Starting phenix.real_space_refine on Tue Dec 31 12:03:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk3_33242/12_2024/7xk3_33242.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk3_33242/12_2024/7xk3_33242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk3_33242/12_2024/7xk3_33242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk3_33242/12_2024/7xk3_33242.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk3_33242/12_2024/7xk3_33242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk3_33242/12_2024/7xk3_33242.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.098 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 6 5.49 5 S 92 5.16 5 C 9617 2.51 5 N 2412 2.21 5 O 2714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14846 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} Conformer: "B" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} bond proxies already assigned to first conformer: 3474 Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2964 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 194 Unusual residues: {'FMN': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9093 SG CYS D 112 42.636 75.974 65.219 1.00 35.57 S ATOM 10059 SG CYS E 26 44.816 71.966 66.205 1.00 30.51 S ATOM 8454 SG CYS D 29 43.184 69.115 62.048 1.00 30.00 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 338 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 338 " occ=0.50 Time building chain proxies: 10.94, per 1000 atoms: 0.74 Number of scatterers: 14846 At special positions: 0 Unit cell: (88, 127.6, 153.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 6 15.00 O 2714 8.00 N 2412 7.00 C 9617 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES D 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb=" FES F 501 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 76 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 70 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 79 " Number of angles added : 12 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 50.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.839A pdb=" N TYR A 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.577A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.684A pdb=" N HIS A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.137A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 355' Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.703A pdb=" N ALA A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 413 removed outlier: 3.748A pdb=" N LEU A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 445 removed outlier: 3.910A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.105A pdb=" N PHE B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 97 removed outlier: 4.071A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.620A pdb=" N LYS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.641A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.885A pdb=" N THR B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.815A pdb=" N PHE B 323 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 325' Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.696A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 removed outlier: 3.656A pdb=" N GLY B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 375 removed outlier: 4.000A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 4.001A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.528A pdb=" N ARG B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.524A pdb=" N VAL C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.857A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 178 through 181 removed outlier: 3.796A pdb=" N GLU C 181 " --> pdb=" O GLY C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.755A pdb=" N SER C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'D' and resid 8 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 28 through 34 Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 removed outlier: 3.785A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.829A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 removed outlier: 4.211A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 120 removed outlier: 3.814A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 125 removed outlier: 3.712A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 157 removed outlier: 3.589A pdb=" N SER D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 4.145A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 14 removed outlier: 3.642A pdb=" N LEU E 7 " --> pdb=" O HIS E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 removed outlier: 3.666A pdb=" N THR E 179 " --> pdb=" O GLY E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 3 through 28 Processing helix chain 'F' and resid 54 through 63 Processing helix chain 'F' and resid 91 through 98 removed outlier: 3.974A pdb=" N HIS F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.840A pdb=" N ILE F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 128' Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.508A pdb=" N GLU F 158 " --> pdb=" O PRO F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 196 removed outlier: 4.071A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 200 Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.869A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 380 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.632A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA A 148 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE A 239 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE A 150 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.568A pdb=" N VAL A 325 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.615A pdb=" N LEU A 31 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 94 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A 74 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.508A pdb=" N PHE A 58 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 366 through 367 removed outlier: 4.826A pdb=" N LEU B 39 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.543A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS C 132 " --> pdb=" O ASP C 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AA8, first strand: chain 'C' and resid 135 through 143 removed outlier: 6.310A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AB1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB2, first strand: chain 'F' and resid 35 through 38 Processing sheet with id=AB3, first strand: chain 'F' and resid 107 through 109 removed outlier: 6.996A pdb=" N ASP F 120 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 224 through 225 Processing sheet with id=AB5, first strand: chain 'F' and resid 224 through 225 removed outlier: 7.581A pdb=" N ILE F 147 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN F 142 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU F 149 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN F 140 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 167 through 172 removed outlier: 3.595A pdb=" N ARG F 210 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 351 through 352 removed outlier: 4.337A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 339 " --> pdb=" O TYR F 351 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 2001 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: 4.28 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 4769 1.37 - 1.57: 10245 1.57 - 1.78: 13 1.78 - 1.99: 150 1.99 - 2.20: 8 Bond restraints: 15185 Sorted by residual: bond pdb=" C4A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.288 1.449 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.534 1.417 0.116 1.45e-02 4.76e+03 6.44e+01 bond pdb=" C10 RBF B 502 " pdb=" N1 RBF B 502 " ideal model delta sigma weight residual 1.304 1.463 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" CA SER C 228 " pdb=" CB SER C 228 " ideal model delta sigma weight residual 1.529 1.420 0.109 1.55e-02 4.16e+03 4.92e+01 bond pdb=" C5A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.350 1.490 -0.140 2.00e-02 2.50e+03 4.89e+01 ... (remaining 15180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 20233 3.33 - 6.66: 301 6.66 - 9.99: 31 9.99 - 13.32: 11 13.32 - 16.65: 6 Bond angle restraints: 20582 Sorted by residual: angle pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.53 13.80 1.14e+00 7.69e-01 1.46e+02 angle pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 89.13 -13.47 1.14e+00 7.69e-01 1.40e+02 angle pdb=" S1 FES F 501 " pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.63 13.70 1.20e+00 6.94e-01 1.30e+02 angle pdb="FE1 FES D 301 " pdb=" S2 FES D 301 " pdb="FE2 FES D 301 " ideal model delta sigma weight residual 75.66 88.67 -13.01 1.14e+00 7.69e-01 1.30e+02 angle pdb=" S1 FES D 301 " pdb="FE2 FES D 301 " pdb=" S2 FES D 301 " ideal model delta sigma weight residual 104.33 91.34 12.99 1.14e+00 7.69e-01 1.30e+02 ... (remaining 20577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8787 35.49 - 70.97: 215 70.97 - 106.45: 31 106.45 - 141.94: 9 141.94 - 177.42: 4 Dihedral angle restraints: 9046 sinusoidal: 3680 harmonic: 5366 Sorted by residual: dihedral pdb=" CA HIS A 215 " pdb=" C HIS A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta harmonic sigma weight residual 180.00 119.33 60.67 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" C10 FMN B 501 " pdb=" C1' FMN B 501 " pdb=" N10 FMN B 501 " pdb=" C2' FMN B 501 " ideal model delta sinusoidal sigma weight residual -102.41 75.02 -177.42 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN C 301 " pdb=" C1' FMN C 301 " pdb=" N10 FMN C 301 " pdb=" C2' FMN C 301 " ideal model delta sinusoidal sigma weight residual 257.59 82.55 175.04 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 9043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2132 0.088 - 0.177: 164 0.177 - 0.265: 16 0.265 - 0.353: 6 0.353 - 0.441: 5 Chirality restraints: 2323 Sorted by residual: chirality pdb=" CA THR C 173 " pdb=" N THR C 173 " pdb=" C THR C 173 " pdb=" CB THR C 173 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CB ILE B 220 " pdb=" CA ILE B 220 " pdb=" CG1 ILE B 220 " pdb=" CG2 ILE B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA ILE B 272 " pdb=" N ILE B 272 " pdb=" C ILE B 272 " pdb=" CB ILE B 272 " both_signs ideal model delta sigma weight residual False 2.43 2.06 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 2320 not shown) Planarity restraints: 2571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.064 2.00e-02 2.50e+03 2.67e-02 3.38e+01 pdb=" C10 FMN C 301 " 0.006 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.027 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.013 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.017 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.018 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.018 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.017 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.038 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.021 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.023 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.013 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " 0.015 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.008 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.022 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.058 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 215 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 216 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 167 " 0.019 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C ALA B 167 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA B 167 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 168 " 0.021 2.00e-02 2.50e+03 ... (remaining 2568 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 3 1.80 - 2.58: 93 2.58 - 3.35: 17851 3.35 - 4.13: 34936 4.13 - 4.90: 67591 Nonbonded interactions: 120474 Sorted by model distance: nonbonded pdb=" SD MET E 17 " pdb="CA CA E 201 " model vdw 1.026 2.870 nonbonded pdb=" CE MET E 17 " pdb="CA CA E 201 " model vdw 1.259 2.930 nonbonded pdb=" CG MET E 17 " pdb="CA CA E 201 " model vdw 1.491 2.910 nonbonded pdb=" O PHE E 28 " pdb=" OG SER E 32 " model vdw 2.203 3.040 nonbonded pdb=" CB MET E 17 " pdb="CA CA E 201 " model vdw 2.237 2.910 ... (remaining 120469 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=0.50 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: 1.860 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: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.300 Find NCS groups from input model: 0.230 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.007 0.161 15185 Z= 0.481 Angle : 0.957 16.654 20582 Z= 0.570 Chirality : 0.054 0.441 2323 Planarity : 0.005 0.096 2571 Dihedral : 17.000 177.424 5624 Min Nonbonded Distance : 1.026 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.29 % Favored : 96.55 % Rotamer: Outliers : 0.58 % Allowed : 4.21 % Favored : 95.21 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -2.55 (0.17), residues: 1885 helix: -0.76 (0.16), residues: 857 sheet: -2.45 (0.34), residues: 174 loop : -2.48 (0.17), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS A 215 PHE 0.020 0.001 PHE B 342 TYR 0.017 0.001 TYR B 216 ARG 0.005 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 1.569 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8111 (ttpp) REVERT: A 249 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8258 (mm-40) REVERT: A 279 MET cc_start: 0.9085 (ttt) cc_final: 0.8848 (ttp) REVERT: A 342 LYS cc_start: 0.8235 (tttm) cc_final: 0.7798 (ttpp) REVERT: A 401 ASP cc_start: 0.7972 (t0) cc_final: 0.7677 (t70) REVERT: B 380 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: C 46 GLN cc_start: 0.8368 (mt0) cc_final: 0.8150 (mt0) REVERT: C 129 ASP cc_start: 0.7613 (p0) cc_final: 0.7195 (p0) REVERT: D 123 MET cc_start: 0.8523 (mmm) cc_final: 0.8309 (mmm) REVERT: D 146 MET cc_start: 0.8370 (mmm) cc_final: 0.8050 (mmm) REVERT: D 209 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.5742 (tmtt) REVERT: E 33 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8351 (mttt) REVERT: E 162 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7643 (mt-10) REVERT: F 34 ASP cc_start: 0.7227 (p0) cc_final: 0.6729 (p0) REVERT: F 252 LEU cc_start: 0.8092 (mm) cc_final: 0.7852 (mm) outliers start: 9 outliers final: 2 residues processed: 220 average time/residue: 0.2952 time to fit residues: 93.0933 Evaluate side-chains 176 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 210 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 88 GLN A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS A 249 GLN B 74 ASN B 78 GLN B 91 GLN B 178 GLN B 219 GLN B 240 GLN B 243 GLN B 313 ASN B 354 ASN C 37 GLN C 68 ASN C 79 ASN C 143 ASN D 176 GLN E 79 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 GLN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15185 Z= 0.215 Angle : 0.559 10.617 20582 Z= 0.287 Chirality : 0.043 0.185 2323 Planarity : 0.005 0.088 2571 Dihedral : 14.629 177.707 2316 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 1.04 % Allowed : 8.61 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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 (0.19), residues: 1885 helix: 0.44 (0.18), residues: 869 sheet: -1.48 (0.40), residues: 167 loop : -1.94 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.009 0.001 HIS A 215 PHE 0.013 0.001 PHE E 28 TYR 0.015 0.001 TYR D 141 ARG 0.004 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8045 (ttpp) REVERT: A 97 ASP cc_start: 0.7171 (p0) cc_final: 0.6722 (p0) REVERT: A 279 MET cc_start: 0.9168 (ttt) cc_final: 0.8933 (ttp) REVERT: A 342 LYS cc_start: 0.8314 (tttm) cc_final: 0.7862 (ttpp) REVERT: B 380 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: D 146 MET cc_start: 0.8365 (mmm) cc_final: 0.8066 (mmm) REVERT: D 210 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.5093 (mm-30) REVERT: E 33 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8270 (mttt) REVERT: E 162 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7693 (mt-10) outliers start: 16 outliers final: 10 residues processed: 191 average time/residue: 0.2729 time to fit residues: 77.6390 Evaluate side-chains 186 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain F residue 347 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 169 optimal weight: 0.2980 chunk 182 optimal weight: 0.0980 chunk 150 optimal weight: 9.9990 chunk 167 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS C 79 ASN ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15185 Z= 0.154 Angle : 0.510 11.063 20582 Z= 0.260 Chirality : 0.042 0.202 2323 Planarity : 0.005 0.113 2571 Dihedral : 13.194 179.151 2311 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 10.49 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.54 (0.19), residues: 1885 helix: 0.97 (0.18), residues: 876 sheet: -0.79 (0.43), residues: 150 loop : -1.73 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.008 0.001 HIS A 215 PHE 0.011 0.001 PHE E 28 TYR 0.014 0.001 TYR D 141 ARG 0.007 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8001 (ttpp) REVERT: A 97 ASP cc_start: 0.7113 (p0) cc_final: 0.6717 (p0) REVERT: A 279 MET cc_start: 0.9125 (ttt) cc_final: 0.8907 (ttp) REVERT: A 342 LYS cc_start: 0.8287 (tttm) cc_final: 0.7849 (ttpp) REVERT: D 146 MET cc_start: 0.8354 (mmm) cc_final: 0.8111 (mmm) REVERT: D 210 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.5305 (mm-30) REVERT: E 33 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8240 (mttt) REVERT: E 162 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7638 (mt-10) outliers start: 13 outliers final: 6 residues processed: 187 average time/residue: 0.2763 time to fit residues: 77.3195 Evaluate side-chains 180 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain F residue 349 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 169 optimal weight: 0.0970 chunk 179 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN C 199 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15185 Z= 0.181 Angle : 0.511 10.988 20582 Z= 0.259 Chirality : 0.042 0.188 2323 Planarity : 0.005 0.115 2571 Dihedral : 11.749 178.939 2308 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 1.23 % Allowed : 10.36 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.24 (0.19), residues: 1885 helix: 1.23 (0.18), residues: 874 sheet: -0.56 (0.45), residues: 140 loop : -1.59 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS F 336 PHE 0.012 0.001 PHE B 213 TYR 0.012 0.001 TYR D 141 ARG 0.004 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7985 (ttpp) REVERT: A 97 ASP cc_start: 0.7136 (p0) cc_final: 0.6733 (p0) REVERT: A 279 MET cc_start: 0.9171 (ttt) cc_final: 0.8953 (ttp) REVERT: A 342 LYS cc_start: 0.8273 (tttm) cc_final: 0.7829 (ttpp) REVERT: E 111 ILE cc_start: 0.6850 (mt) cc_final: 0.6590 (mp) REVERT: E 162 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7646 (mt-10) outliers start: 19 outliers final: 13 residues processed: 192 average time/residue: 0.2615 time to fit residues: 75.8529 Evaluate side-chains 189 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 349 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 124 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15185 Z= 0.204 Angle : 0.514 11.113 20582 Z= 0.261 Chirality : 0.042 0.214 2323 Planarity : 0.005 0.118 2571 Dihedral : 10.924 178.190 2305 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 1.42 % Allowed : 11.59 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.06 (0.19), residues: 1885 helix: 1.34 (0.18), residues: 874 sheet: -0.41 (0.45), residues: 140 loop : -1.46 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS F 336 PHE 0.014 0.001 PHE E 28 TYR 0.012 0.001 TYR F 179 ARG 0.005 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7996 (ttpp) REVERT: A 97 ASP cc_start: 0.7105 (p0) cc_final: 0.6709 (p0) REVERT: A 342 LYS cc_start: 0.8291 (tttm) cc_final: 0.7842 (ttpp) REVERT: B 380 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: E 17 MET cc_start: 0.8032 (mmm) cc_final: 0.7715 (mmm) REVERT: E 162 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7608 (mt-10) REVERT: F 214 MET cc_start: 0.7939 (mtm) cc_final: 0.7662 (mtm) outliers start: 22 outliers final: 15 residues processed: 191 average time/residue: 0.2599 time to fit residues: 74.8172 Evaluate side-chains 188 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 349 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 0.0980 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 HIS C 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15185 Z= 0.388 Angle : 0.603 11.370 20582 Z= 0.305 Chirality : 0.046 0.202 2323 Planarity : 0.005 0.136 2571 Dihedral : 11.067 179.933 2305 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.55 % Allowed : 12.10 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.26 (0.19), residues: 1885 helix: 1.12 (0.18), residues: 868 sheet: -0.62 (0.45), residues: 145 loop : -1.46 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 103 HIS 0.006 0.001 HIS F 336 PHE 0.018 0.002 PHE F 318 TYR 0.012 0.002 TYR D 93 ARG 0.006 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 1.542 Fit side-chains REVERT: A 75 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8048 (ttpp) REVERT: A 97 ASP cc_start: 0.7184 (p0) cc_final: 0.6765 (p0) REVERT: A 342 LYS cc_start: 0.8380 (tttm) cc_final: 0.7911 (ttpp) REVERT: B 380 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: E 162 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7691 (mt-10) outliers start: 24 outliers final: 19 residues processed: 190 average time/residue: 0.2868 time to fit residues: 82.2090 Evaluate side-chains 192 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 349 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15185 Z= 0.146 Angle : 0.482 11.625 20582 Z= 0.248 Chirality : 0.041 0.178 2323 Planarity : 0.005 0.114 2571 Dihedral : 10.303 177.681 2305 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.04 % Allowed : 12.82 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: 0.17 (0.19), residues: 1885 helix: 1.50 (0.18), residues: 869 sheet: -0.48 (0.45), residues: 145 loop : -1.25 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS F 336 PHE 0.013 0.001 PHE E 28 TYR 0.014 0.001 TYR D 141 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7954 (ttpp) REVERT: A 97 ASP cc_start: 0.7062 (p0) cc_final: 0.6680 (p0) REVERT: A 249 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8167 (mm110) REVERT: A 342 LYS cc_start: 0.8256 (tttm) cc_final: 0.7813 (ttpp) REVERT: E 17 MET cc_start: 0.7968 (mmm) cc_final: 0.7716 (mmm) REVERT: E 162 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7547 (mt-10) REVERT: F 34 ASP cc_start: 0.7123 (p0) cc_final: 0.6809 (p0) REVERT: F 112 GLN cc_start: 0.8022 (mp10) cc_final: 0.7191 (mp10) REVERT: F 377 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7800 (ttp) outliers start: 16 outliers final: 14 residues processed: 191 average time/residue: 0.2644 time to fit residues: 76.0658 Evaluate side-chains 190 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15185 Z= 0.303 Angle : 0.560 11.856 20582 Z= 0.283 Chirality : 0.044 0.160 2323 Planarity : 0.005 0.137 2571 Dihedral : 10.475 179.139 2305 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 1.49 % Allowed : 12.88 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: 0.05 (0.19), residues: 1885 helix: 1.35 (0.18), residues: 872 sheet: -0.47 (0.45), residues: 143 loop : -1.26 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.007 0.001 HIS F 336 PHE 0.017 0.001 PHE E 28 TYR 0.013 0.001 TYR F 179 ARG 0.004 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.662 Fit side-chains REVERT: A 75 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8006 (ttpp) REVERT: A 97 ASP cc_start: 0.7171 (p0) cc_final: 0.6745 (p0) REVERT: A 342 LYS cc_start: 0.8353 (tttm) cc_final: 0.7889 (ttpp) REVERT: B 380 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: E 17 MET cc_start: 0.7997 (mmm) cc_final: 0.7539 (mmm) REVERT: E 162 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7648 (mt-10) REVERT: F 112 GLN cc_start: 0.8062 (mp10) cc_final: 0.7197 (mp10) REVERT: F 377 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7865 (ttp) outliers start: 23 outliers final: 16 residues processed: 190 average time/residue: 0.2667 time to fit residues: 75.7661 Evaluate side-chains 194 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15185 Z= 0.249 Angle : 0.531 10.809 20582 Z= 0.270 Chirality : 0.043 0.157 2323 Planarity : 0.005 0.133 2571 Dihedral : 10.383 178.918 2305 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 1.49 % Allowed : 12.69 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: 0.12 (0.19), residues: 1885 helix: 1.39 (0.18), residues: 873 sheet: -0.43 (0.45), residues: 143 loop : -1.22 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.007 0.001 HIS F 336 PHE 0.016 0.001 PHE E 28 TYR 0.013 0.001 TYR F 179 ARG 0.005 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.756 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7999 (ttpp) REVERT: A 97 ASP cc_start: 0.7115 (p0) cc_final: 0.6721 (p0) REVERT: A 342 LYS cc_start: 0.8324 (tttm) cc_final: 0.7866 (ttpp) REVERT: B 380 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: E 17 MET cc_start: 0.7979 (mmm) cc_final: 0.7586 (mmm) REVERT: E 162 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7592 (mt-10) REVERT: F 112 GLN cc_start: 0.8053 (mp10) cc_final: 0.7186 (mp10) REVERT: F 377 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7844 (ttp) outliers start: 23 outliers final: 18 residues processed: 188 average time/residue: 0.2746 time to fit residues: 77.3048 Evaluate side-chains 195 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 170 optimal weight: 0.0070 chunk 147 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15185 Z= 0.167 Angle : 0.493 10.604 20582 Z= 0.252 Chirality : 0.041 0.161 2323 Planarity : 0.005 0.124 2571 Dihedral : 10.034 177.438 2305 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 1.42 % Allowed : 13.01 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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 (0.19), residues: 1885 helix: 1.59 (0.18), residues: 871 sheet: -0.37 (0.45), residues: 143 loop : -1.13 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.006 0.001 HIS F 336 PHE 0.014 0.001 PHE E 28 TYR 0.013 0.001 TYR F 217 ARG 0.003 0.000 ARG B 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7965 (ttpp) REVERT: A 97 ASP cc_start: 0.7089 (p0) cc_final: 0.6688 (p0) REVERT: A 342 LYS cc_start: 0.8289 (tttm) cc_final: 0.7839 (ttpp) REVERT: B 261 MET cc_start: 0.8380 (mmm) cc_final: 0.7929 (tpt) REVERT: B 380 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: D 209 LYS cc_start: 0.7393 (tmtt) cc_final: 0.7048 (tptm) REVERT: E 17 MET cc_start: 0.7946 (mmm) cc_final: 0.7706 (mmm) REVERT: E 162 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7607 (mt-10) REVERT: F 34 ASP cc_start: 0.7065 (p0) cc_final: 0.6767 (p0) REVERT: F 112 GLN cc_start: 0.8015 (mp10) cc_final: 0.7170 (mp10) REVERT: F 377 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7823 (ttp) outliers start: 22 outliers final: 19 residues processed: 190 average time/residue: 0.2661 time to fit residues: 75.7220 Evaluate side-chains 195 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.159264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120506 restraints weight = 25783.996| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.87 r_work: 0.3108 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15185 Z= 0.300 Angle : 0.560 11.045 20582 Z= 0.285 Chirality : 0.044 0.159 2323 Planarity : 0.005 0.131 2571 Dihedral : 10.302 178.890 2305 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 1.42 % Allowed : 13.33 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: 0.20 (0.19), residues: 1885 helix: 1.43 (0.18), residues: 867 sheet: -0.35 (0.45), residues: 143 loop : -1.14 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.007 0.001 HIS F 336 PHE 0.016 0.001 PHE E 28 TYR 0.012 0.002 TYR F 179 ARG 0.005 0.000 ARG B 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.96 seconds wall clock time: 54 minutes 26.72 seconds (3266.72 seconds total)