Starting phenix.real_space_refine on Wed Feb 4 18:33:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9olh_70593/02_2026/9olh_70593.cif Found real_map, /net/cci-nas-00/data/ceres_data/9olh_70593/02_2026/9olh_70593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9olh_70593/02_2026/9olh_70593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9olh_70593/02_2026/9olh_70593.map" model { file = "/net/cci-nas-00/data/ceres_data/9olh_70593/02_2026/9olh_70593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9olh_70593/02_2026/9olh_70593.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.042 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 9 5.49 5 Mg 3 5.21 5 S 81 5.16 5 C 7627 2.51 5 N 2057 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12067 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3358 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1485 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain: "G" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 153 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "H" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 260 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.75, per 1000 atoms: 0.23 Number of scatterers: 12067 At special positions: 0 Unit cell: (109.172, 101.374, 150.39, 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 81 16.00 P 9 15.00 Mg 3 11.99 O 2290 8.00 N 2057 7.00 C 7627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 557.5 milliseconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2832 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 9 sheets defined 58.5% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.714A pdb=" N ASN A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.561A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.814A pdb=" N GLU A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.376A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.539A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.628A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.515A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.070A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.979A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.718A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.535A pdb=" N GLY A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.753A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.159A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.920A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.955A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.548A pdb=" N GLU B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.144A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 4.653A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.617A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.703A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.555A pdb=" N VAL B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.619A pdb=" N TYR B 281 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.598A pdb=" N ASN B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 299' Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.637A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.186A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.330A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 4.076A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 28 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.632A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 128 removed outlier: 3.803A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 162 removed outlier: 4.388A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.598A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.732A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.504A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.796A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.952A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.598A pdb=" N GLY C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 337 removed outlier: 3.651A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 399 removed outlier: 4.226A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.917A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.622A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 23 removed outlier: 3.585A pdb=" N TRP F 17 " --> pdb=" O ARG F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 33 Processing helix chain 'F' and resid 52 through 68 removed outlier: 3.775A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 76 Processing helix chain 'F' and resid 85 through 107 removed outlier: 4.104A pdb=" N GLU F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU F 97 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 115 through 120 removed outlier: 3.543A pdb=" N LEU F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 115 through 120' Processing helix chain 'F' and resid 122 through 146 removed outlier: 3.634A pdb=" N PHE F 126 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG F 144 " --> pdb=" O GLN F 140 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 150 Processing helix chain 'F' and resid 151 through 159 removed outlier: 3.767A pdb=" N GLU F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 191 removed outlier: 3.566A pdb=" N ALA F 167 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 158 Processing helix chain 'H' and resid 157 through 186 removed outlier: 3.520A pdb=" N ASN H 180 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG H 183 " --> pdb=" O LYS H 179 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU H 186 " --> pdb=" O PHE H 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.172A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.548A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.151A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 5 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.550A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.921A pdb=" N ILE C 5 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N SER C 140 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS C 200 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.703A pdb=" N LYS C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 269 through 273 removed outlier: 6.547A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1779 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: 1.75 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 3268 1.33 - 1.48: 3902 1.48 - 1.63: 5037 1.63 - 1.79: 68 1.79 - 1.94: 66 Bond restraints: 12341 Sorted by residual: bond pdb=" C2' GTP C 501 " pdb=" C3' GTP C 501 " ideal model delta sigma weight residual 1.524 1.220 0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " ideal model delta sigma weight residual 1.524 1.222 0.302 2.00e-02 2.50e+03 2.28e+02 bond pdb=" PG GSP B 501 " pdb=" S1G GSP B 501 " ideal model delta sigma weight residual 1.700 1.940 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " ideal model delta sigma weight residual 1.524 1.389 0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.524 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 12336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 16428 2.51 - 5.03: 276 5.03 - 7.54: 29 7.54 - 10.06: 12 10.06 - 12.57: 1 Bond angle restraints: 16746 Sorted by residual: angle pdb=" O1A GSP B 501 " pdb=" PA GSP B 501 " pdb=" O2A GSP B 501 " ideal model delta sigma weight residual 109.50 122.07 -12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N VAL B 175 " pdb=" CA VAL B 175 " pdb=" C VAL B 175 " ideal model delta sigma weight residual 106.21 110.26 -4.05 1.07e+00 8.73e-01 1.43e+01 angle pdb=" C ARG A 320 " pdb=" N GLY A 321 " pdb=" CA GLY A 321 " ideal model delta sigma weight residual 122.63 118.86 3.77 1.03e+00 9.43e-01 1.34e+01 angle pdb=" C LEU B 130 " pdb=" N GLN B 131 " pdb=" CA GLN B 131 " ideal model delta sigma weight residual 122.24 116.58 5.66 1.57e+00 4.06e-01 1.30e+01 angle pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 111.00 101.08 9.92 3.00e+00 1.11e-01 1.09e+01 ... (remaining 16741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 7092 35.63 - 71.25: 241 71.25 - 106.88: 10 106.88 - 142.50: 4 142.50 - 178.13: 4 Dihedral angle restraints: 7351 sinusoidal: 2949 harmonic: 4402 Sorted by residual: dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -108.86 178.13 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -112.81 -177.93 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.45 172.04 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 7348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1296 0.051 - 0.103: 442 0.103 - 0.154: 89 0.154 - 0.205: 4 0.205 - 0.256: 3 Chirality restraints: 1834 Sorted by residual: chirality pdb=" C4' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O4' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C4' GTP C 501 " pdb=" C3' GTP C 501 " pdb=" C5' GTP C 501 " pdb=" O4' GTP C 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' GSP B 501 " pdb=" C2' GSP B 501 " pdb=" C4' GSP B 501 " pdb=" O3' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.68 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1831 not shown) Planarity restraints: 2165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO A 325 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 324 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.14e+00 pdb=" N PRO C 325 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 325 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 325 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 71 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.71e+00 pdb=" N PRO A 72 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.027 5.00e-02 4.00e+02 ... (remaining 2162 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 6 2.18 - 2.86: 4460 2.86 - 3.54: 16997 3.54 - 4.22: 29049 4.22 - 4.90: 51158 Nonbonded interactions: 101670 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.499 2.170 nonbonded pdb=" O1B GTP A 501 " pdb=" O1G GTP A 501 " model vdw 2.001 3.040 nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 2.007 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.051 2.170 nonbonded pdb=" OE1 GLU B 410 " pdb=" NE2 GLN F 112 " model vdw 2.072 3.120 ... (remaining 101665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.680 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5062 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 0.304 12341 Z= 0.571 Angle : 0.864 12.570 16746 Z= 0.480 Chirality : 0.051 0.256 1834 Planarity : 0.005 0.086 2165 Dihedral : 18.126 178.126 4519 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.42 % Allowed : 16.34 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.18), residues: 1504 helix: -1.47 (0.15), residues: 749 sheet: -1.70 (0.32), residues: 194 loop : -2.03 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 121 TYR 0.016 0.002 TYR F 131 PHE 0.020 0.002 PHE A 404 TRP 0.019 0.003 TRP A 21 HIS 0.009 0.002 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.01252 (12341) covalent geometry : angle 0.86367 (16746) hydrogen bonds : bond 0.15405 ( 607) hydrogen bonds : angle 6.73877 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 324 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.6384 (m-80) cc_final: 0.6039 (m-10) REVERT: A 353 VAL cc_start: 0.6492 (t) cc_final: 0.6251 (m) REVERT: C 277 SER cc_start: 0.4904 (OUTLIER) cc_final: 0.2557 (p) REVERT: C 428 LEU cc_start: 0.7494 (tp) cc_final: 0.7252 (tt) outliers start: 57 outliers final: 6 residues processed: 365 average time/residue: 0.1054 time to fit residues: 54.1509 Evaluate side-chains 184 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 362 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN A 50 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 228 ASN A 249 ASN A 256 GLN A 300 ASN A 329 ASN B 28 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 334 GLN B 337 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 375 GLN C 15 GLN C 28 HIS ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 197 HIS C 228 ASN C 256 GLN C 300 ASN C 309 HIS C 329 ASN F 112 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 GLN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.100722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.055775 restraints weight = 44222.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.055704 restraints weight = 31819.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.056411 restraints weight = 24745.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.057043 restraints weight = 20680.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.057342 restraints weight = 18752.365| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12341 Z= 0.196 Angle : 0.745 10.392 16746 Z= 0.371 Chirality : 0.045 0.152 1834 Planarity : 0.005 0.055 2165 Dihedral : 11.836 175.342 1697 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.41 % Allowed : 22.15 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1504 helix: 0.20 (0.18), residues: 770 sheet: -0.94 (0.33), residues: 204 loop : -1.43 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 121 TYR 0.027 0.002 TYR A 24 PHE 0.023 0.002 PHE A 351 TRP 0.023 0.002 TRP B 21 HIS 0.008 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00421 (12341) covalent geometry : angle 0.74457 (16746) hydrogen bonds : bond 0.04711 ( 607) hydrogen bonds : angle 5.05346 ( 1779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9300 (m-30) cc_final: 0.8964 (p0) REVERT: B 64 ILE cc_start: 0.8926 (mt) cc_final: 0.8710 (tt) REVERT: B 164 MET cc_start: 0.8183 (tpp) cc_final: 0.7197 (mmm) REVERT: B 165 ASN cc_start: 0.9228 (p0) cc_final: 0.8960 (p0) REVERT: B 200 TYR cc_start: 0.8723 (m-80) cc_final: 0.8349 (m-80) REVERT: B 202 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 203 ASP cc_start: 0.8939 (t0) cc_final: 0.8700 (t0) REVERT: B 330 MET cc_start: 0.9428 (mmm) cc_final: 0.9226 (mmm) REVERT: C 25 CYS cc_start: 0.9235 (m) cc_final: 0.9001 (p) REVERT: C 52 PHE cc_start: 0.8614 (m-10) cc_final: 0.8407 (m-10) REVERT: C 153 LEU cc_start: 0.9471 (tt) cc_final: 0.9029 (pp) REVERT: C 238 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8276 (mt) REVERT: C 377 MET cc_start: 0.8953 (tmm) cc_final: 0.8223 (tmm) REVERT: C 413 MET cc_start: 0.7824 (mmm) cc_final: 0.7231 (mmm) REVERT: C 425 MET cc_start: 0.9286 (tpp) cc_final: 0.8844 (tpp) REVERT: F 20 LEU cc_start: 0.8175 (mt) cc_final: 0.7757 (pp) outliers start: 44 outliers final: 22 residues processed: 204 average time/residue: 0.1016 time to fit residues: 30.5947 Evaluate side-chains 155 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain F residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 84 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 148 optimal weight: 30.0000 chunk 59 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 334 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS C 258 ASN C 301 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.093523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.048470 restraints weight = 45367.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.049249 restraints weight = 32084.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.050212 restraints weight = 26532.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.050579 restraints weight = 22997.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.051114 restraints weight = 20913.308| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12341 Z= 0.223 Angle : 0.709 13.490 16746 Z= 0.355 Chirality : 0.045 0.176 1834 Planarity : 0.005 0.056 2165 Dihedral : 11.518 177.828 1691 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.64 % Allowed : 21.77 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.21), residues: 1504 helix: 0.67 (0.18), residues: 767 sheet: -0.51 (0.35), residues: 194 loop : -1.06 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 276 TYR 0.027 0.002 TYR A 210 PHE 0.025 0.002 PHE C 255 TRP 0.034 0.003 TRP B 21 HIS 0.010 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00447 (12341) covalent geometry : angle 0.70904 (16746) hydrogen bonds : bond 0.04157 ( 607) hydrogen bonds : angle 4.85896 ( 1779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9491 (tp) cc_final: 0.9011 (mt) REVERT: A 90 GLU cc_start: 0.9457 (tp30) cc_final: 0.9193 (tp30) REVERT: A 203 MET cc_start: 0.8844 (pmm) cc_final: 0.8403 (pmm) REVERT: A 221 ARG cc_start: 0.8438 (ptm-80) cc_final: 0.8111 (mtp-110) REVERT: A 388 TRP cc_start: 0.9183 (m-10) cc_final: 0.8859 (m-90) REVERT: A 398 MET cc_start: 0.8897 (mmt) cc_final: 0.8497 (mmm) REVERT: B 164 MET cc_start: 0.8780 (tpp) cc_final: 0.7600 (mmm) REVERT: B 165 ASN cc_start: 0.9481 (p0) cc_final: 0.9253 (p0) REVERT: B 200 TYR cc_start: 0.8762 (m-80) cc_final: 0.8298 (m-80) REVERT: B 266 PHE cc_start: 0.8672 (m-10) cc_final: 0.8372 (m-80) REVERT: B 293 MET cc_start: 0.8710 (mmm) cc_final: 0.8366 (mmm) REVERT: B 323 MET cc_start: 0.9242 (mmm) cc_final: 0.8749 (mmm) REVERT: B 330 MET cc_start: 0.9518 (mmm) cc_final: 0.9249 (mmm) REVERT: B 388 MET cc_start: 0.9446 (mmt) cc_final: 0.9094 (mmt) REVERT: C 25 CYS cc_start: 0.9250 (m) cc_final: 0.8974 (p) REVERT: C 52 PHE cc_start: 0.8797 (m-10) cc_final: 0.8576 (m-10) REVERT: C 68 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8275 (m) REVERT: C 161 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: C 256 GLN cc_start: 0.9443 (pt0) cc_final: 0.9238 (pt0) REVERT: C 285 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.7001 (mm-40) REVERT: C 377 MET cc_start: 0.8972 (tmm) cc_final: 0.8358 (tmm) REVERT: C 425 MET cc_start: 0.9190 (tpp) cc_final: 0.8711 (tpp) REVERT: G 149 ASN cc_start: -0.2436 (OUTLIER) cc_final: -0.2969 (p0) outliers start: 47 outliers final: 29 residues processed: 172 average time/residue: 0.0946 time to fit residues: 25.1587 Evaluate side-chains 149 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 161 TYR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 149 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 31 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.092064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.048203 restraints weight = 45474.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.048808 restraints weight = 33769.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.049365 restraints weight = 27053.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.049376 restraints weight = 22839.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.049376 restraints weight = 22794.702| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12341 Z= 0.186 Angle : 0.685 11.340 16746 Z= 0.335 Chirality : 0.044 0.213 1834 Planarity : 0.004 0.050 2165 Dihedral : 11.458 179.048 1691 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.41 % Allowed : 23.63 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1504 helix: 0.86 (0.18), residues: 772 sheet: -0.27 (0.35), residues: 194 loop : -0.76 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 390 TYR 0.022 0.002 TYR A 210 PHE 0.022 0.001 PHE A 351 TRP 0.048 0.002 TRP B 21 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00399 (12341) covalent geometry : angle 0.68524 (16746) hydrogen bonds : bond 0.03905 ( 607) hydrogen bonds : angle 4.75731 ( 1779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 24 TYR cc_start: 0.9284 (m-80) cc_final: 0.9020 (m-80) REVERT: A 86 LEU cc_start: 0.9436 (tp) cc_final: 0.8909 (mt) REVERT: A 388 TRP cc_start: 0.9084 (m-10) cc_final: 0.8756 (m-90) REVERT: A 398 MET cc_start: 0.8937 (mmt) cc_final: 0.8589 (mmm) REVERT: B 116 VAL cc_start: 0.9673 (t) cc_final: 0.9406 (p) REVERT: B 164 MET cc_start: 0.9000 (tpp) cc_final: 0.7725 (mmm) REVERT: B 165 ASN cc_start: 0.9519 (p0) cc_final: 0.9283 (p0) REVERT: B 200 TYR cc_start: 0.8686 (m-80) cc_final: 0.8219 (m-80) REVERT: B 293 MET cc_start: 0.8697 (mmm) cc_final: 0.8400 (mmm) REVERT: B 313 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.9038 (m) REVERT: B 323 MET cc_start: 0.9085 (mmm) cc_final: 0.8534 (tpt) REVERT: B 330 MET cc_start: 0.9396 (mmm) cc_final: 0.9081 (mmm) REVERT: B 388 MET cc_start: 0.9314 (mmt) cc_final: 0.8846 (mmt) REVERT: C 25 CYS cc_start: 0.9326 (m) cc_final: 0.9107 (p) REVERT: C 52 PHE cc_start: 0.8713 (m-10) cc_final: 0.8469 (m-10) REVERT: C 116 ASP cc_start: 0.9618 (m-30) cc_final: 0.9230 (p0) REVERT: C 315 CYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8175 (m) REVERT: C 349 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8404 (t) REVERT: C 377 MET cc_start: 0.9052 (tmm) cc_final: 0.8414 (tmm) REVERT: C 425 MET cc_start: 0.9243 (tpp) cc_final: 0.8642 (tpp) outliers start: 44 outliers final: 24 residues processed: 159 average time/residue: 0.0894 time to fit residues: 22.0812 Evaluate side-chains 142 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 134 optimal weight: 50.0000 chunk 68 optimal weight: 9.9990 chunk 128 optimal weight: 40.0000 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.088091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.043614 restraints weight = 48216.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.044283 restraints weight = 35426.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.044685 restraints weight = 29428.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.044996 restraints weight = 26596.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.045359 restraints weight = 24999.007| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.7335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 12341 Z= 0.221 Angle : 0.706 9.854 16746 Z= 0.349 Chirality : 0.044 0.164 1834 Planarity : 0.004 0.051 2165 Dihedral : 11.485 176.097 1691 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.56 % Allowed : 23.86 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1504 helix: 0.84 (0.18), residues: 763 sheet: -0.36 (0.35), residues: 204 loop : -0.62 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 46 TYR 0.015 0.002 TYR B 106 PHE 0.015 0.002 PHE A 202 TRP 0.040 0.002 TRP B 21 HIS 0.008 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00469 (12341) covalent geometry : angle 0.70595 (16746) hydrogen bonds : bond 0.03976 ( 607) hydrogen bonds : angle 4.72723 ( 1779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9354 (OUTLIER) cc_final: 0.9080 (p0) REVERT: A 224 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8112 (m-10) REVERT: A 388 TRP cc_start: 0.9121 (m-10) cc_final: 0.8777 (m-90) REVERT: A 425 MET cc_start: 0.8593 (tpp) cc_final: 0.8361 (tpp) REVERT: B 64 ILE cc_start: 0.9180 (mt) cc_final: 0.8979 (tt) REVERT: B 73 MET cc_start: 0.9283 (mmm) cc_final: 0.8762 (mpp) REVERT: B 164 MET cc_start: 0.9096 (tpp) cc_final: 0.7776 (mmm) REVERT: B 165 ASN cc_start: 0.9542 (p0) cc_final: 0.9340 (p0) REVERT: B 200 TYR cc_start: 0.8867 (m-80) cc_final: 0.8467 (m-80) REVERT: B 233 MET cc_start: 0.9278 (mmt) cc_final: 0.8841 (mmm) REVERT: B 267 MET cc_start: 0.9191 (mtt) cc_final: 0.8866 (mpp) REVERT: B 293 MET cc_start: 0.8838 (mmm) cc_final: 0.8423 (mmm) REVERT: B 323 MET cc_start: 0.9051 (mmm) cc_final: 0.8467 (tpt) REVERT: B 330 MET cc_start: 0.9454 (mmm) cc_final: 0.9151 (mmm) REVERT: B 388 MET cc_start: 0.9349 (mmt) cc_final: 0.8873 (mmt) REVERT: C 87 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8938 (m-80) REVERT: C 116 ASP cc_start: 0.9627 (m-30) cc_final: 0.9275 (p0) REVERT: C 285 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7165 (mt0) REVERT: C 322 ASP cc_start: 0.8538 (t70) cc_final: 0.7317 (p0) REVERT: C 349 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8326 (t) REVERT: C 425 MET cc_start: 0.9304 (tpp) cc_final: 0.8280 (tpp) REVERT: C 428 LEU cc_start: 0.9551 (tt) cc_final: 0.9147 (pp) outliers start: 46 outliers final: 30 residues processed: 152 average time/residue: 0.0900 time to fit residues: 21.4889 Evaluate side-chains 136 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain F residue 187 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 147 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN F 132 HIS F 171 ASN ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.089326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.044396 restraints weight = 46472.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.044967 restraints weight = 34215.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.045737 restraints weight = 28523.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.045938 restraints weight = 25643.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.046153 restraints weight = 24235.009| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.7713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12341 Z= 0.148 Angle : 0.672 10.127 16746 Z= 0.322 Chirality : 0.043 0.151 1834 Planarity : 0.004 0.043 2165 Dihedral : 11.267 176.994 1690 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.49 % Allowed : 24.48 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1504 helix: 1.11 (0.18), residues: 770 sheet: -0.27 (0.35), residues: 199 loop : -0.50 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 121 TYR 0.016 0.002 TYR A 210 PHE 0.041 0.001 PHE A 351 TRP 0.031 0.002 TRP B 21 HIS 0.007 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00318 (12341) covalent geometry : angle 0.67162 (16746) hydrogen bonds : bond 0.03512 ( 607) hydrogen bonds : angle 4.51571 ( 1779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9417 (tp) cc_final: 0.8969 (mt) REVERT: A 153 LEU cc_start: 0.9527 (pp) cc_final: 0.9319 (pp) REVERT: A 210 TYR cc_start: 0.9241 (m-80) cc_final: 0.8698 (m-80) REVERT: A 388 TRP cc_start: 0.9046 (m-10) cc_final: 0.8670 (m-90) REVERT: A 425 MET cc_start: 0.8591 (tpp) cc_final: 0.8335 (tpp) REVERT: B 73 MET cc_start: 0.9271 (mmm) cc_final: 0.8746 (mpp) REVERT: B 164 MET cc_start: 0.9093 (tpp) cc_final: 0.7809 (mmm) REVERT: B 165 ASN cc_start: 0.9569 (p0) cc_final: 0.9324 (p0) REVERT: B 200 TYR cc_start: 0.8856 (m-80) cc_final: 0.8381 (m-80) REVERT: B 233 MET cc_start: 0.9300 (mmt) cc_final: 0.8709 (mmm) REVERT: B 293 MET cc_start: 0.8835 (mmm) cc_final: 0.8418 (mmm) REVERT: B 330 MET cc_start: 0.9466 (mmm) cc_final: 0.9129 (mmm) REVERT: B 388 MET cc_start: 0.9311 (mmt) cc_final: 0.8830 (mmt) REVERT: C 116 ASP cc_start: 0.9673 (m-30) cc_final: 0.9381 (p0) REVERT: C 161 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: C 256 GLN cc_start: 0.9267 (pt0) cc_final: 0.8939 (pt0) REVERT: C 322 ASP cc_start: 0.8793 (t70) cc_final: 0.7753 (p0) REVERT: C 349 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8175 (t) REVERT: C 425 MET cc_start: 0.9303 (tpp) cc_final: 0.8680 (tpp) REVERT: H 177 MET cc_start: 0.5764 (mmp) cc_final: 0.4980 (ptt) outliers start: 45 outliers final: 30 residues processed: 158 average time/residue: 0.0983 time to fit residues: 23.8726 Evaluate side-chains 132 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 161 TYR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 132 HIS Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.088085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.043759 restraints weight = 47259.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.044179 restraints weight = 34773.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.044942 restraints weight = 29186.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.045141 restraints weight = 26245.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.045254 restraints weight = 24583.317| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.8082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12341 Z= 0.182 Angle : 0.703 12.029 16746 Z= 0.340 Chirality : 0.044 0.215 1834 Planarity : 0.004 0.043 2165 Dihedral : 11.270 173.390 1690 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.72 % Allowed : 24.86 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1504 helix: 1.07 (0.18), residues: 774 sheet: -0.20 (0.35), residues: 204 loop : -0.32 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 156 TYR 0.018 0.002 TYR F 131 PHE 0.013 0.001 PHE B 133 TRP 0.067 0.002 TRP B 21 HIS 0.008 0.001 HIS F 132 Details of bonding type rmsd covalent geometry : bond 0.00387 (12341) covalent geometry : angle 0.70281 (16746) hydrogen bonds : bond 0.03669 ( 607) hydrogen bonds : angle 4.50535 ( 1779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9426 (tp) cc_final: 0.8995 (mt) REVERT: A 210 TYR cc_start: 0.9300 (m-80) cc_final: 0.8797 (m-80) REVERT: A 302 MET cc_start: 0.8945 (mmm) cc_final: 0.8470 (mmm) REVERT: A 388 TRP cc_start: 0.9043 (m-10) cc_final: 0.8681 (m-90) REVERT: A 425 MET cc_start: 0.8568 (tpp) cc_final: 0.8302 (tpp) REVERT: B 133 PHE cc_start: 0.8851 (m-80) cc_final: 0.8194 (m-80) REVERT: B 164 MET cc_start: 0.9160 (tpp) cc_final: 0.7694 (mmm) REVERT: B 165 ASN cc_start: 0.9567 (p0) cc_final: 0.9292 (p0) REVERT: B 200 TYR cc_start: 0.8904 (m-80) cc_final: 0.8321 (m-80) REVERT: B 233 MET cc_start: 0.9291 (mmt) cc_final: 0.8783 (mmm) REVERT: B 267 MET cc_start: 0.9203 (mtt) cc_final: 0.8657 (mpp) REVERT: B 293 MET cc_start: 0.8894 (mmm) cc_final: 0.8556 (mmm) REVERT: B 299 MET cc_start: 0.7577 (pmm) cc_final: 0.7285 (pmm) REVERT: B 300 MET cc_start: 0.8900 (mmm) cc_final: 0.7575 (mpp) REVERT: B 330 MET cc_start: 0.9464 (mmm) cc_final: 0.9137 (mmm) REVERT: B 388 MET cc_start: 0.9303 (mmt) cc_final: 0.8762 (mmt) REVERT: C 5 ILE cc_start: 0.9347 (mm) cc_final: 0.9004 (mm) REVERT: C 87 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8840 (m-80) REVERT: C 116 ASP cc_start: 0.9673 (m-30) cc_final: 0.9418 (p0) REVERT: C 161 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.8682 (m-10) REVERT: C 322 ASP cc_start: 0.8855 (t70) cc_final: 0.7888 (p0) REVERT: C 349 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8263 (t) REVERT: C 425 MET cc_start: 0.9298 (tpp) cc_final: 0.8670 (tpp) REVERT: H 177 MET cc_start: 0.5712 (mmp) cc_final: 0.4955 (ptt) outliers start: 48 outliers final: 36 residues processed: 149 average time/residue: 0.0926 time to fit residues: 21.8895 Evaluate side-chains 135 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 161 TYR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain G residue 156 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 0.0980 chunk 108 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 124 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 overall best weight: 2.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.090379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.045668 restraints weight = 47103.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.046043 restraints weight = 34510.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.046126 restraints weight = 27961.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.046143 restraints weight = 26511.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.046143 restraints weight = 25737.962| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.8181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12341 Z= 0.116 Angle : 0.690 12.414 16746 Z= 0.326 Chirality : 0.044 0.181 1834 Planarity : 0.004 0.041 2165 Dihedral : 11.139 175.736 1690 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.71 % Allowed : 26.41 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.22), residues: 1504 helix: 1.21 (0.19), residues: 766 sheet: -0.09 (0.37), residues: 192 loop : -0.16 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.024 0.001 TYR A 224 PHE 0.019 0.001 PHE B 20 TRP 0.074 0.002 TRP B 21 HIS 0.011 0.001 HIS C 393 Details of bonding type rmsd covalent geometry : bond 0.00257 (12341) covalent geometry : angle 0.69032 (16746) hydrogen bonds : bond 0.03431 ( 607) hydrogen bonds : angle 4.36667 ( 1779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9423 (tp) cc_final: 0.9014 (mt) REVERT: A 210 TYR cc_start: 0.9203 (m-80) cc_final: 0.8765 (m-80) REVERT: A 302 MET cc_start: 0.8847 (mmm) cc_final: 0.8588 (mmm) REVERT: A 388 TRP cc_start: 0.9012 (m-10) cc_final: 0.8676 (m-90) REVERT: A 425 MET cc_start: 0.8733 (tpp) cc_final: 0.8503 (tpp) REVERT: B 133 PHE cc_start: 0.8881 (m-80) cc_final: 0.8011 (m-80) REVERT: B 164 MET cc_start: 0.9203 (tpp) cc_final: 0.7169 (mpp) REVERT: B 165 ASN cc_start: 0.9587 (p0) cc_final: 0.9252 (p0) REVERT: B 200 TYR cc_start: 0.8892 (m-80) cc_final: 0.8185 (m-80) REVERT: B 233 MET cc_start: 0.9278 (mmt) cc_final: 0.8755 (mmm) REVERT: B 293 MET cc_start: 0.8864 (mmm) cc_final: 0.8548 (mmm) REVERT: B 299 MET cc_start: 0.7306 (pmm) cc_final: 0.6887 (pmm) REVERT: B 300 MET cc_start: 0.8889 (mmm) cc_final: 0.7650 (mpp) REVERT: B 330 MET cc_start: 0.9490 (mmm) cc_final: 0.9147 (mmm) REVERT: B 388 MET cc_start: 0.9338 (mmt) cc_final: 0.8849 (mmt) REVERT: C 87 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: C 116 ASP cc_start: 0.9698 (m-30) cc_final: 0.9437 (p0) REVERT: C 161 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8784 (m-10) REVERT: C 256 GLN cc_start: 0.9267 (pt0) cc_final: 0.8836 (pt0) REVERT: C 322 ASP cc_start: 0.8894 (t70) cc_final: 0.7864 (p0) REVERT: C 425 MET cc_start: 0.9295 (tpp) cc_final: 0.8619 (tpp) REVERT: H 177 MET cc_start: 0.5662 (mmp) cc_final: 0.4911 (ptt) outliers start: 35 outliers final: 31 residues processed: 139 average time/residue: 0.0934 time to fit residues: 20.5893 Evaluate side-chains 137 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 161 TYR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 156 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.089122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.044376 restraints weight = 46146.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.044804 restraints weight = 33784.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.045312 restraints weight = 28192.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.045601 restraints weight = 25238.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.045964 restraints weight = 24137.024| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.8414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12341 Z= 0.131 Angle : 0.689 12.425 16746 Z= 0.325 Chirality : 0.044 0.251 1834 Planarity : 0.004 0.056 2165 Dihedral : 11.099 175.859 1690 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.87 % Allowed : 25.79 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1504 helix: 1.28 (0.19), residues: 766 sheet: -0.04 (0.38), residues: 187 loop : -0.15 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 276 TYR 0.019 0.001 TYR A 224 PHE 0.017 0.001 PHE B 133 TRP 0.068 0.002 TRP B 21 HIS 0.006 0.001 HIS C 393 Details of bonding type rmsd covalent geometry : bond 0.00290 (12341) covalent geometry : angle 0.68854 (16746) hydrogen bonds : bond 0.03375 ( 607) hydrogen bonds : angle 4.36044 ( 1779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9369 (tp) cc_final: 0.8956 (mt) REVERT: A 210 TYR cc_start: 0.9236 (m-80) cc_final: 0.8648 (m-80) REVERT: A 302 MET cc_start: 0.8866 (mmm) cc_final: 0.8539 (mmm) REVERT: A 388 TRP cc_start: 0.9005 (m-10) cc_final: 0.8640 (m-90) REVERT: A 425 MET cc_start: 0.8724 (tpp) cc_final: 0.8484 (tpp) REVERT: B 133 PHE cc_start: 0.8990 (m-80) cc_final: 0.8074 (m-80) REVERT: B 164 MET cc_start: 0.9227 (tpp) cc_final: 0.6996 (mpp) REVERT: B 165 ASN cc_start: 0.9564 (p0) cc_final: 0.9178 (p0) REVERT: B 200 TYR cc_start: 0.8838 (m-80) cc_final: 0.8126 (m-80) REVERT: B 233 MET cc_start: 0.9260 (mmt) cc_final: 0.8785 (mmm) REVERT: B 293 MET cc_start: 0.8857 (mmm) cc_final: 0.8539 (mmm) REVERT: B 299 MET cc_start: 0.7320 (pmm) cc_final: 0.6948 (pmm) REVERT: B 300 MET cc_start: 0.8887 (mmm) cc_final: 0.7612 (mpp) REVERT: B 323 MET cc_start: 0.9062 (mmm) cc_final: 0.8719 (mmm) REVERT: B 330 MET cc_start: 0.9463 (mmm) cc_final: 0.9136 (mmm) REVERT: B 388 MET cc_start: 0.9288 (mmt) cc_final: 0.9050 (mmt) REVERT: C 87 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8812 (m-80) REVERT: C 116 ASP cc_start: 0.9646 (m-30) cc_final: 0.9409 (p0) REVERT: C 256 GLN cc_start: 0.9247 (pt0) cc_final: 0.8966 (pt0) REVERT: C 322 ASP cc_start: 0.8792 (t70) cc_final: 0.8236 (p0) REVERT: C 425 MET cc_start: 0.9322 (tpp) cc_final: 0.8719 (tpp) REVERT: H 177 MET cc_start: 0.5719 (mmp) cc_final: 0.5000 (ptt) outliers start: 37 outliers final: 34 residues processed: 137 average time/residue: 0.0782 time to fit residues: 17.4959 Evaluate side-chains 135 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 132 HIS Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain G residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 62 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 133 optimal weight: 40.0000 chunk 115 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 148 optimal weight: 50.0000 chunk 3 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 133 GLN ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.094253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.044924 restraints weight = 66901.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.046045 restraints weight = 45426.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.046332 restraints weight = 38228.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.046930 restraints weight = 34750.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.046928 restraints weight = 33128.628| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.8719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12341 Z= 0.152 Angle : 0.704 12.071 16746 Z= 0.332 Chirality : 0.044 0.212 1834 Planarity : 0.004 0.055 2165 Dihedral : 11.090 176.292 1690 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.71 % Allowed : 26.10 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1504 helix: 1.23 (0.19), residues: 766 sheet: -0.09 (0.38), residues: 187 loop : -0.15 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 276 TYR 0.017 0.002 TYR A 224 PHE 0.014 0.001 PHE A 149 TRP 0.072 0.002 TRP B 21 HIS 0.008 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00328 (12341) covalent geometry : angle 0.70429 (16746) hydrogen bonds : bond 0.03438 ( 607) hydrogen bonds : angle 4.39901 ( 1779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9384 (tp) cc_final: 0.8959 (mt) REVERT: A 210 TYR cc_start: 0.9288 (m-80) cc_final: 0.8739 (m-80) REVERT: A 302 MET cc_start: 0.8752 (mmm) cc_final: 0.8524 (mmm) REVERT: A 388 TRP cc_start: 0.9040 (m-10) cc_final: 0.8676 (m-90) REVERT: A 425 MET cc_start: 0.8697 (tpp) cc_final: 0.8444 (tpp) REVERT: B 133 PHE cc_start: 0.8953 (m-80) cc_final: 0.8013 (m-80) REVERT: B 164 MET cc_start: 0.9295 (tpp) cc_final: 0.7224 (mpp) REVERT: B 165 ASN cc_start: 0.9608 (p0) cc_final: 0.9240 (p0) REVERT: B 200 TYR cc_start: 0.8957 (m-80) cc_final: 0.8205 (m-80) REVERT: B 233 MET cc_start: 0.9249 (mmt) cc_final: 0.8749 (mmm) REVERT: B 293 MET cc_start: 0.8900 (mmm) cc_final: 0.8574 (mmm) REVERT: B 300 MET cc_start: 0.8831 (mmm) cc_final: 0.7556 (mpp) REVERT: B 323 MET cc_start: 0.9073 (mmm) cc_final: 0.8717 (mmm) REVERT: B 330 MET cc_start: 0.9536 (mmm) cc_final: 0.9211 (mmm) REVERT: B 388 MET cc_start: 0.9398 (mmt) cc_final: 0.9143 (mmt) REVERT: C 5 ILE cc_start: 0.9466 (mm) cc_final: 0.9127 (mm) REVERT: C 256 GLN cc_start: 0.9263 (pt0) cc_final: 0.8988 (pt0) REVERT: C 322 ASP cc_start: 0.8922 (t70) cc_final: 0.8356 (p0) REVERT: C 413 MET cc_start: 0.6263 (mmp) cc_final: 0.5713 (mmm) REVERT: C 425 MET cc_start: 0.9288 (tpp) cc_final: 0.8637 (tpp) REVERT: H 177 MET cc_start: 0.5850 (mmp) cc_final: 0.5189 (ptt) outliers start: 35 outliers final: 34 residues processed: 128 average time/residue: 0.0868 time to fit residues: 18.0271 Evaluate side-chains 130 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain F residue 132 HIS Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain G residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.093705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.045705 restraints weight = 66409.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.046328 restraints weight = 47037.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.046245 restraints weight = 36716.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.047954 restraints weight = 37810.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.047399 restraints weight = 35108.002| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.8936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12341 Z= 0.156 Angle : 0.710 12.551 16746 Z= 0.336 Chirality : 0.044 0.249 1834 Planarity : 0.004 0.048 2165 Dihedral : 11.046 178.318 1688 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.94 % Allowed : 25.72 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1504 helix: 1.24 (0.19), residues: 766 sheet: -0.20 (0.37), residues: 192 loop : -0.07 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.017 0.002 TYR A 224 PHE 0.020 0.001 PHE B 20 TRP 0.087 0.003 TRP B 21 HIS 0.008 0.001 HIS C 393 Details of bonding type rmsd covalent geometry : bond 0.00337 (12341) covalent geometry : angle 0.71030 (16746) hydrogen bonds : bond 0.03471 ( 607) hydrogen bonds : angle 4.40699 ( 1779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3330.02 seconds wall clock time: 57 minutes 57.67 seconds (3477.67 seconds total)