Starting phenix.real_space_refine on Sun Nov 17 19:30:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/11_2024/8fyc_29564.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/11_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_29564/11_2024/8fyc_29564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/11_2024/8fyc_29564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/11_2024/8fyc_29564.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyc_29564/11_2024/8fyc_29564.cif" } 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. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.37, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.7 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: 6.50 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: 4.96 Time building geometry restraints manager: 4.29 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: 0.00 - 1.62: 20214 1.62 - 3.24: 765 3.24 - 4.86: 100 4.86 - 6.49: 26 6.49 - 8.11: 5 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 3.040 nonbonded pdb=" OH TYR E 223 " pdb=" N2 DG G 27 " model vdw 2.229 3.120 nonbonded pdb=" NH1 ARG E 34 " pdb=" O ARG E 69 " model vdw 2.229 3.120 nonbonded pdb=" OH TYR C 229 " pdb=" OD2 ASP C 275 " model vdw 2.231 3.040 nonbonded pdb=" O ARG C 256 " pdb=" OG1 THR C 259 " model vdw 2.233 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.780 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.150 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 301 time to evaluate : 1.425 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: 0.3078 time to fit residues: 129.8288 Evaluate side-chains 223 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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: 0.0050 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 overall best weight: 2.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 222 GLN K 287 ASN ** B 183 ASN ** 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 214 HIS ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 127 GLN F 183 ASN F 184 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1842 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= 0.274 Angle : 0.651 6.938 21110 Z= 0.368 Chirality : 0.043 0.160 2379 Planarity : 0.005 0.046 2203 Dihedral : 23.969 179.272 3215 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % 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: -0.75 (0.21), residues: 1459 helix: 0.44 (0.19), residues: 665 sheet: -1.27 (0.33), residues: 216 loop : -1.18 (0.24), residues: 578 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 0.020 0.002 PHE K 202 TYR 0.018 0.002 TYR B 194 ARG 0.007 0.001 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 274 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 271 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7590 (mmt180) REVERT: D 69 ASP cc_start: 0.8401 (t70) cc_final: 0.8174 (t70) REVERT: B 125 MET cc_start: 0.8610 (mpp) cc_final: 0.8381 (mpp) REVERT: B 134 ASP cc_start: 0.9090 (m-30) cc_final: 0.8576 (t0) REVERT: B 141 GLN cc_start: 0.9403 (tm-30) cc_final: 0.9120 (tm-30) REVERT: B 217 HIS cc_start: 0.9153 (t-90) cc_final: 0.8812 (t70) REVERT: C 81 LEU cc_start: 0.8833 (mm) cc_final: 0.8616 (mm) REVERT: C 282 ILE cc_start: 0.9107 (mm) cc_final: 0.8768 (mm) REVERT: E 83 TRP cc_start: 0.8427 (m-90) cc_final: 0.7679 (m-90) REVERT: E 272 MET cc_start: 0.9140 (mpp) cc_final: 0.8858 (mpp) REVERT: F 15 LEU cc_start: 0.9279 (mt) cc_final: 0.9044 (mt) REVERT: F 19 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7944 (mm-30) outliers start: 1 outliers final: 1 residues processed: 274 average time/residue: 0.2768 time to fit residues: 110.0683 Evaluate side-chains 206 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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: 4.9990 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 222 GLN K 237 HIS ** B 108 GLN ** 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 146 HIS C 253 GLN F 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15146 Z= 0.343 Angle : 0.680 7.487 21110 Z= 0.377 Chirality : 0.043 0.160 2379 Planarity : 0.005 0.081 2203 Dihedral : 24.346 175.564 3215 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % 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: -1.02 (0.21), residues: 1459 helix: 0.21 (0.19), residues: 672 sheet: -1.46 (0.33), residues: 217 loop : -1.31 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 83 HIS 0.008 0.001 HIS F 217 PHE 0.019 0.002 PHE K 224 TYR 0.018 0.002 TYR F 91 ARG 0.012 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 261 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 1.565 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: K 271 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7637 (mmt180) REVERT: D 41 GLU cc_start: 0.8480 (mp0) cc_final: 0.7899 (mp0) REVERT: D 63 ARG cc_start: 0.8317 (mmt180) cc_final: 0.7634 (mmm160) REVERT: D 69 ASP cc_start: 0.8505 (t70) cc_final: 0.8238 (t70) REVERT: A 8 LEU cc_start: 0.9017 (mt) cc_final: 0.8780 (mp) REVERT: A 20 THR cc_start: 0.9073 (p) cc_final: 0.8840 (t) REVERT: B 134 ASP cc_start: 0.9054 (m-30) cc_final: 0.8583 (t0) REVERT: B 217 HIS cc_start: 0.9218 (t-90) cc_final: 0.8885 (t70) REVERT: C 141 GLN cc_start: 0.8983 (mp10) cc_final: 0.8774 (mp10) REVERT: C 147 GLU cc_start: 0.8407 (mp0) cc_final: 0.7996 (tt0) REVERT: C 282 ILE cc_start: 0.9151 (mm) cc_final: 0.8817 (mm) REVERT: E 34 ARG cc_start: 0.7477 (ptt-90) cc_final: 0.6970 (ptt-90) REVERT: E 69 ARG cc_start: 0.7528 (tpm170) cc_final: 0.7245 (tpm170) REVERT: E 128 MET cc_start: 0.9001 (tpp) cc_final: 0.8737 (tpp) REVERT: F 15 LEU cc_start: 0.9346 (mt) cc_final: 0.9098 (mt) REVERT: F 19 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8165 (mm-30) REVERT: F 198 HIS cc_start: 0.8301 (t70) cc_final: 0.8076 (t-90) outliers start: 1 outliers final: 1 residues processed: 261 average time/residue: 0.2906 time to fit residues: 110.1457 Evaluate side-chains 209 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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: 7.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 145 optimal weight: 0.1980 chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- 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 222 GLN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** 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** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15146 Z= 0.379 Angle : 0.701 7.418 21110 Z= 0.387 Chirality : 0.044 0.170 2379 Planarity : 0.005 0.057 2203 Dihedral : 24.640 176.729 3215 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.88 % 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: -1.26 (0.21), residues: 1459 helix: 0.03 (0.19), residues: 677 sheet: -1.54 (0.33), residues: 214 loop : -1.48 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 83 HIS 0.007 0.001 HIS C 146 PHE 0.029 0.002 PHE B 24 TYR 0.022 0.002 TYR C 126 ARG 0.008 0.001 ARG F 96 *********************** 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 261 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 1.681 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: K 147 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6828 (tm-30) REVERT: K 271 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7803 (mmt180) REVERT: D 38 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.8112 (tmm-80) REVERT: D 41 GLU cc_start: 0.8507 (mp0) cc_final: 0.7722 (mp0) REVERT: D 63 ARG cc_start: 0.8328 (mmt180) cc_final: 0.7588 (mmm160) REVERT: D 69 ASP cc_start: 0.8582 (t70) cc_final: 0.8065 (t70) REVERT: A 8 LEU cc_start: 0.9053 (mt) cc_final: 0.8824 (mp) REVERT: A 20 THR cc_start: 0.9078 (p) cc_final: 0.8850 (t) REVERT: B 84 VAL cc_start: 0.8560 (m) cc_final: 0.7657 (m) REVERT: B 206 LEU cc_start: 0.8934 (mt) cc_final: 0.8451 (mt) REVERT: B 217 HIS cc_start: 0.9178 (t-90) cc_final: 0.8882 (t70) REVERT: C 184 GLN cc_start: 0.9154 (pm20) cc_final: 0.8808 (pm20) REVERT: C 282 ILE cc_start: 0.9143 (mm) cc_final: 0.8812 (mm) REVERT: C 295 LEU cc_start: 0.9269 (mm) cc_final: 0.8978 (mt) REVERT: E 69 ARG cc_start: 0.7498 (tpm170) cc_final: 0.7273 (tpm170) REVERT: E 128 MET cc_start: 0.8951 (tpp) cc_final: 0.8709 (tpp) REVERT: F 15 LEU cc_start: 0.9341 (mt) cc_final: 0.9078 (mt) REVERT: F 128 MET cc_start: 0.7637 (pmm) cc_final: 0.7411 (pmm) outliers start: 1 outliers final: 1 residues processed: 261 average time/residue: 0.2977 time to fit residues: 111.5602 Evaluate side-chains 204 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 0.0570 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 190 HIS ** 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** F 33 ASN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15146 Z= 0.204 Angle : 0.631 9.041 21110 Z= 0.342 Chirality : 0.042 0.174 2379 Planarity : 0.004 0.056 2203 Dihedral : 24.592 179.402 3215 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -0.96 (0.21), residues: 1459 helix: 0.27 (0.19), residues: 675 sheet: -1.40 (0.32), residues: 218 loop : -1.30 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 83 HIS 0.006 0.001 HIS C 68 PHE 0.020 0.002 PHE K 224 TYR 0.022 0.002 TYR E 229 ARG 0.007 0.000 ARG C 169 *********************** 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 268 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6238 (mtt180) cc_final: 0.4282 (mtm180) REVERT: K 147 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6914 (tm-30) REVERT: K 220 LEU cc_start: 0.6444 (tt) cc_final: 0.6219 (tt) REVERT: K 271 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7834 (mmt180) REVERT: D 19 LEU cc_start: 0.8973 (mp) cc_final: 0.8771 (mp) REVERT: D 38 ARG cc_start: 0.8605 (tmm-80) cc_final: 0.8146 (tmm-80) REVERT: D 41 GLU cc_start: 0.8505 (mp0) cc_final: 0.7743 (mp0) REVERT: D 69 ASP cc_start: 0.8457 (t70) cc_final: 0.8203 (t70) REVERT: A 77 ARG cc_start: 0.8389 (mtt90) cc_final: 0.7886 (mtt-85) REVERT: B 84 VAL cc_start: 0.8181 (m) cc_final: 0.6943 (m) REVERT: B 108 GLN cc_start: 0.8970 (pt0) cc_final: 0.8729 (pt0) REVERT: B 134 ASP cc_start: 0.9063 (m-30) cc_final: 0.8406 (t0) REVERT: B 163 ASN cc_start: 0.9021 (m-40) cc_final: 0.8792 (m-40) REVERT: B 206 LEU cc_start: 0.8852 (mt) cc_final: 0.8384 (mt) REVERT: B 217 HIS cc_start: 0.9135 (t-90) cc_final: 0.8827 (t70) REVERT: C 23 THR cc_start: 0.9391 (p) cc_final: 0.9177 (t) REVERT: C 282 ILE cc_start: 0.9104 (mm) cc_final: 0.8820 (mm) REVERT: E 272 MET cc_start: 0.8808 (mpp) cc_final: 0.8544 (mpp) REVERT: F 15 LEU cc_start: 0.9304 (mt) cc_final: 0.9090 (mt) REVERT: F 198 HIS cc_start: 0.8087 (t-90) cc_final: 0.7823 (t-90) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2740 time to fit residues: 107.0799 Evaluate side-chains 214 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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: 7.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 222 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 253 GLN F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3344 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= 0.214 Angle : 0.616 7.410 21110 Z= 0.336 Chirality : 0.042 0.193 2379 Planarity : 0.005 0.097 2203 Dihedral : 24.552 178.587 3215 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -0.87 (0.21), residues: 1459 helix: 0.38 (0.19), residues: 679 sheet: -1.44 (0.32), residues: 222 loop : -1.29 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 44 HIS 0.006 0.001 HIS C 68 PHE 0.021 0.002 PHE K 224 TYR 0.040 0.002 TYR B 194 ARG 0.009 0.000 ARG D 77 *********************** 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 264 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.493 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: K 142 ARG cc_start: 0.6271 (mtt180) cc_final: 0.4374 (mtm180) REVERT: K 147 GLU cc_start: 0.7248 (tm-30) cc_final: 0.7040 (tm-30) REVERT: K 220 LEU cc_start: 0.6524 (tt) cc_final: 0.6285 (tt) REVERT: K 271 ARG cc_start: 0.8392 (mtt180) cc_final: 0.7864 (mmt180) REVERT: D 6 ILE cc_start: 0.8880 (mt) cc_final: 0.8654 (mt) REVERT: D 19 LEU cc_start: 0.8972 (mp) cc_final: 0.8770 (mp) REVERT: D 38 ARG cc_start: 0.8609 (tmm-80) cc_final: 0.8105 (tmm-80) REVERT: D 41 GLU cc_start: 0.8525 (mp0) cc_final: 0.7702 (mp0) REVERT: D 58 MET cc_start: 0.8049 (ttp) cc_final: 0.7556 (tpp) REVERT: A 20 THR cc_start: 0.9110 (p) cc_final: 0.8864 (t) REVERT: B 84 VAL cc_start: 0.8185 (m) cc_final: 0.7052 (m) REVERT: B 134 ASP cc_start: 0.9022 (m-30) cc_final: 0.8391 (t0) REVERT: B 163 ASN cc_start: 0.9000 (m-40) cc_final: 0.8765 (m-40) REVERT: B 206 LEU cc_start: 0.8852 (mt) cc_final: 0.8299 (mt) REVERT: B 217 HIS cc_start: 0.9160 (t-90) cc_final: 0.8841 (t70) REVERT: C 282 ILE cc_start: 0.9106 (mm) cc_final: 0.8826 (mm) REVERT: E 297 ASP cc_start: 0.8942 (m-30) cc_final: 0.8702 (p0) REVERT: F 198 HIS cc_start: 0.8109 (t-90) cc_final: 0.7825 (t-90) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2708 time to fit residues: 104.2563 Evaluate side-chains 210 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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: 8.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN F 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15146 Z= 0.203 Angle : 0.621 7.191 21110 Z= 0.339 Chirality : 0.041 0.167 2379 Planarity : 0.004 0.056 2203 Dihedral : 24.536 179.338 3215 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: -0.76 (0.21), residues: 1459 helix: 0.44 (0.19), residues: 678 sheet: -1.28 (0.32), residues: 222 loop : -1.24 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 83 HIS 0.005 0.001 HIS C 68 PHE 0.022 0.001 PHE K 224 TYR 0.033 0.002 TYR B 194 ARG 0.006 0.000 ARG B 150 *********************** 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 277 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6141 (mtt180) cc_final: 0.4183 (mtm180) REVERT: K 147 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6979 (tm-30) REVERT: K 161 PHE cc_start: 0.7961 (t80) cc_final: 0.7521 (t80) REVERT: K 220 LEU cc_start: 0.6549 (tt) cc_final: 0.6276 (tt) REVERT: K 271 ARG cc_start: 0.8419 (mtt180) cc_final: 0.7885 (mmt180) REVERT: D 4 THR cc_start: 0.8362 (t) cc_final: 0.7569 (t) REVERT: D 6 ILE cc_start: 0.8777 (mt) cc_final: 0.8527 (mt) REVERT: D 41 GLU cc_start: 0.8451 (mp0) cc_final: 0.8233 (mp0) REVERT: D 58 MET cc_start: 0.8110 (ttp) cc_final: 0.7532 (tpp) REVERT: A 20 THR cc_start: 0.9121 (p) cc_final: 0.8861 (t) REVERT: B 134 ASP cc_start: 0.9223 (m-30) cc_final: 0.8499 (t0) REVERT: B 163 ASN cc_start: 0.8965 (m-40) cc_final: 0.8752 (m-40) REVERT: B 217 HIS cc_start: 0.9054 (t-90) cc_final: 0.8689 (t70) REVERT: C 23 THR cc_start: 0.9379 (p) cc_final: 0.9126 (t) REVERT: C 83 TRP cc_start: 0.8348 (m100) cc_final: 0.8059 (m100) REVERT: C 282 ILE cc_start: 0.9110 (mm) cc_final: 0.8752 (mm) REVERT: E 297 ASP cc_start: 0.8920 (m-30) cc_final: 0.8710 (p0) REVERT: F 15 LEU cc_start: 0.9235 (mt) cc_final: 0.8989 (mt) REVERT: F 19 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7313 (mm-30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2840 time to fit residues: 115.5371 Evaluate side-chains 219 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 120 optimal weight: 0.0370 chunk 139 optimal weight: 0.2980 chunk 146 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 212 HIS B 190 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** E 29 HIS ** 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: 0.7463 moved from start: 0.3677 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= 0.188 Angle : 0.625 8.109 21110 Z= 0.339 Chirality : 0.042 0.211 2379 Planarity : 0.004 0.058 2203 Dihedral : 24.485 179.721 3215 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: -0.67 (0.21), residues: 1459 helix: 0.51 (0.19), residues: 682 sheet: -1.11 (0.33), residues: 223 loop : -1.25 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 44 HIS 0.005 0.001 HIS C 68 PHE 0.026 0.001 PHE K 224 TYR 0.031 0.001 TYR B 194 ARG 0.010 0.001 ARG D 40 *********************** 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 288 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.700 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: K 142 ARG cc_start: 0.6200 (mtt180) cc_final: 0.4254 (mtm180) REVERT: K 147 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6974 (tm-30) REVERT: K 161 PHE cc_start: 0.8008 (t80) cc_final: 0.7588 (t80) REVERT: K 219 PHE cc_start: 0.4058 (t80) cc_final: 0.3548 (t80) REVERT: K 220 LEU cc_start: 0.6545 (tt) cc_final: 0.6295 (tt) REVERT: K 271 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7885 (mmp-170) REVERT: D 28 THR cc_start: 0.9136 (p) cc_final: 0.8877 (t) REVERT: D 41 GLU cc_start: 0.8378 (mp0) cc_final: 0.7872 (mp0) REVERT: D 58 MET cc_start: 0.8123 (ttp) cc_final: 0.7622 (tpp) REVERT: A 20 THR cc_start: 0.9103 (p) cc_final: 0.8846 (t) REVERT: A 44 TRP cc_start: 0.8210 (t60) cc_final: 0.7864 (t60) REVERT: A 49 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8063 (mt-10) REVERT: A 71 LEU cc_start: 0.8480 (tp) cc_final: 0.7097 (tp) REVERT: B 134 ASP cc_start: 0.9186 (m-30) cc_final: 0.8424 (t0) REVERT: B 163 ASN cc_start: 0.8940 (m-40) cc_final: 0.8725 (m-40) REVERT: B 186 LEU cc_start: 0.8951 (tt) cc_final: 0.8666 (tp) REVERT: B 217 HIS cc_start: 0.8959 (t-90) cc_final: 0.8600 (t70) REVERT: C 60 LEU cc_start: 0.9044 (mt) cc_final: 0.8811 (mt) REVERT: C 83 TRP cc_start: 0.8302 (m100) cc_final: 0.8079 (m100) REVERT: C 277 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8119 (tp-100) REVERT: E 90 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7037 (mtm110) REVERT: E 297 ASP cc_start: 0.8958 (m-30) cc_final: 0.8750 (p0) REVERT: F 15 LEU cc_start: 0.9191 (mt) cc_final: 0.8926 (mt) REVERT: F 17 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7592 (ptp-170) REVERT: F 19 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7224 (mm-30) REVERT: F 115 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8952 (tm-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3050 time to fit residues: 126.5767 Evaluate side-chains 223 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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: 0.7980 chunk 142 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** 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 183 ASN C 253 GLN ** E 29 HIS ** 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: 0.7499 moved from start: 0.3781 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= 0.217 Angle : 0.643 9.403 21110 Z= 0.348 Chirality : 0.042 0.255 2379 Planarity : 0.004 0.063 2203 Dihedral : 24.502 178.593 3215 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 0.51 (0.19), residues: 680 sheet: -1.24 (0.33), residues: 223 loop : -1.20 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 83 HIS 0.006 0.001 HIS C 68 PHE 0.026 0.002 PHE K 224 TYR 0.036 0.002 TYR B 155 ARG 0.007 0.000 ARG B 150 *********************** 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 275 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.493 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 142 ARG cc_start: 0.6139 (mtt180) cc_final: 0.4171 (mtm180) REVERT: K 147 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6976 (tm-30) REVERT: K 161 PHE cc_start: 0.7950 (t80) cc_final: 0.7515 (t80) REVERT: K 188 GLU cc_start: 0.4195 (tp30) cc_final: 0.3748 (tp30) REVERT: K 219 PHE cc_start: 0.3840 (t80) cc_final: 0.3557 (t80) REVERT: K 220 LEU cc_start: 0.6458 (tt) cc_final: 0.6197 (tt) REVERT: K 271 ARG cc_start: 0.8453 (mtt180) cc_final: 0.7886 (mmp-170) REVERT: D 28 THR cc_start: 0.9106 (p) cc_final: 0.8855 (t) REVERT: D 38 ARG cc_start: 0.8528 (tmm-80) cc_final: 0.7891 (tmm-80) REVERT: D 41 GLU cc_start: 0.8394 (mp0) cc_final: 0.7558 (mp0) REVERT: D 51 MET cc_start: 0.7912 (ptp) cc_final: 0.7584 (ptp) REVERT: D 58 MET cc_start: 0.8190 (ttp) cc_final: 0.7743 (tpp) REVERT: D 69 ASP cc_start: 0.8294 (t70) cc_final: 0.7968 (t70) REVERT: A 49 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8068 (mt-10) REVERT: A 71 LEU cc_start: 0.8347 (tp) cc_final: 0.6554 (tp) REVERT: B 134 ASP cc_start: 0.9190 (m-30) cc_final: 0.8403 (t0) REVERT: B 163 ASN cc_start: 0.8943 (m-40) cc_final: 0.8729 (m-40) REVERT: B 217 HIS cc_start: 0.8955 (t-90) cc_final: 0.8607 (t70) REVERT: B 223 TYR cc_start: 0.8116 (m-80) cc_final: 0.7643 (m-80) REVERT: C 277 GLN cc_start: 0.8441 (tp-100) cc_final: 0.8178 (tp-100) REVERT: E 90 ARG cc_start: 0.7758 (ttm110) cc_final: 0.7343 (mmm160) REVERT: F 15 LEU cc_start: 0.9214 (mt) cc_final: 0.8948 (mt) REVERT: F 19 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7353 (mm-30) REVERT: F 54 MET cc_start: 0.8331 (mmm) cc_final: 0.7810 (mmt) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2734 time to fit residues: 109.2458 Evaluate side-chains 212 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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: 9.9990 chunk 71 optimal weight: 0.0770 chunk 104 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 145 optimal weight: 0.0040 chunk 126 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9954 ------------------------------------------------------------------------------- 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 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** E 29 HIS ** 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: 0.7471 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15146 Z= 0.198 Angle : 0.646 9.469 21110 Z= 0.348 Chirality : 0.043 0.267 2379 Planarity : 0.004 0.061 2203 Dihedral : 24.495 179.858 3215 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.63 (0.21), residues: 1459 helix: 0.57 (0.19), residues: 679 sheet: -1.16 (0.33), residues: 223 loop : -1.22 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 296 HIS 0.005 0.001 HIS C 146 PHE 0.023 0.001 PHE K 224 TYR 0.030 0.001 TYR B 155 ARG 0.007 0.001 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 265 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6250 (mtt180) cc_final: 0.4314 (mtm180) REVERT: K 147 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7165 (tm-30) REVERT: K 161 PHE cc_start: 0.7985 (t80) cc_final: 0.7538 (t80) REVERT: K 188 GLU cc_start: 0.4205 (tp30) cc_final: 0.3773 (tp30) REVERT: K 219 PHE cc_start: 0.3760 (t80) cc_final: 0.3552 (t80) REVERT: K 220 LEU cc_start: 0.6467 (tt) cc_final: 0.6194 (tt) REVERT: K 271 ARG cc_start: 0.8469 (mtt180) cc_final: 0.7895 (mmp-170) REVERT: D 6 ILE cc_start: 0.8895 (pt) cc_final: 0.8544 (pt) REVERT: D 28 THR cc_start: 0.9086 (p) cc_final: 0.8818 (t) REVERT: D 38 ARG cc_start: 0.8521 (tmm-80) cc_final: 0.7919 (tmm-80) REVERT: D 41 GLU cc_start: 0.8453 (mp0) cc_final: 0.7586 (mp0) REVERT: D 58 MET cc_start: 0.8118 (ttp) cc_final: 0.7517 (tpp) REVERT: D 69 ASP cc_start: 0.8253 (t70) cc_final: 0.8011 (t70) REVERT: A 20 THR cc_start: 0.9102 (p) cc_final: 0.8864 (t) REVERT: B 134 ASP cc_start: 0.9196 (m-30) cc_final: 0.8434 (t0) REVERT: B 163 ASN cc_start: 0.8935 (m-40) cc_final: 0.8725 (m-40) REVERT: B 217 HIS cc_start: 0.9029 (t-90) cc_final: 0.8668 (t-90) REVERT: B 223 TYR cc_start: 0.7825 (m-80) cc_final: 0.7572 (m-80) REVERT: C 81 LEU cc_start: 0.8887 (mm) cc_final: 0.8684 (mm) REVERT: C 277 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8127 (tp-100) REVERT: E 90 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7221 (mtm110) REVERT: E 171 TYR cc_start: 0.7945 (p90) cc_final: 0.7733 (p90) REVERT: F 15 LEU cc_start: 0.9152 (mt) cc_final: 0.8876 (mt) REVERT: F 116 ARG cc_start: 0.9342 (mmm-85) cc_final: 0.8973 (ppt170) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2745 time to fit residues: 105.4643 Evaluate side-chains 210 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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: 0.8980 chunk 116 optimal weight: 0.4980 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 126 optimal weight: 0.0000 chunk 52 optimal weight: 0.0070 chunk 129 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 212 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.103508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080299 restraints weight = 82200.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.082734 restraints weight = 45044.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.084235 restraints weight = 30475.680| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15146 Z= 0.191 Angle : 0.644 9.367 21110 Z= 0.347 Chirality : 0.042 0.231 2379 Planarity : 0.004 0.060 2203 Dihedral : 24.443 179.170 3215 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.61 (0.21), residues: 1459 helix: 0.58 (0.19), residues: 681 sheet: -1.12 (0.33), residues: 220 loop : -1.24 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 83 HIS 0.007 0.001 HIS C 146 PHE 0.023 0.001 PHE K 224 TYR 0.029 0.002 TYR B 155 ARG 0.006 0.000 ARG B 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3062.18 seconds wall clock time: 56 minutes 41.37 seconds (3401.37 seconds total)