Z= 0.204 Angle : 0.614 8.833 21110 Z= 0.332 Chirality : 0.041 0.262 2379 Planarity : 0.004 0.062 2203 Dihedral : 24.465 179.009 3215 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1459 helix: 0.82 (0.20), residues: 679 sheet: -1.31 (0.33), residues: 216 loop : -1.15 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 296 HIS 0.006 0.001 HIS E 29 PHE 0.025 0.001 PHE K 224 TYR 0.030 0.002 TYR B 155 ARG 0.005 0.000 ARG D 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 161 PHE cc_start: 0.8032 (t80) cc_final: 0.7562 (t80) REVERT: K 220 LEU cc_start: 0.6569 (tt) cc_final: 0.6319 (tt) REVERT: K 271 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7822 (mmm160) REVERT: D 38 ARG cc_start: 0.8594 (tmm-80) cc_final: 0.7945 (tmm-80) REVERT: D 41 GLU cc_start: 0.8377 (mp0) cc_final: 0.7573 (mp0) REVERT: D 69 ASP cc_start: 0.8324 (t70) cc_final: 0.8039 (t70) REVERT: A 45 ARG cc_start: 0.8440 (tpp80) cc_final: 0.8114 (mmm-85) REVERT: A 49 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8461 (mm-30) REVERT: B 134 ASP cc_start: 0.9114 (m-30) cc_final: 0.8650 (t0) REVERT: B 163 ASN cc_start: 0.8851 (m-40) cc_final: 0.8631 (m-40) REVERT: B 217 HIS cc_start: 0.9159 (t-90) cc_final: 0.8848 (t70) REVERT: C 282 ILE cc_start: 0.9090 (mm) cc_final: 0.8780 (mm) REVERT: E 69 ARG cc_start: 0.7409 (tpm170) cc_final: 0.7098 (tpm170) REVERT: E 171 TYR cc_start: 0.8344 (p90) cc_final: 0.7917 (p90) REVERT: F 15 LEU cc_start: 0.9120 (mt) cc_final: 0.8893 (mt) REVERT: F 19 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7587 (mm-30) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2677 time to fit residues: 101.3946 Evaluate side-chains 204 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.100433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078571 restraints weight = 66223.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.080647 restraints weight = 39915.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.081856 restraints weight = 28559.016| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15146 Z= 0.207 Angle : 0.611 8.657 21110 Z= 0.330 Chirality : 0.041 0.176 2379 Planarity : 0.004 0.056 2203 Dihedral : 24.487 178.875 3215 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), residues: 1459 helix: 0.85 (0.20), residues: 678 sheet: -1.37 (0.32), residues: 220 loop : -1.10 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 83 HIS 0.006 0.001 HIS E 29 PHE 0.025 0.001 PHE K 224 TYR 0.029 0.002 TYR B 155 ARG 0.005 0.000 ARG C 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2934.98 seconds wall clock time: 54 minutes 15.46 seconds (3255.46 seconds total)