Starting phenix.real_space_refine on Wed Feb 12 18:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8n_24898/02_2025/7s8n_24898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8n_24898/02_2025/7s8n_24898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8n_24898/02_2025/7s8n_24898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8n_24898/02_2025/7s8n_24898.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8n_24898/02_2025/7s8n_24898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8n_24898/02_2025/7s8n_24898.cif" } resolution = 2.9 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= 0.026 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5232 2.51 5 N 1386 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8154 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2475 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1872 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'8IU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.34, per 1000 atoms: 0.78 Number of scatterers: 8154 At special positions: 0 Unit cell: (91.91, 121.03, 128.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1483 8.00 N 1386 7.00 C 5232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.5% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.593A pdb=" N THR B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.592A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.671A pdb=" N ALA B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.837A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.586A pdb=" N ASP B 162 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.601A pdb=" N THR B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 4.024A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.633A pdb=" N LYS C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.567A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.878A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'R' and resid 30 through 57 removed outlier: 4.115A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 Processing helix chain 'R' and resid 103 through 133 removed outlier: 4.009A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 211 Processing helix chain 'R' and resid 219 through 245 Proline residue: R 238 - end of helix Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.547A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.600A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.660A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.838A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.657A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.822A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.793A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.593A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.590A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.519A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.876A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.652A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.652A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 147 409 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2615 1.34 - 1.46: 2011 1.46 - 1.58: 3634 1.58 - 1.70: 1 1.70 - 1.82: 72 Bond restraints: 8333 Sorted by residual: bond pdb=" C03 8IU R 401 " pdb=" C04 8IU R 401 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C04 8IU R 401 " pdb=" N05 8IU R 401 " ideal model delta sigma weight residual 1.457 1.647 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C21 8IU R 401 " pdb=" N05 8IU R 401 " ideal model delta sigma weight residual 1.470 1.319 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C03 8IU R 401 " pdb=" N02 8IU R 401 " ideal model delta sigma weight residual 1.448 1.546 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" N19 8IU R 401 " pdb=" N20 8IU R 401 " ideal model delta sigma weight residual 1.341 1.437 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 8328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 10881 1.99 - 3.98: 394 3.98 - 5.98: 52 5.98 - 7.97: 18 7.97 - 9.96: 4 Bond angle restraints: 11349 Sorted by residual: angle pdb=" N PHE C 234 " pdb=" CA PHE C 234 " pdb=" C PHE C 234 " ideal model delta sigma weight residual 110.48 116.07 -5.59 1.48e+00 4.57e-01 1.43e+01 angle pdb=" N VAL B 219 " pdb=" CA VAL B 219 " pdb=" C VAL B 219 " ideal model delta sigma weight residual 112.90 110.00 2.90 9.60e-01 1.09e+00 9.15e+00 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 109.81 116.45 -6.64 2.21e+00 2.05e-01 9.04e+00 angle pdb=" C GLY R 236 " pdb=" N LEU R 237 " pdb=" CA LEU R 237 " ideal model delta sigma weight residual 121.80 114.49 7.31 2.44e+00 1.68e-01 8.98e+00 angle pdb=" CA CYS E 217 " pdb=" CB CYS E 217 " pdb=" SG CYS E 217 " ideal model delta sigma weight residual 114.40 120.99 -6.59 2.30e+00 1.89e-01 8.21e+00 ... (remaining 11344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4379 17.20 - 34.41: 401 34.41 - 51.61: 59 51.61 - 68.81: 5 68.81 - 86.01: 3 Dihedral angle restraints: 4847 sinusoidal: 1702 harmonic: 3145 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 147.42 -54.42 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CA MET E 128 " pdb=" C MET E 128 " pdb=" N THR E 129 " pdb=" CA THR E 129 " ideal model delta harmonic sigma weight residual -180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASP B 199 " pdb=" C ASP B 199 " pdb=" N ILE B 200 " pdb=" CA ILE B 200 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 4844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 662 0.037 - 0.075: 432 0.075 - 0.112: 169 0.112 - 0.149: 50 0.149 - 0.187: 10 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA PRO R 238 " pdb=" N PRO R 238 " pdb=" C PRO R 238 " pdb=" CB PRO R 238 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CG LEU R 160 " pdb=" CB LEU R 160 " pdb=" CD1 LEU R 160 " pdb=" CD2 LEU R 160 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 1320 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 233 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C LEU R 233 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU R 233 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU R 234 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 172 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO E 173 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 173 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 173 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 151 " 0.024 2.00e-02 2.50e+03 1.57e-02 4.31e+00 pdb=" CG PHE C 151 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE C 151 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 151 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 151 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 151 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 151 " 0.009 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1084 2.74 - 3.28: 7119 3.28 - 3.82: 12207 3.82 - 4.36: 13688 4.36 - 4.90: 26018 Nonbonded interactions: 60116 Sorted by model distance: nonbonded pdb=" O VAL B 198 " pdb=" OG SER B 201 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 2.220 3.040 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.273 3.040 nonbonded pdb=" ND2 ASN R 48 " pdb=" OD2 ASP R 75 " model vdw 2.331 3.120 nonbonded pdb=" O THR C 86 " pdb=" OG1 THR C 87 " model vdw 2.383 3.040 ... (remaining 60111 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.530 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.012 0.219 8333 Z= 0.758 Angle : 0.896 9.959 11349 Z= 0.478 Chirality : 0.056 0.187 1323 Planarity : 0.005 0.056 1426 Dihedral : 13.071 86.015 2811 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.33 (0.25), residues: 1070 helix: 1.55 (0.28), residues: 362 sheet: 0.01 (0.31), residues: 256 loop : -1.89 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP R 243 HIS 0.016 0.003 HIS C 54 PHE 0.033 0.003 PHE C 235 TYR 0.016 0.003 TYR E 163 ARG 0.012 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.848 Fit side-chains REVERT: B 10 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7682 (mtmm) REVERT: B 35 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8138 (mtp85) REVERT: B 80 ASN cc_start: 0.8131 (m-40) cc_final: 0.7897 (m110) REVERT: B 128 ILE cc_start: 0.8210 (tp) cc_final: 0.7948 (tp) REVERT: C 23 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7814 (ttpt) REVERT: C 219 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6801 (mtt90) REVERT: C 291 ASP cc_start: 0.7896 (p0) cc_final: 0.7674 (p0) REVERT: R 55 LEU cc_start: 0.8354 (mt) cc_final: 0.8107 (mt) REVERT: E 3 GLN cc_start: 0.7989 (mt0) cc_final: 0.7766 (mt0) REVERT: E 185 SER cc_start: 0.8242 (m) cc_final: 0.7962 (p) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 1.1083 time to fit residues: 210.1619 Evaluate side-chains 157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 101 ASN C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094924 restraints weight = 12081.170| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.86 r_work: 0.3090 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8333 Z= 0.210 Angle : 0.596 7.218 11349 Z= 0.319 Chirality : 0.043 0.140 1323 Planarity : 0.004 0.041 1426 Dihedral : 4.684 31.538 1182 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.95 % Allowed : 8.91 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1070 helix: 2.35 (0.29), residues: 366 sheet: 0.32 (0.30), residues: 279 loop : -1.62 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.005 0.001 HIS C 54 PHE 0.013 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.008 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.888 Fit side-chains REVERT: B 10 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7723 (mttm) REVERT: B 35 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8512 (mtp85) REVERT: B 128 ILE cc_start: 0.8411 (tp) cc_final: 0.8177 (tp) REVERT: C 23 LYS cc_start: 0.8299 (ttpt) cc_final: 0.8023 (ttmm) REVERT: E 93 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8117 (ttt) outliers start: 16 outliers final: 7 residues processed: 164 average time/residue: 1.1620 time to fit residues: 202.8660 Evaluate side-chains 157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 93 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.093317 restraints weight = 12263.129| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.85 r_work: 0.3065 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8333 Z= 0.304 Angle : 0.622 6.721 11349 Z= 0.330 Chirality : 0.044 0.138 1323 Planarity : 0.004 0.041 1426 Dihedral : 4.564 30.549 1182 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.69 % Allowed : 12.70 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.65 (0.27), residues: 1070 helix: 2.56 (0.29), residues: 366 sheet: 0.46 (0.31), residues: 282 loop : -1.60 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 243 HIS 0.007 0.002 HIS C 54 PHE 0.017 0.002 PHE C 151 TYR 0.017 0.002 TYR E 178 ARG 0.005 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.751 Fit side-chains REVERT: B 128 ILE cc_start: 0.8472 (tp) cc_final: 0.8259 (tp) REVERT: B 195 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7443 (ttpt) REVERT: C 23 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8046 (ttpt) REVERT: C 72 SER cc_start: 0.8696 (m) cc_final: 0.8486 (p) REVERT: C 146 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 165 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8180 (p) REVERT: E 93 MET cc_start: 0.8486 (ttp) cc_final: 0.8189 (ttt) REVERT: E 179 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7085 (mtp180) REVERT: E 211 ASP cc_start: 0.7607 (t0) cc_final: 0.7205 (t0) outliers start: 22 outliers final: 10 residues processed: 163 average time/residue: 1.1620 time to fit residues: 201.4764 Evaluate side-chains 162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.091589 restraints weight = 12194.267| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.86 r_work: 0.3036 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8333 Z= 0.385 Angle : 0.664 7.734 11349 Z= 0.352 Chirality : 0.046 0.141 1323 Planarity : 0.004 0.043 1426 Dihedral : 4.616 25.659 1182 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.42 % Allowed : 15.14 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.27), residues: 1070 helix: 2.38 (0.29), residues: 373 sheet: 0.62 (0.31), residues: 281 loop : -1.68 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 243 HIS 0.010 0.002 HIS C 54 PHE 0.020 0.002 PHE C 151 TYR 0.017 0.002 TYR E 178 ARG 0.006 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.903 Fit side-chains REVERT: B 10 LYS cc_start: 0.8277 (mtpm) cc_final: 0.7961 (mttm) REVERT: B 195 LYS cc_start: 0.7772 (ttpt) cc_final: 0.7413 (ttpt) REVERT: C 23 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8091 (ttpt) REVERT: C 146 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8351 (mp) REVERT: C 165 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8184 (p) REVERT: C 256 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7080 (mtt180) REVERT: R 55 LEU cc_start: 0.8363 (mt) cc_final: 0.8086 (mt) REVERT: R 272 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7950 (t) REVERT: E 3 GLN cc_start: 0.8537 (mt0) cc_final: 0.8291 (mt0) REVERT: E 93 MET cc_start: 0.8503 (ttp) cc_final: 0.8227 (ttt) REVERT: E 179 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: E 211 ASP cc_start: 0.7657 (t0) cc_final: 0.7263 (t0) outliers start: 28 outliers final: 13 residues processed: 168 average time/residue: 1.1584 time to fit residues: 207.1569 Evaluate side-chains 171 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 181 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094468 restraints weight = 12099.585| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.85 r_work: 0.3077 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8333 Z= 0.210 Angle : 0.562 6.609 11349 Z= 0.298 Chirality : 0.042 0.135 1323 Planarity : 0.004 0.039 1426 Dihedral : 4.269 23.879 1182 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.93 % Allowed : 16.97 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.92 (0.27), residues: 1070 helix: 2.77 (0.29), residues: 366 sheet: 0.70 (0.31), residues: 283 loop : -1.52 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.004 0.001 HIS C 54 PHE 0.012 0.001 PHE C 151 TYR 0.012 0.001 TYR B 163 ARG 0.003 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.033 Fit side-chains REVERT: B 10 LYS cc_start: 0.8052 (mtpm) cc_final: 0.7764 (mttm) REVERT: B 195 LYS cc_start: 0.7745 (ttpt) cc_final: 0.7380 (ttpt) REVERT: C 23 LYS cc_start: 0.8381 (ttpt) cc_final: 0.8061 (ttpt) REVERT: C 72 SER cc_start: 0.8686 (m) cc_final: 0.8468 (p) REVERT: R 55 LEU cc_start: 0.8327 (mt) cc_final: 0.8040 (mt) REVERT: R 272 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7990 (t) REVERT: E 3 GLN cc_start: 0.8507 (mt0) cc_final: 0.8273 (mt0) REVERT: E 93 MET cc_start: 0.8482 (ttp) cc_final: 0.8207 (ttt) REVERT: E 179 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7009 (mtp180) REVERT: E 211 ASP cc_start: 0.7566 (t0) cc_final: 0.7187 (t0) outliers start: 24 outliers final: 13 residues processed: 157 average time/residue: 1.2060 time to fit residues: 200.9502 Evaluate side-chains 161 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092297 restraints weight = 12073.912| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.92 r_work: 0.3044 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8333 Z= 0.338 Angle : 0.625 7.127 11349 Z= 0.331 Chirality : 0.045 0.153 1323 Planarity : 0.004 0.040 1426 Dihedral : 4.437 24.015 1182 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.66 % Allowed : 17.70 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.27), residues: 1070 helix: 2.68 (0.29), residues: 367 sheet: 0.75 (0.31), residues: 279 loop : -1.53 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 243 HIS 0.007 0.002 HIS C 54 PHE 0.018 0.002 PHE C 151 TYR 0.017 0.002 TYR E 178 ARG 0.005 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.841 Fit side-chains REVERT: B 10 LYS cc_start: 0.8200 (mtpm) cc_final: 0.7880 (mttm) REVERT: B 195 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7346 (ttpt) REVERT: C 23 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8077 (ttpt) REVERT: C 146 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8343 (mp) REVERT: C 165 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8159 (p) REVERT: C 256 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7119 (mtt180) REVERT: R 55 LEU cc_start: 0.8312 (mt) cc_final: 0.8001 (mt) REVERT: R 272 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7943 (t) REVERT: E 3 GLN cc_start: 0.8547 (mt0) cc_final: 0.8304 (mt0) REVERT: E 93 MET cc_start: 0.8496 (ttp) cc_final: 0.8209 (ttt) REVERT: E 179 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7149 (mtp180) REVERT: E 201 THR cc_start: 0.8281 (t) cc_final: 0.8051 (p) REVERT: E 211 ASP cc_start: 0.7657 (t0) cc_final: 0.7257 (t0) outliers start: 30 outliers final: 16 residues processed: 164 average time/residue: 1.1440 time to fit residues: 199.5192 Evaluate side-chains 169 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 100 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094891 restraints weight = 12132.917| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.93 r_work: 0.3092 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8333 Z= 0.179 Angle : 0.540 6.546 11349 Z= 0.285 Chirality : 0.041 0.132 1323 Planarity : 0.004 0.053 1426 Dihedral : 4.110 23.537 1182 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.30 % Allowed : 18.44 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.08 (0.27), residues: 1070 helix: 2.88 (0.29), residues: 367 sheet: 0.76 (0.31), residues: 288 loop : -1.41 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE C 241 TYR 0.011 0.001 TYR E 95 ARG 0.013 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.967 Fit side-chains REVERT: B 10 LYS cc_start: 0.7947 (mtpm) cc_final: 0.7656 (mttm) REVERT: B 195 LYS cc_start: 0.7700 (ttpt) cc_final: 0.7336 (ttpt) REVERT: C 23 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7956 (ttmm) REVERT: C 72 SER cc_start: 0.8704 (m) cc_final: 0.8465 (p) REVERT: C 146 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8343 (mp) REVERT: C 165 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8185 (p) REVERT: R 55 LEU cc_start: 0.8298 (mt) cc_final: 0.8050 (mt) REVERT: R 272 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7938 (t) REVERT: E 3 GLN cc_start: 0.8551 (mt0) cc_final: 0.8306 (mt0) REVERT: E 93 MET cc_start: 0.8474 (ttp) cc_final: 0.8188 (ttt) REVERT: E 179 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.6766 (mtp180) REVERT: E 211 ASP cc_start: 0.7535 (t0) cc_final: 0.7163 (t0) outliers start: 27 outliers final: 12 residues processed: 163 average time/residue: 1.1841 time to fit residues: 204.9698 Evaluate side-chains 161 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.095193 restraints weight = 12304.700| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.94 r_work: 0.3094 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8333 Z= 0.177 Angle : 0.536 7.094 11349 Z= 0.282 Chirality : 0.041 0.132 1323 Planarity : 0.004 0.042 1426 Dihedral : 4.031 23.508 1182 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.44 % Allowed : 18.68 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.17 (0.27), residues: 1070 helix: 2.97 (0.29), residues: 367 sheet: 0.76 (0.31), residues: 288 loop : -1.34 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE R 64 TYR 0.014 0.001 TYR B 163 ARG 0.008 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.019 Fit side-chains REVERT: B 10 LYS cc_start: 0.7861 (mtpm) cc_final: 0.7588 (mttm) REVERT: B 195 LYS cc_start: 0.7635 (ttpt) cc_final: 0.7340 (ttpt) REVERT: C 23 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7929 (ttmm) REVERT: C 72 SER cc_start: 0.8711 (m) cc_final: 0.8472 (p) REVERT: C 146 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8355 (mp) REVERT: C 165 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8193 (p) REVERT: R 55 LEU cc_start: 0.8265 (mt) cc_final: 0.7984 (mt) REVERT: R 272 SER cc_start: 0.8267 (OUTLIER) cc_final: 0.8020 (t) REVERT: E 3 GLN cc_start: 0.8566 (mt0) cc_final: 0.8329 (mt0) REVERT: E 51 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8104 (tp) REVERT: E 93 MET cc_start: 0.8481 (ttp) cc_final: 0.8200 (ttt) REVERT: E 179 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.6786 (mtp180) REVERT: E 201 THR cc_start: 0.8317 (t) cc_final: 0.8086 (p) REVERT: E 211 ASP cc_start: 0.7527 (t0) cc_final: 0.7164 (t0) outliers start: 20 outliers final: 13 residues processed: 152 average time/residue: 1.2494 time to fit residues: 201.8200 Evaluate side-chains 156 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093951 restraints weight = 12377.930| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.95 r_work: 0.3080 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8333 Z= 0.218 Angle : 0.563 7.305 11349 Z= 0.295 Chirality : 0.042 0.133 1323 Planarity : 0.004 0.061 1426 Dihedral : 4.102 23.596 1182 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.30 % Allowed : 18.80 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.15 (0.27), residues: 1070 helix: 2.99 (0.29), residues: 365 sheet: 0.78 (0.31), residues: 288 loop : -1.39 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 243 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.013 0.001 TYR E 178 ARG 0.016 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.845 Fit side-chains REVERT: B 10 LYS cc_start: 0.7993 (mtpm) cc_final: 0.7706 (mttm) REVERT: B 195 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7366 (ttpt) REVERT: C 23 LYS cc_start: 0.8298 (ttpt) cc_final: 0.7937 (ttmm) REVERT: C 72 SER cc_start: 0.8735 (m) cc_final: 0.8482 (p) REVERT: C 165 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8171 (p) REVERT: C 219 ARG cc_start: 0.7770 (mtt90) cc_final: 0.7519 (mtt90) REVERT: R 55 LEU cc_start: 0.8287 (mt) cc_final: 0.7995 (mt) REVERT: R 272 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.8036 (t) REVERT: E 3 GLN cc_start: 0.8560 (mt0) cc_final: 0.8330 (mt0) REVERT: E 93 MET cc_start: 0.8491 (ttp) cc_final: 0.8208 (ttt) REVERT: E 179 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.6817 (mtp180) REVERT: E 201 THR cc_start: 0.8318 (t) cc_final: 0.8085 (p) REVERT: E 211 ASP cc_start: 0.7557 (t0) cc_final: 0.7194 (t0) outliers start: 27 outliers final: 17 residues processed: 152 average time/residue: 1.1770 time to fit residues: 189.9986 Evaluate side-chains 159 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 60 optimal weight: 0.0000 chunk 48 optimal weight: 0.0470 chunk 3 optimal weight: 0.8980 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097040 restraints weight = 12149.044| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.93 r_work: 0.3126 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8333 Z= 0.149 Angle : 0.516 7.325 11349 Z= 0.271 Chirality : 0.041 0.141 1323 Planarity : 0.004 0.062 1426 Dihedral : 3.880 23.563 1182 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.20 % Allowed : 20.15 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.30 (0.27), residues: 1070 helix: 3.09 (0.29), residues: 366 sheet: 0.79 (0.31), residues: 293 loop : -1.25 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE C 241 TYR 0.011 0.001 TYR B 163 ARG 0.016 0.000 ARG B 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.972 Fit side-chains REVERT: B 10 LYS cc_start: 0.7705 (mtpm) cc_final: 0.7437 (mttm) REVERT: B 15 ARG cc_start: 0.8406 (ttt90) cc_final: 0.8174 (ttm-80) REVERT: B 195 LYS cc_start: 0.7597 (ttpt) cc_final: 0.6955 (ttpt) REVERT: B 199 ASP cc_start: 0.7590 (p0) cc_final: 0.7249 (p0) REVERT: C 23 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7917 (ttmm) REVERT: C 72 SER cc_start: 0.8718 (m) cc_final: 0.8464 (p) REVERT: C 165 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8193 (p) REVERT: C 312 ASP cc_start: 0.7962 (t0) cc_final: 0.7747 (t70) REVERT: R 162 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.7018 (mp) REVERT: R 272 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.8035 (t) REVERT: E 3 GLN cc_start: 0.8551 (mt0) cc_final: 0.8305 (mt0) REVERT: E 93 MET cc_start: 0.8476 (ttp) cc_final: 0.8195 (ttt) REVERT: E 179 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.6494 (mtp180) REVERT: E 201 THR cc_start: 0.8298 (t) cc_final: 0.8067 (p) REVERT: E 211 ASP cc_start: 0.7475 (t0) cc_final: 0.7098 (t0) outliers start: 18 outliers final: 9 residues processed: 149 average time/residue: 1.2632 time to fit residues: 199.1746 Evaluate side-chains 152 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.093271 restraints weight = 12259.641| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.94 r_work: 0.3060 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8333 Z= 0.290 Angle : 0.607 7.682 11349 Z= 0.318 Chirality : 0.043 0.139 1323 Planarity : 0.004 0.067 1426 Dihedral : 4.185 23.623 1182 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.20 % Allowed : 20.51 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.18 (0.27), residues: 1070 helix: 2.99 (0.29), residues: 367 sheet: 0.82 (0.31), residues: 282 loop : -1.36 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 243 HIS 0.008 0.002 HIS E 35 PHE 0.016 0.002 PHE C 234 TYR 0.016 0.002 TYR E 178 ARG 0.016 0.001 ARG B 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6028.71 seconds wall clock time: 107 minutes 24.07 seconds (6444.07 seconds total)