Starting phenix.real_space_refine on Wed Jul 30 07:18:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k20_22638/07_2025/7k20_22638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k20_22638/07_2025/7k20_22638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k20_22638/07_2025/7k20_22638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k20_22638/07_2025/7k20_22638.map" model { file = "/net/cci-nas-00/data/ceres_data/7k20_22638/07_2025/7k20_22638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k20_22638/07_2025/7k20_22638.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7480 2.51 5 N 1984 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11828 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.81, per 1000 atoms: 0.66 Number of scatterers: 11828 At special positions: 0 Unit cell: (100.32, 77.33, 164.065, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 8 15.00 Mg 4 11.99 O 2268 8.00 N 1984 7.00 C 7480 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 20 sheets defined 41.5% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.995A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.636A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.677A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.676A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.765A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.751A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.732A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.506A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.629A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.751A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 359 through 366 removed outlier: 4.013A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.920A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.620A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.517A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 4.016A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.977A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.554A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.665A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.545A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.883A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.913A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.551A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.607A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.667A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 359 through 366 removed outlier: 4.032A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.837A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS B 374 " --> pdb=" O HIS B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.558A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.629A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.983A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 removed outlier: 3.558A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.726A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.514A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.737A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.658A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.664A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.222A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.516A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 364 removed outlier: 4.107A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 removed outlier: 3.584A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS C 374 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.503A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.987A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 146 removed outlier: 3.639A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.772A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.538A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.897A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 removed outlier: 3.653A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.639A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.598A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.549A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 359 through 366 removed outlier: 4.090A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 removed outlier: 4.105A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS D 374 " --> pdb=" O HIS D 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.569A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.113A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.564A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.688A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.317A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 31 removed outlier: 7.103A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.506A pdb=" N ASP D 154 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 429 hydrogen bonds defined for protein. 1083 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: 3.58 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3356 1.33 - 1.45: 2025 1.45 - 1.57: 6555 1.57 - 1.68: 12 1.68 - 1.80: 148 Bond restraints: 12096 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C2 1T4 B 803 " pdb=" N1 1T4 B 803 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" CB THR C 160 " pdb=" CG2 THR C 160 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.21e+00 ... (remaining 12091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 15593 2.11 - 4.22: 728 4.22 - 6.32: 77 6.32 - 8.43: 23 8.43 - 10.54: 7 Bond angle restraints: 16428 Sorted by residual: angle pdb=" C19 1T4 C 803 " pdb=" C17 1T4 C 803 " pdb=" N1 1T4 C 803 " ideal model delta sigma weight residual 114.67 125.21 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C19 1T4 B 803 " pdb=" C17 1T4 B 803 " pdb=" N1 1T4 B 803 " ideal model delta sigma weight residual 114.67 125.13 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 102.31 10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C19 1T4 A 803 " pdb=" C17 1T4 A 803 " pdb=" N1 1T4 A 803 " ideal model delta sigma weight residual 114.67 124.77 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " ideal model delta sigma weight residual 112.70 102.72 9.98 3.00e+00 1.11e-01 1.11e+01 ... (remaining 16423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.28: 6950 18.28 - 36.56: 219 36.56 - 54.85: 37 54.85 - 73.13: 9 73.13 - 91.41: 5 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" O1B ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " pdb=" PA ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 -151.41 91.41 1 2.00e+01 2.50e-03 2.46e+01 dihedral pdb=" CA PHE C 124 " pdb=" C PHE C 124 " pdb=" N GLU C 125 " pdb=" CA GLU C 125 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PHE A 124 " pdb=" C PHE A 124 " pdb=" N GLU A 125 " pdb=" CA GLU A 125 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1166 0.058 - 0.115: 532 0.115 - 0.172: 93 0.172 - 0.230: 10 0.230 - 0.287: 7 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB ILE C 250 " pdb=" CA ILE C 250 " pdb=" CG1 ILE C 250 " pdb=" CG2 ILE C 250 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 250 " pdb=" CA ILE A 250 " pdb=" CG1 ILE A 250 " pdb=" CG2 ILE A 250 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1805 not shown) Planarity restraints: 2092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " -0.027 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP B 340 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 243 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO C 243 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.032 5.00e-02 4.00e+02 ... (remaining 2089 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 465 2.69 - 3.24: 11220 3.24 - 3.80: 18891 3.80 - 4.35: 25732 4.35 - 4.90: 43113 Nonbonded interactions: 99421 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.141 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.158 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.159 2.170 nonbonded pdb=" OE2 GLU C 270 " pdb=" OG1 THR D 203 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 802 " model vdw 2.244 3.040 ... (remaining 99416 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.410 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.013 0.224 12100 Z= 0.671 Angle : 1.021 10.540 16428 Z= 0.521 Chirality : 0.064 0.287 1808 Planarity : 0.007 0.061 2092 Dihedral : 10.523 91.411 4468 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: -5.12 (0.16), residues: 1468 helix: -4.45 (0.09), residues: 636 sheet: -2.85 (0.27), residues: 236 loop : -2.06 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP B 340 HIS 0.007 0.002 HIS C 40 PHE 0.030 0.004 PHE D 266 TYR 0.018 0.003 TYR C 218 ARG 0.017 0.002 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.29859 ( 421) hydrogen bonds : angle 10.75294 ( 1083) covalent geometry : bond 0.01289 (12096) covalent geometry : angle 1.02058 (16428) Misc. bond : bond 0.21022 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.9017 (mmm) cc_final: 0.8717 (mmm) REVERT: C 184 ASP cc_start: 0.8042 (m-30) cc_final: 0.7790 (m-30) REVERT: C 286 ASP cc_start: 0.7268 (t0) cc_final: 0.6896 (t0) REVERT: C 355 MET cc_start: 0.8304 (mmm) cc_final: 0.8081 (mmm) REVERT: D 113 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8507 (mptt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2691 time to fit residues: 51.9429 Evaluate side-chains 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN D 59 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.079025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.065620 restraints weight = 24958.701| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.38 r_work: 0.2813 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12100 Z= 0.125 Angle : 0.573 6.373 16428 Z= 0.286 Chirality : 0.045 0.137 1808 Planarity : 0.005 0.050 2092 Dihedral : 8.201 78.092 1672 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.40 % Allowed : 5.73 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.19), residues: 1468 helix: -3.08 (0.15), residues: 612 sheet: -1.81 (0.30), residues: 236 loop : -1.18 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 340 HIS 0.004 0.001 HIS D 87 PHE 0.008 0.001 PHE A 266 TYR 0.009 0.001 TYR A 169 ARG 0.004 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 421) hydrogen bonds : angle 5.57391 ( 1083) covalent geometry : bond 0.00280 (12096) covalent geometry : angle 0.57289 (16428) Misc. bond : bond 0.00047 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 1.296 Fit side-chains REVERT: A 123 MET cc_start: 0.9429 (mmt) cc_final: 0.9189 (mmt) REVERT: A 283 MET cc_start: 0.8755 (mmm) cc_final: 0.8524 (mmm) REVERT: B 157 ASP cc_start: 0.8404 (t70) cc_final: 0.7981 (t0) REVERT: B 227 MET cc_start: 0.8988 (mmm) cc_final: 0.8398 (mmm) REVERT: B 372 ARG cc_start: 0.8490 (ptp-170) cc_final: 0.8198 (ptt-90) REVERT: C 355 MET cc_start: 0.8912 (mmm) cc_final: 0.8678 (mmm) REVERT: D 184 ASP cc_start: 0.8808 (m-30) cc_final: 0.8602 (m-30) REVERT: D 227 MET cc_start: 0.9017 (mmm) cc_final: 0.8774 (mmm) REVERT: D 313 MET cc_start: 0.9190 (mmm) cc_final: 0.8975 (mmm) outliers start: 5 outliers final: 1 residues processed: 124 average time/residue: 0.2400 time to fit residues: 43.2539 Evaluate side-chains 83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 93 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 102 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS B 161 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.066175 restraints weight = 25462.737| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.40 r_work: 0.2820 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12100 Z= 0.103 Angle : 0.529 6.124 16428 Z= 0.256 Chirality : 0.044 0.136 1808 Planarity : 0.004 0.049 2092 Dihedral : 7.416 74.538 1672 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.88 % Allowed : 6.61 % Favored : 92.52 % 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: -2.31 (0.20), residues: 1468 helix: -2.13 (0.18), residues: 612 sheet: -1.44 (0.30), residues: 236 loop : -0.63 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.003 0.001 HIS D 87 PHE 0.008 0.001 PHE C 124 TYR 0.007 0.001 TYR A 294 ARG 0.003 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.02796 ( 421) hydrogen bonds : angle 4.76361 ( 1083) covalent geometry : bond 0.00236 (12096) covalent geometry : angle 0.52901 (16428) Misc. bond : bond 0.00036 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.747 Fit side-chains REVERT: A 283 MET cc_start: 0.8727 (mmm) cc_final: 0.8460 (mmm) REVERT: B 157 ASP cc_start: 0.8406 (t70) cc_final: 0.8144 (t0) REVERT: B 227 MET cc_start: 0.8992 (mmm) cc_final: 0.8652 (mmm) REVERT: B 372 ARG cc_start: 0.8413 (ptp-170) cc_final: 0.8025 (ptt-90) REVERT: C 288 ASP cc_start: 0.7583 (p0) cc_final: 0.7379 (p0) REVERT: C 355 MET cc_start: 0.8886 (mmm) cc_final: 0.8656 (mmm) REVERT: D 269 MET cc_start: 0.8440 (mtp) cc_final: 0.7908 (mtm) REVERT: D 313 MET cc_start: 0.9159 (mmm) cc_final: 0.8928 (mmm) outliers start: 11 outliers final: 5 residues processed: 113 average time/residue: 0.2678 time to fit residues: 45.4198 Evaluate side-chains 95 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 0.0070 chunk 138 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.066005 restraints weight = 25230.871| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.35 r_work: 0.2822 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12100 Z= 0.112 Angle : 0.516 6.211 16428 Z= 0.248 Chirality : 0.044 0.132 1808 Planarity : 0.004 0.048 2092 Dihedral : 7.071 75.255 1672 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.72 % Allowed : 7.40 % Favored : 91.88 % 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: -1.50 (0.22), residues: 1468 helix: -1.46 (0.21), residues: 588 sheet: -1.17 (0.30), residues: 236 loop : -0.18 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS D 87 PHE 0.007 0.001 PHE C 124 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.02552 ( 421) hydrogen bonds : angle 4.39683 ( 1083) covalent geometry : bond 0.00261 (12096) covalent geometry : angle 0.51606 (16428) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 1.458 Fit side-chains REVERT: A 123 MET cc_start: 0.9511 (mmt) cc_final: 0.9178 (mmt) REVERT: A 157 ASP cc_start: 0.8277 (t70) cc_final: 0.7888 (t0) REVERT: A 349 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8315 (mp) REVERT: B 157 ASP cc_start: 0.8471 (t70) cc_final: 0.7973 (t0) REVERT: B 227 MET cc_start: 0.8967 (mmm) cc_final: 0.8600 (mmm) REVERT: B 372 ARG cc_start: 0.8441 (ptp-170) cc_final: 0.8051 (ptt-90) REVERT: C 288 ASP cc_start: 0.7435 (p0) cc_final: 0.7223 (p0) REVERT: C 355 MET cc_start: 0.8902 (mmm) cc_final: 0.8661 (mmm) REVERT: D 82 MET cc_start: 0.9413 (tpt) cc_final: 0.9070 (tpt) REVERT: D 269 MET cc_start: 0.8469 (mtp) cc_final: 0.7933 (mtm) REVERT: D 313 MET cc_start: 0.9133 (mmm) cc_final: 0.8873 (mmm) outliers start: 9 outliers final: 4 residues processed: 107 average time/residue: 0.2617 time to fit residues: 42.5568 Evaluate side-chains 94 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 297 ASN D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.078721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.065676 restraints weight = 25398.481| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.35 r_work: 0.2813 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12100 Z= 0.116 Angle : 0.515 6.284 16428 Z= 0.245 Chirality : 0.044 0.131 1808 Planarity : 0.004 0.045 2092 Dihedral : 6.818 75.086 1672 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.80 % Allowed : 8.12 % Favored : 91.08 % 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: -1.10 (0.22), residues: 1468 helix: -1.17 (0.22), residues: 584 sheet: -0.89 (0.31), residues: 236 loop : 0.06 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.003 0.001 HIS D 87 PHE 0.007 0.001 PHE C 124 TYR 0.006 0.001 TYR D 294 ARG 0.002 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.02480 ( 421) hydrogen bonds : angle 4.21889 ( 1083) covalent geometry : bond 0.00272 (12096) covalent geometry : angle 0.51513 (16428) Misc. bond : bond 0.00021 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.529 Fit side-chains REVERT: A 123 MET cc_start: 0.9518 (mmt) cc_final: 0.9238 (mmt) REVERT: A 157 ASP cc_start: 0.8239 (t70) cc_final: 0.7899 (t0) REVERT: A 283 MET cc_start: 0.8750 (mmm) cc_final: 0.8547 (mmt) REVERT: A 349 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8357 (mp) REVERT: B 157 ASP cc_start: 0.8462 (t70) cc_final: 0.7980 (t0) REVERT: B 227 MET cc_start: 0.8930 (mmm) cc_final: 0.8624 (mmm) REVERT: B 372 ARG cc_start: 0.8443 (ptp-170) cc_final: 0.8088 (ptt-90) REVERT: C 355 MET cc_start: 0.8918 (mmm) cc_final: 0.8642 (mmm) REVERT: D 82 MET cc_start: 0.9404 (tpt) cc_final: 0.9068 (tpt) REVERT: D 269 MET cc_start: 0.8449 (mtp) cc_final: 0.7895 (mtm) REVERT: D 313 MET cc_start: 0.9189 (mmm) cc_final: 0.8981 (mmm) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 0.2600 time to fit residues: 42.2434 Evaluate side-chains 101 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 105 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN D 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.065048 restraints weight = 25565.981| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.36 r_work: 0.2799 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12100 Z= 0.137 Angle : 0.520 6.300 16428 Z= 0.250 Chirality : 0.044 0.131 1808 Planarity : 0.004 0.044 2092 Dihedral : 6.794 77.442 1672 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.27 % Allowed : 8.52 % Favored : 90.21 % 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: -0.71 (0.22), residues: 1468 helix: -0.89 (0.22), residues: 576 sheet: -0.65 (0.31), residues: 236 loop : 0.28 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.003 0.001 HIS D 87 PHE 0.007 0.001 PHE D 200 TYR 0.009 0.001 TYR B 294 ARG 0.002 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.02532 ( 421) hydrogen bonds : angle 4.20592 ( 1083) covalent geometry : bond 0.00323 (12096) covalent geometry : angle 0.52020 (16428) Misc. bond : bond 0.00021 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 2.287 Fit side-chains REVERT: A 123 MET cc_start: 0.9493 (mmt) cc_final: 0.9209 (mmt) REVERT: A 157 ASP cc_start: 0.8387 (t70) cc_final: 0.8079 (t0) REVERT: A 283 MET cc_start: 0.8766 (mmm) cc_final: 0.8558 (mmt) REVERT: A 349 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8212 (mp) REVERT: B 157 ASP cc_start: 0.8411 (t70) cc_final: 0.7967 (t0) REVERT: B 227 MET cc_start: 0.8938 (mmm) cc_final: 0.8626 (mmm) REVERT: B 372 ARG cc_start: 0.8450 (ptp-170) cc_final: 0.8108 (ptt-90) REVERT: C 355 MET cc_start: 0.8918 (mmm) cc_final: 0.8663 (mmm) REVERT: D 82 MET cc_start: 0.9405 (tpt) cc_final: 0.9051 (tpt) REVERT: D 269 MET cc_start: 0.8480 (mtp) cc_final: 0.7997 (mtm) REVERT: D 313 MET cc_start: 0.9227 (mmm) cc_final: 0.9012 (mmm) outliers start: 16 outliers final: 10 residues processed: 108 average time/residue: 0.2949 time to fit residues: 48.8303 Evaluate side-chains 103 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 71 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.077881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.064838 restraints weight = 25643.387| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.34 r_work: 0.2793 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12100 Z= 0.149 Angle : 0.533 6.683 16428 Z= 0.256 Chirality : 0.045 0.130 1808 Planarity : 0.004 0.044 2092 Dihedral : 6.803 77.635 1672 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.04 % Allowed : 9.00 % Favored : 89.97 % 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: -0.48 (0.22), residues: 1468 helix: -0.67 (0.22), residues: 576 sheet: -0.48 (0.31), residues: 236 loop : 0.37 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.003 0.001 HIS D 87 PHE 0.008 0.001 PHE A 124 TYR 0.007 0.001 TYR B 294 ARG 0.003 0.000 ARG C 290 Details of bonding type rmsd hydrogen bonds : bond 0.02556 ( 421) hydrogen bonds : angle 4.19979 ( 1083) covalent geometry : bond 0.00353 (12096) covalent geometry : angle 0.53332 (16428) Misc. bond : bond 0.00020 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.510 Fit side-chains REVERT: A 123 MET cc_start: 0.9488 (mmt) cc_final: 0.9210 (mmt) REVERT: A 157 ASP cc_start: 0.8416 (t70) cc_final: 0.8129 (t0) REVERT: A 283 MET cc_start: 0.8750 (mmm) cc_final: 0.8535 (mmt) REVERT: B 157 ASP cc_start: 0.8397 (t70) cc_final: 0.7960 (t0) REVERT: B 372 ARG cc_start: 0.8455 (ptp-170) cc_final: 0.8109 (ptt-90) REVERT: C 355 MET cc_start: 0.8939 (mmm) cc_final: 0.8673 (mmm) outliers start: 13 outliers final: 11 residues processed: 103 average time/residue: 0.2375 time to fit residues: 36.7526 Evaluate side-chains 102 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.076674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063437 restraints weight = 25673.265| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.33 r_work: 0.2757 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12100 Z= 0.239 Angle : 0.589 6.397 16428 Z= 0.287 Chirality : 0.047 0.131 1808 Planarity : 0.004 0.041 2092 Dihedral : 7.204 84.962 1672 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.59 % Allowed : 8.68 % Favored : 89.73 % 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: -0.57 (0.22), residues: 1468 helix: -0.80 (0.22), residues: 588 sheet: -0.43 (0.32), residues: 236 loop : 0.34 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 340 HIS 0.004 0.001 HIS C 40 PHE 0.009 0.001 PHE D 200 TYR 0.009 0.001 TYR B 294 ARG 0.003 0.001 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.02927 ( 421) hydrogen bonds : angle 4.42695 ( 1083) covalent geometry : bond 0.00561 (12096) covalent geometry : angle 0.58876 (16428) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.384 Fit side-chains REVERT: A 157 ASP cc_start: 0.8370 (t70) cc_final: 0.8159 (t0) REVERT: A 283 MET cc_start: 0.8809 (mmm) cc_final: 0.8598 (mmt) REVERT: A 349 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8287 (mp) REVERT: A 372 ARG cc_start: 0.8428 (ptp-170) cc_final: 0.8200 (ptt-90) REVERT: B 157 ASP cc_start: 0.8530 (t70) cc_final: 0.8177 (t0) REVERT: B 372 ARG cc_start: 0.8471 (ptp-170) cc_final: 0.8139 (ptt-90) REVERT: C 355 MET cc_start: 0.8982 (mmm) cc_final: 0.8698 (mmm) REVERT: D 313 MET cc_start: 0.9196 (mmm) cc_final: 0.8920 (mmm) outliers start: 20 outliers final: 10 residues processed: 108 average time/residue: 0.2297 time to fit residues: 37.7052 Evaluate side-chains 102 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.065244 restraints weight = 25489.513| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.34 r_work: 0.2802 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12100 Z= 0.122 Angle : 0.527 6.883 16428 Z= 0.253 Chirality : 0.044 0.130 1808 Planarity : 0.003 0.044 2092 Dihedral : 6.693 75.939 1672 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.27 % Allowed : 9.00 % Favored : 89.73 % 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: -0.28 (0.23), residues: 1468 helix: -0.44 (0.23), residues: 580 sheet: -0.28 (0.32), residues: 236 loop : 0.37 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 PHE 0.007 0.001 PHE D 200 TYR 0.008 0.001 TYR D 294 ARG 0.003 0.000 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.02462 ( 421) hydrogen bonds : angle 4.22509 ( 1083) covalent geometry : bond 0.00291 (12096) covalent geometry : angle 0.52742 (16428) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.250 Fit side-chains REVERT: A 157 ASP cc_start: 0.8369 (t70) cc_final: 0.8096 (t0) REVERT: A 283 MET cc_start: 0.8748 (mmm) cc_final: 0.8539 (mmt) REVERT: A 349 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8266 (mp) REVERT: B 157 ASP cc_start: 0.8467 (t70) cc_final: 0.8061 (t0) REVERT: B 372 ARG cc_start: 0.8468 (ptp-170) cc_final: 0.8139 (ptt-90) REVERT: C 313 MET cc_start: 0.9264 (mmm) cc_final: 0.9044 (tpp) REVERT: C 355 MET cc_start: 0.8939 (mmm) cc_final: 0.8646 (mmm) REVERT: D 123 MET cc_start: 0.9373 (mmt) cc_final: 0.9153 (mmt) REVERT: D 313 MET cc_start: 0.9214 (mmm) cc_final: 0.8947 (mmm) outliers start: 16 outliers final: 13 residues processed: 107 average time/residue: 0.2159 time to fit residues: 34.8550 Evaluate side-chains 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 71 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.063942 restraints weight = 25353.571| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.31 r_work: 0.2770 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12100 Z= 0.213 Angle : 0.574 6.682 16428 Z= 0.280 Chirality : 0.046 0.134 1808 Planarity : 0.004 0.041 2092 Dihedral : 7.027 83.337 1672 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.35 % Allowed : 9.24 % Favored : 89.41 % 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: -0.34 (0.23), residues: 1468 helix: -0.55 (0.22), residues: 588 sheet: -0.21 (0.33), residues: 236 loop : 0.36 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE C 124 TYR 0.008 0.001 TYR B 294 ARG 0.004 0.001 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.02818 ( 421) hydrogen bonds : angle 4.37499 ( 1083) covalent geometry : bond 0.00503 (12096) covalent geometry : angle 0.57386 (16428) Misc. bond : bond 0.00016 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 2.389 Fit side-chains REVERT: A 157 ASP cc_start: 0.8363 (t70) cc_final: 0.8140 (t0) REVERT: A 283 MET cc_start: 0.8787 (mmm) cc_final: 0.8571 (mmt) REVERT: A 349 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8277 (mp) REVERT: A 372 ARG cc_start: 0.8421 (ptp-170) cc_final: 0.8207 (ptt-90) REVERT: B 157 ASP cc_start: 0.8507 (t70) cc_final: 0.8129 (t0) REVERT: B 372 ARG cc_start: 0.8486 (ptp-170) cc_final: 0.8152 (ptt-90) REVERT: C 355 MET cc_start: 0.8971 (mmm) cc_final: 0.8665 (mmm) REVERT: D 313 MET cc_start: 0.9199 (mmm) cc_final: 0.8924 (mmm) outliers start: 17 outliers final: 14 residues processed: 103 average time/residue: 0.2983 time to fit residues: 46.7689 Evaluate side-chains 104 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.065255 restraints weight = 25256.473| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.33 r_work: 0.2802 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12100 Z= 0.123 Angle : 0.529 6.714 16428 Z= 0.256 Chirality : 0.044 0.132 1808 Planarity : 0.003 0.042 2092 Dihedral : 6.681 76.369 1672 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.35 % Allowed : 9.08 % Favored : 89.57 % 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: -0.18 (0.23), residues: 1468 helix: -0.33 (0.23), residues: 580 sheet: -0.15 (0.33), residues: 236 loop : 0.35 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.007 0.001 PHE C 124 TYR 0.009 0.001 TYR B 306 ARG 0.005 0.000 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.02475 ( 421) hydrogen bonds : angle 4.20805 ( 1083) covalent geometry : bond 0.00296 (12096) covalent geometry : angle 0.52907 (16428) Misc. bond : bond 0.00017 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5563.45 seconds wall clock time: 100 minutes 15.40 seconds (6015.40 seconds total)