Starting phenix.real_space_refine on Sun Aug 24 14:18:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umu_42384/08_2025/8umu_42384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umu_42384/08_2025/8umu_42384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8umu_42384/08_2025/8umu_42384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umu_42384/08_2025/8umu_42384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8umu_42384/08_2025/8umu_42384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umu_42384/08_2025/8umu_42384.map" } resolution = 3.16 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= -0.000 sd= 0.052 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 11 5.49 5 Mg 3 5.21 5 S 136 5.16 5 C 12926 2.51 5 N 3528 2.21 5 O 3917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20521 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4074 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 482} Chain breaks: 5 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: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2492 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2563 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "D" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2526 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 13, 'TRANS': 313} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.01, per 1000 atoms: 0.24 Number of scatterers: 20521 At special positions: 0 Unit cell: (117.576, 128.34, 140.76, 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 136 16.00 P 11 15.00 Mg 3 11.99 O 3917 8.00 N 3528 7.00 C 12926 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: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.4 microseconds 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 14 sheets defined 51.0% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.607A pdb=" N PHE A 286 " --> pdb=" O TRP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.539A pdb=" N GLU A 293 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 294 " --> pdb=" O TYR A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 294' Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 311 through 316 removed outlier: 4.326A pdb=" N VAL A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 441 through 453 removed outlier: 3.628A pdb=" N ILE A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.953A pdb=" N GLN A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.600A pdb=" N LEU A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 4.006A pdb=" N TYR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 Processing helix chain 'A' and resid 628 through 643 removed outlier: 4.108A pdb=" N GLY A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 654 Processing helix chain 'A' and resid 666 through 690 Processing helix chain 'A' and resid 692 through 698 removed outlier: 3.522A pdb=" N LEU A 695 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 696 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 697 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 698 - end of helix No H-bonds generated for 'chain 'A' and resid 692 through 698' Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.088A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 744 removed outlier: 3.712A pdb=" N GLU A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 752 removed outlier: 3.840A pdb=" N ARG A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.996A pdb=" N GLU A 823 " --> pdb=" O ASN A 820 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 824 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 125 removed outlier: 4.727A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.523A pdb=" N SER B 145 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET B 146 " --> pdb=" O ALA B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.371A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 removed outlier: 3.609A pdb=" N GLN B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.604A pdb=" N ILE B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 244 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.802A pdb=" N ALA B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 4.147A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 removed outlier: 3.643A pdb=" N GLY B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.876A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 37 through 50 removed outlier: 3.723A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 removed outlier: 4.048A pdb=" N THR C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 85 removed outlier: 3.630A pdb=" N SER C 85 " --> pdb=" O GLU C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 85' Processing helix chain 'C' and resid 103 through 110 removed outlier: 3.554A pdb=" N SER C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.599A pdb=" N ALA C 129 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 130' Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.757A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 182 through 193 removed outlier: 3.884A pdb=" N LEU C 186 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 209 removed outlier: 4.264A pdb=" N MET C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 removed outlier: 3.543A pdb=" N GLN C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 removed outlier: 3.534A pdb=" N VAL C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.859A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 313 removed outlier: 3.699A pdb=" N SER C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.581A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.871A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.509A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 3.508A pdb=" N VAL D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.809A pdb=" N SER D 154 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 155' Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 223 through 234 removed outlier: 4.012A pdb=" N SER D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.775A pdb=" N ALA D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.671A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.596A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 298 removed outlier: 3.584A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 316 removed outlier: 3.531A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.672A pdb=" N GLN D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.554A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.583A pdb=" N ARG E 15 " --> pdb=" O SER E 12 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 12 through 16' Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.020A pdb=" N CYS E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 103 through 118 removed outlier: 4.263A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.759A pdb=" N GLN E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 127' Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.669A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 removed outlier: 3.883A pdb=" N ARG E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 removed outlier: 3.775A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.608A pdb=" N CYS E 220 " --> pdb=" O ALA E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.943A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.396A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 16 removed outlier: 3.621A pdb=" N LYS F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 removed outlier: 3.691A pdb=" N LEU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 190 through 194 removed outlier: 3.525A pdb=" N ALA F 194 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 219 No H-bonds generated for 'chain 'F' and resid 217 through 219' Processing helix chain 'G' and resid 9 through 18 removed outlier: 3.827A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.504A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 155 removed outlier: 4.195A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 153 removed outlier: 3.770A pdb=" N HIS H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 209 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.694A pdb=" N LEU A 168 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 399 removed outlier: 6.681A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 369 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 508 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 371 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.289A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.493A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 122 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.514A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.153A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN D 73 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N PHE D 197 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.449A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.232A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 104 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN G 179 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.697A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.374A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN F 177 " --> pdb=" O GLU H 115 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN F 179 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP H 113 " --> pdb=" O ASN F 179 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS F 181 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL H 111 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.607A pdb=" N GLU G 3 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER H 172 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ALA H 157 " --> pdb=" O SER H 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.753A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 66 through 71 removed outlier: 7.276A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.43 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: 5306 1.33 - 1.49: 6129 1.49 - 1.64: 9212 1.64 - 1.79: 86 1.79 - 1.95: 120 Bond restraints: 20853 Sorted by residual: bond pdb=" CA SER B 238 " pdb=" C SER B 238 " ideal model delta sigma weight residual 1.524 1.425 0.099 1.24e-02 6.50e+03 6.38e+01 bond pdb=" CA GLN B 237 " pdb=" C GLN B 237 " ideal model delta sigma weight residual 1.524 1.440 0.084 1.24e-02 6.50e+03 4.59e+01 bond pdb=" CA ASP G 21 " pdb=" C ASP G 21 " ideal model delta sigma weight residual 1.522 1.436 0.085 1.31e-02 5.83e+03 4.25e+01 bond pdb=" N ILE G 23 " pdb=" CA ILE G 23 " ideal model delta sigma weight residual 1.460 1.527 -0.068 1.25e-02 6.40e+03 2.93e+01 bond pdb=" N LYS F 14 " pdb=" CA LYS F 14 " ideal model delta sigma weight residual 1.459 1.398 0.061 1.21e-02 6.83e+03 2.55e+01 ... (remaining 20848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 27416 2.67 - 5.33: 655 5.33 - 8.00: 113 8.00 - 10.67: 34 10.67 - 13.34: 5 Bond angle restraints: 28223 Sorted by residual: angle pdb=" N GLU F 17 " pdb=" CA GLU F 17 " pdb=" C GLU F 17 " ideal model delta sigma weight residual 113.23 100.51 12.72 1.24e+00 6.50e-01 1.05e+02 angle pdb=" N LYS G 20 " pdb=" CA LYS G 20 " pdb=" C LYS G 20 " ideal model delta sigma weight residual 111.71 121.98 -10.27 1.15e+00 7.56e-01 7.97e+01 angle pdb=" N ILE F 78 " pdb=" CA ILE F 78 " pdb=" C ILE F 78 " ideal model delta sigma weight residual 113.22 105.48 7.74 1.23e+00 6.61e-01 3.96e+01 angle pdb=" C GLN B 237 " pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " ideal model delta sigma weight residual 110.96 101.47 9.49 1.54e+00 4.22e-01 3.80e+01 angle pdb=" C SER B 238 " pdb=" CA SER B 238 " pdb=" CB SER B 238 " ideal model delta sigma weight residual 110.96 101.65 9.31 1.54e+00 4.22e-01 3.65e+01 ... (remaining 28218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 11661 24.53 - 49.06: 1057 49.06 - 73.59: 136 73.59 - 98.13: 22 98.13 - 122.66: 2 Dihedral angle restraints: 12878 sinusoidal: 5265 harmonic: 7613 Sorted by residual: dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 177.35 122.66 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" O1B ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PB ADP E2000 " pdb=" PA ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 -175.46 115.45 1 2.00e+01 2.50e-03 3.43e+01 dihedral pdb=" C GLN B 237 " pdb=" N GLN B 237 " pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " ideal model delta harmonic sigma weight residual -122.60 -109.96 -12.64 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 12875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3025 0.104 - 0.207: 246 0.207 - 0.310: 15 0.310 - 0.414: 3 0.414 - 0.517: 3 Chirality restraints: 3292 Sorted by residual: chirality pdb=" CA PHE B 240 " pdb=" N PHE B 240 " pdb=" C PHE B 240 " pdb=" CB PHE B 240 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA LYS G 20 " pdb=" N LYS G 20 " pdb=" C LYS G 20 " pdb=" CB LYS G 20 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CB ILE H 241 " pdb=" CA ILE H 241 " pdb=" CG1 ILE H 241 " pdb=" CG2 ILE H 241 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.32e+00 ... (remaining 3289 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 405 " -0.083 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO A 406 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 406 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 406 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " -0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 699 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 360 " -0.051 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO A 361 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.043 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 333 2.66 - 3.22: 17654 3.22 - 3.78: 32380 3.78 - 4.34: 42928 4.34 - 4.90: 71115 Nonbonded interactions: 164410 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.104 2.170 nonbonded pdb="MG MG B 401 " pdb=" O3G AGS B 402 " model vdw 2.167 2.170 nonbonded pdb=" O THR E 168 " pdb=" OG1 THR E 168 " model vdw 2.257 3.040 nonbonded pdb=" O TYR E 254 " pdb=" OG1 THR E 258 " model vdw 2.271 3.040 nonbonded pdb=" O GLU D 259 " pdb=" OG1 THR D 263 " model vdw 2.285 3.040 ... (remaining 164405 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 'F' selection = (chain 'G' and resid 1 through 256) selection = (chain 'H' and resid 1 through 256) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.250 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.006 0.099 20853 Z= 0.315 Angle : 1.015 13.336 28223 Z= 0.577 Chirality : 0.059 0.517 3292 Planarity : 0.008 0.124 3607 Dihedral : 17.808 122.657 7922 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.84 % Allowed : 27.36 % Favored : 71.80 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.89 (0.15), residues: 2577 helix: -1.65 (0.12), residues: 1169 sheet: -0.06 (0.22), residues: 555 loop : -1.15 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 846 TYR 0.040 0.002 TYR F 249 PHE 0.049 0.003 PHE B 223 TRP 0.018 0.002 TRP E 251 HIS 0.011 0.002 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00561 (20853) covalent geometry : angle 1.01544 (28223) hydrogen bonds : bond 0.12962 ( 1119) hydrogen bonds : angle 6.98563 ( 3231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 342 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.6499 (mmm) cc_final: 0.6147 (mmm) REVERT: C 51 ASP cc_start: 0.6192 (t0) cc_final: 0.5873 (t0) REVERT: E 317 TYR cc_start: 0.8270 (t80) cc_final: 0.7417 (t80) REVERT: F 121 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7109 (tt) REVERT: G 27 CYS cc_start: 0.7266 (m) cc_final: 0.6569 (t) REVERT: H 2 PHE cc_start: 0.5988 (t80) cc_final: 0.5520 (t80) REVERT: H 133 TYR cc_start: 0.3392 (m-80) cc_final: 0.1611 (m-10) outliers start: 19 outliers final: 5 residues processed: 353 average time/residue: 0.1393 time to fit residues: 73.7250 Evaluate side-chains 292 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 286 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain H residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 182 GLN B 204 ASN B 226 GLN B 234 ASN C 55 HIS C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 194 HIS F 131 GLN ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.202663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.158040 restraints weight = 29713.025| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.08 r_work: 0.3845 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20853 Z= 0.211 Angle : 0.689 10.911 28223 Z= 0.351 Chirality : 0.044 0.172 3292 Planarity : 0.006 0.075 3607 Dihedral : 7.976 104.445 2880 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.96 % Allowed : 25.12 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.75 (0.16), residues: 2577 helix: -0.38 (0.14), residues: 1191 sheet: 0.13 (0.22), residues: 554 loop : -0.82 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 193 TYR 0.026 0.002 TYR F 249 PHE 0.021 0.002 PHE B 223 TRP 0.014 0.002 TRP D 40 HIS 0.009 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00494 (20853) covalent geometry : angle 0.68939 (28223) hydrogen bonds : bond 0.04277 ( 1119) hydrogen bonds : angle 5.35914 ( 3231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 314 time to evaluate : 0.538 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 632 PHE cc_start: 0.5149 (t80) cc_final: 0.4477 (t80) REVERT: A 815 TYR cc_start: 0.6919 (m-80) cc_final: 0.6705 (m-80) REVERT: B 136 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7412 (mtmt) REVERT: B 145 SER cc_start: 0.8168 (OUTLIER) cc_final: 0.7767 (m) REVERT: B 336 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: C 20 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6254 (mt) REVERT: C 51 ASP cc_start: 0.6686 (t0) cc_final: 0.6129 (t0) REVERT: C 311 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6225 (mtp180) REVERT: D 95 LEU cc_start: 0.4875 (tp) cc_final: 0.4309 (mt) REVERT: D 178 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.5364 (mp) REVERT: E 205 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6752 (tt) REVERT: E 317 TYR cc_start: 0.8090 (t80) cc_final: 0.7674 (t80) REVERT: G 27 CYS cc_start: 0.7716 (m) cc_final: 0.7058 (t) REVERT: H 2 PHE cc_start: 0.6560 (t80) cc_final: 0.5874 (t80) REVERT: H 91 ARG cc_start: 0.7706 (tmt170) cc_final: 0.7456 (tmt170) REVERT: H 133 TYR cc_start: 0.4101 (m-80) cc_final: 0.2720 (m-10) outliers start: 90 outliers final: 48 residues processed: 381 average time/residue: 0.1435 time to fit residues: 83.3183 Evaluate side-chains 340 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 285 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 7 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 176 optimal weight: 0.0470 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.203874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.165071 restraints weight = 29591.579| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.65 r_work: 0.3913 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20853 Z= 0.136 Angle : 0.596 10.576 28223 Z= 0.303 Chirality : 0.042 0.145 3292 Planarity : 0.005 0.063 3607 Dihedral : 7.503 100.875 2875 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.87 % Allowed : 25.47 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.25 (0.16), residues: 2577 helix: 0.18 (0.15), residues: 1194 sheet: 0.20 (0.22), residues: 553 loop : -0.72 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 193 TYR 0.018 0.001 TYR G 249 PHE 0.022 0.001 PHE H 207 TRP 0.013 0.002 TRP E 4 HIS 0.008 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00316 (20853) covalent geometry : angle 0.59627 (28223) hydrogen bonds : bond 0.03676 ( 1119) hydrogen bonds : angle 5.00682 ( 3231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 315 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 PHE cc_start: 0.5114 (t80) cc_final: 0.4505 (t80) REVERT: A 815 TYR cc_start: 0.6916 (m-80) cc_final: 0.6631 (m-80) REVERT: B 127 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7479 (ttpt) REVERT: B 136 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7171 (mtmt) REVERT: B 145 SER cc_start: 0.8157 (OUTLIER) cc_final: 0.7765 (m) REVERT: C 20 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6180 (mt) REVERT: C 29 GLN cc_start: 0.7293 (mm-40) cc_final: 0.7092 (mm110) REVERT: C 51 ASP cc_start: 0.6443 (t0) cc_final: 0.5855 (t0) REVERT: D 95 LEU cc_start: 0.4871 (tp) cc_final: 0.4319 (mt) REVERT: D 193 ARG cc_start: 0.6470 (ttt-90) cc_final: 0.5543 (ttt180) REVERT: D 272 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7782 (pm20) REVERT: E 205 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6871 (tt) REVERT: E 317 TYR cc_start: 0.7997 (t80) cc_final: 0.7266 (t80) REVERT: G 27 CYS cc_start: 0.7636 (m) cc_final: 0.6990 (t) REVERT: H 2 PHE cc_start: 0.6257 (t80) cc_final: 0.5492 (t80) REVERT: H 8 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6802 (tm-30) REVERT: H 91 ARG cc_start: 0.7622 (tmt170) cc_final: 0.7211 (tmt170) REVERT: H 133 TYR cc_start: 0.4193 (m-80) cc_final: 0.2755 (m-10) outliers start: 88 outliers final: 49 residues processed: 379 average time/residue: 0.1271 time to fit residues: 73.6509 Evaluate side-chains 350 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 24 optimal weight: 6.9990 chunk 249 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 169 optimal weight: 0.1980 chunk 176 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 71 HIS E 194 HIS ** F 213 ASN ** 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 = 0.4522 r_free = 0.4522 target = 0.203629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.164490 restraints weight = 29737.620| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.61 r_work: 0.3904 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20853 Z= 0.134 Angle : 0.576 8.855 28223 Z= 0.293 Chirality : 0.041 0.140 3292 Planarity : 0.004 0.061 3607 Dihedral : 7.160 90.248 2874 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.40 % Allowed : 24.81 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.06 (0.17), residues: 2577 helix: 0.47 (0.15), residues: 1194 sheet: 0.31 (0.23), residues: 545 loop : -0.57 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 91 TYR 0.021 0.001 TYR G 249 PHE 0.026 0.001 PHE H 207 TRP 0.021 0.002 TRP E 4 HIS 0.007 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00315 (20853) covalent geometry : angle 0.57639 (28223) hydrogen bonds : bond 0.03477 ( 1119) hydrogen bonds : angle 4.82267 ( 3231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 322 time to evaluate : 0.557 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 815 TYR cc_start: 0.6866 (m-80) cc_final: 0.6603 (m-80) REVERT: B 127 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7523 (ttpt) REVERT: B 136 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7238 (mtmt) REVERT: B 216 ASP cc_start: 0.5732 (p0) cc_final: 0.5488 (p0) REVERT: C 20 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6197 (mt) REVERT: C 51 ASP cc_start: 0.6472 (t0) cc_final: 0.5866 (t0) REVERT: C 85 SER cc_start: 0.7375 (m) cc_final: 0.7050 (p) REVERT: D 272 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: E 154 LYS cc_start: 0.8384 (ptpt) cc_final: 0.8174 (ptpt) REVERT: G 27 CYS cc_start: 0.7653 (m) cc_final: 0.7003 (t) REVERT: H 2 PHE cc_start: 0.6310 (t80) cc_final: 0.5551 (t80) REVERT: H 91 ARG cc_start: 0.7615 (tmt170) cc_final: 0.6983 (tmt170) REVERT: H 133 TYR cc_start: 0.4178 (m-80) cc_final: 0.2811 (m-10) outliers start: 100 outliers final: 60 residues processed: 392 average time/residue: 0.1258 time to fit residues: 75.5281 Evaluate side-chains 366 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 38 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN E 71 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.203339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.164887 restraints weight = 29632.053| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.65 r_work: 0.3903 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20853 Z= 0.132 Angle : 0.584 9.383 28223 Z= 0.294 Chirality : 0.042 0.154 3292 Planarity : 0.004 0.087 3607 Dihedral : 6.844 77.753 2872 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.66 % Allowed : 25.21 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.21 (0.17), residues: 2577 helix: 0.60 (0.15), residues: 1196 sheet: 0.34 (0.23), residues: 545 loop : -0.48 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 454 TYR 0.029 0.001 TYR E 155 PHE 0.030 0.001 PHE H 207 TRP 0.023 0.002 TRP E 4 HIS 0.007 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00306 (20853) covalent geometry : angle 0.58379 (28223) hydrogen bonds : bond 0.03402 ( 1119) hydrogen bonds : angle 4.75269 ( 3231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 325 time to evaluate : 0.668 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 483 MET cc_start: 0.7102 (tpp) cc_final: 0.6642 (tpp) REVERT: A 815 TYR cc_start: 0.6834 (m-80) cc_final: 0.6536 (m-80) REVERT: B 127 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7512 (ttpt) REVERT: B 136 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7277 (mtmt) REVERT: B 216 ASP cc_start: 0.5685 (p0) cc_final: 0.5418 (p0) REVERT: C 20 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6211 (mt) REVERT: C 51 ASP cc_start: 0.6427 (t0) cc_final: 0.5909 (t0) REVERT: C 85 SER cc_start: 0.7389 (m) cc_final: 0.7114 (p) REVERT: C 165 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7701 (tp) REVERT: D 272 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: E 154 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7274 (pttt) REVERT: G 27 CYS cc_start: 0.7660 (m) cc_final: 0.7038 (t) REVERT: H 91 ARG cc_start: 0.7594 (tmt170) cc_final: 0.7055 (tmt170) REVERT: H 133 TYR cc_start: 0.4124 (m-80) cc_final: 0.2772 (m-10) REVERT: H 162 CYS cc_start: 0.7023 (t) cc_final: 0.6572 (p) outliers start: 106 outliers final: 75 residues processed: 407 average time/residue: 0.1321 time to fit residues: 82.4707 Evaluate side-chains 386 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 44 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 52 optimal weight: 0.0060 chunk 206 optimal weight: 0.1980 chunk 91 optimal weight: 0.0060 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 overall best weight: 1.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 347 GLN E 71 HIS E 194 HIS E 213 HIS H 44 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.202832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.159069 restraints weight = 29687.312| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.00 r_work: 0.3851 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20853 Z= 0.139 Angle : 0.591 11.118 28223 Z= 0.297 Chirality : 0.042 0.173 3292 Planarity : 0.004 0.064 3607 Dihedral : 6.644 64.252 2872 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.84 % Allowed : 25.52 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.30 (0.17), residues: 2577 helix: 0.69 (0.15), residues: 1194 sheet: 0.30 (0.23), residues: 547 loop : -0.39 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 168 TYR 0.026 0.001 TYR E 155 PHE 0.020 0.001 PHE G 2 TRP 0.023 0.002 TRP E 4 HIS 0.009 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00328 (20853) covalent geometry : angle 0.59131 (28223) hydrogen bonds : bond 0.03416 ( 1119) hydrogen bonds : angle 4.71475 ( 3231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 317 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6625 (tt) REVERT: A 483 MET cc_start: 0.7163 (tpp) cc_final: 0.6733 (tpp) REVERT: A 815 TYR cc_start: 0.6858 (m-80) cc_final: 0.6524 (m-80) REVERT: B 127 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7517 (ttpt) REVERT: B 136 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7264 (mtmt) REVERT: B 145 SER cc_start: 0.8056 (OUTLIER) cc_final: 0.7748 (m) REVERT: B 216 ASP cc_start: 0.5728 (p0) cc_final: 0.5197 (p0) REVERT: C 20 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6289 (mt) REVERT: C 51 ASP cc_start: 0.6530 (t0) cc_final: 0.5938 (t0) REVERT: C 85 SER cc_start: 0.7393 (m) cc_final: 0.7131 (p) REVERT: C 165 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7714 (tp) REVERT: D 272 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: E 104 ASP cc_start: 0.8450 (p0) cc_final: 0.8232 (p0) REVERT: G 27 CYS cc_start: 0.7722 (m) cc_final: 0.7094 (t) REVERT: H 8 GLN cc_start: 0.7277 (tm-30) cc_final: 0.6932 (tm-30) REVERT: H 91 ARG cc_start: 0.7719 (tmt170) cc_final: 0.7219 (tmt170) REVERT: H 133 TYR cc_start: 0.4220 (m-80) cc_final: 0.2934 (m-10) REVERT: H 162 CYS cc_start: 0.7054 (t) cc_final: 0.6602 (p) outliers start: 110 outliers final: 80 residues processed: 400 average time/residue: 0.1303 time to fit residues: 79.8994 Evaluate side-chains 387 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 300 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 10 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 347 GLN E 71 HIS E 213 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.202578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.159463 restraints weight = 29739.415| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.88 r_work: 0.3867 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20853 Z= 0.138 Angle : 0.593 9.945 28223 Z= 0.297 Chirality : 0.042 0.163 3292 Planarity : 0.004 0.061 3607 Dihedral : 6.523 63.793 2872 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.84 % Allowed : 25.65 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.31 (0.17), residues: 2577 helix: 0.70 (0.15), residues: 1200 sheet: 0.32 (0.23), residues: 543 loop : -0.41 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 117 TYR 0.025 0.001 TYR E 155 PHE 0.026 0.002 PHE B 223 TRP 0.022 0.002 TRP E 4 HIS 0.008 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00326 (20853) covalent geometry : angle 0.59312 (28223) hydrogen bonds : bond 0.03405 ( 1119) hydrogen bonds : angle 4.72010 ( 3231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 313 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6633 (tt) REVERT: A 483 MET cc_start: 0.7124 (tpp) cc_final: 0.6804 (tpp) REVERT: A 815 TYR cc_start: 0.6892 (m-80) cc_final: 0.6534 (m-80) REVERT: B 127 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7513 (ttpt) REVERT: B 136 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7274 (mtmt) REVERT: B 145 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7724 (m) REVERT: B 216 ASP cc_start: 0.5690 (p0) cc_final: 0.5149 (p0) REVERT: C 20 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6230 (mt) REVERT: C 51 ASP cc_start: 0.6469 (t0) cc_final: 0.5888 (t0) REVERT: C 85 SER cc_start: 0.7436 (m) cc_final: 0.7185 (p) REVERT: D 272 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: E 48 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.7024 (mtmt) REVERT: E 104 ASP cc_start: 0.8413 (p0) cc_final: 0.8154 (p0) REVERT: E 127 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6551 (ttt90) REVERT: F 8 GLN cc_start: 0.7136 (tp-100) cc_final: 0.6920 (tp-100) REVERT: G 27 CYS cc_start: 0.7665 (m) cc_final: 0.7062 (t) REVERT: H 40 MET cc_start: 0.6214 (tpt) cc_final: 0.5314 (tmm) REVERT: H 91 ARG cc_start: 0.7731 (tmt170) cc_final: 0.7236 (tmt170) REVERT: H 116 MET cc_start: 0.7192 (tpt) cc_final: 0.6410 (tpt) REVERT: H 162 CYS cc_start: 0.7111 (t) cc_final: 0.6610 (p) REVERT: H 210 ARG cc_start: 0.7316 (mmp80) cc_final: 0.7093 (mmp80) REVERT: H 227 LEU cc_start: 0.7155 (tt) cc_final: 0.6911 (tt) outliers start: 110 outliers final: 87 residues processed: 397 average time/residue: 0.1292 time to fit residues: 78.1545 Evaluate side-chains 394 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 299 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN E 71 HIS E 194 HIS E 213 HIS ** H 36 ASN ** 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 = 0.4494 r_free = 0.4494 target = 0.200736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155148 restraints weight = 29676.225| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.58 r_work: 0.3856 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20853 Z= 0.167 Angle : 0.622 10.207 28223 Z= 0.311 Chirality : 0.043 0.185 3292 Planarity : 0.005 0.078 3607 Dihedral : 6.473 63.792 2872 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.06 % Allowed : 25.91 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.22 (0.17), residues: 2577 helix: 0.67 (0.15), residues: 1197 sheet: 0.20 (0.23), residues: 536 loop : -0.43 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 550 TYR 0.029 0.002 TYR G 249 PHE 0.025 0.002 PHE G 2 TRP 0.023 0.002 TRP E 4 HIS 0.008 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00396 (20853) covalent geometry : angle 0.62162 (28223) hydrogen bonds : bond 0.03564 ( 1119) hydrogen bonds : angle 4.79768 ( 3231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 315 time to evaluate : 0.585 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 482 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6640 (tt) REVERT: A 483 MET cc_start: 0.7167 (tpp) cc_final: 0.6742 (tpp) REVERT: B 127 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7545 (ttpt) REVERT: B 136 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7511 (mtmt) REVERT: B 145 SER cc_start: 0.8123 (OUTLIER) cc_final: 0.7757 (m) REVERT: B 216 ASP cc_start: 0.5720 (p0) cc_final: 0.5174 (p0) REVERT: B 325 MET cc_start: 0.7946 (mtm) cc_final: 0.7421 (mpp) REVERT: C 20 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6250 (mt) REVERT: C 51 ASP cc_start: 0.6530 (t0) cc_final: 0.5921 (t0) REVERT: C 85 SER cc_start: 0.7449 (m) cc_final: 0.7198 (p) REVERT: C 225 MET cc_start: 0.7886 (tmm) cc_final: 0.7668 (tmm) REVERT: D 272 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: E 104 ASP cc_start: 0.8420 (p0) cc_final: 0.8153 (p0) REVERT: E 127 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6585 (ttt90) REVERT: F 8 GLN cc_start: 0.7189 (tp-100) cc_final: 0.6954 (tp-100) REVERT: F 243 ASP cc_start: 0.7470 (p0) cc_final: 0.7245 (p0) REVERT: G 27 CYS cc_start: 0.7742 (m) cc_final: 0.7126 (t) REVERT: H 8 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6773 (tm-30) REVERT: H 91 ARG cc_start: 0.7787 (tmt170) cc_final: 0.7283 (tmt170) REVERT: H 116 MET cc_start: 0.7196 (tpt) cc_final: 0.6434 (tpt) REVERT: H 133 TYR cc_start: 0.4252 (m-80) cc_final: 0.2721 (m-10) REVERT: H 162 CYS cc_start: 0.7082 (t) cc_final: 0.6581 (p) REVERT: H 207 PHE cc_start: 0.7970 (m-80) cc_final: 0.7670 (m-10) outliers start: 115 outliers final: 92 residues processed: 406 average time/residue: 0.1244 time to fit residues: 76.9793 Evaluate side-chains 399 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 300 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 151 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 51 optimal weight: 0.0270 chunk 54 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 347 GLN E 71 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.202908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159106 restraints weight = 29595.348| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.01 r_work: 0.3861 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20853 Z= 0.125 Angle : 0.600 10.975 28223 Z= 0.300 Chirality : 0.042 0.169 3292 Planarity : 0.004 0.061 3607 Dihedral : 6.347 63.065 2872 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.31 % Allowed : 26.66 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.39 (0.17), residues: 2577 helix: 0.83 (0.15), residues: 1198 sheet: 0.22 (0.23), residues: 528 loop : -0.34 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 210 TYR 0.022 0.001 TYR G 249 PHE 0.022 0.001 PHE B 223 TRP 0.020 0.001 TRP E 4 HIS 0.007 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00289 (20853) covalent geometry : angle 0.60024 (28223) hydrogen bonds : bond 0.03306 ( 1119) hydrogen bonds : angle 4.70110 ( 3231) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 323 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6626 (tt) REVERT: A 483 MET cc_start: 0.7126 (tpp) cc_final: 0.6756 (tpp) REVERT: B 127 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7559 (ttpt) REVERT: B 136 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7509 (mtmt) REVERT: B 145 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7762 (m) REVERT: B 216 ASP cc_start: 0.5659 (p0) cc_final: 0.5111 (p0) REVERT: B 285 LEU cc_start: 0.8608 (mp) cc_final: 0.8391 (mt) REVERT: B 325 MET cc_start: 0.7948 (mtm) cc_final: 0.7429 (mpp) REVERT: C 51 ASP cc_start: 0.6508 (t0) cc_final: 0.5941 (t0) REVERT: C 85 SER cc_start: 0.7445 (m) cc_final: 0.7213 (p) REVERT: C 225 MET cc_start: 0.7922 (tmm) cc_final: 0.7707 (tmm) REVERT: C 320 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7908 (mt) REVERT: D 272 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: E 9 ARG cc_start: 0.5816 (ttt-90) cc_final: 0.5472 (ttt-90) REVERT: E 48 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6765 (mtmt) REVERT: E 104 ASP cc_start: 0.8368 (p0) cc_final: 0.8127 (p0) REVERT: E 127 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6562 (ttt90) REVERT: E 227 LEU cc_start: 0.7577 (mm) cc_final: 0.7332 (mp) REVERT: F 8 GLN cc_start: 0.7201 (tp-100) cc_final: 0.6961 (tp-100) REVERT: F 243 ASP cc_start: 0.7503 (p0) cc_final: 0.7279 (p0) REVERT: G 27 CYS cc_start: 0.7625 (m) cc_final: 0.7048 (t) REVERT: H 8 GLN cc_start: 0.7199 (tm-30) cc_final: 0.6859 (tm-30) REVERT: H 68 MET cc_start: 0.7089 (mtm) cc_final: 0.6757 (pmm) REVERT: H 91 ARG cc_start: 0.7649 (tmt170) cc_final: 0.7226 (tmt170) REVERT: H 133 TYR cc_start: 0.4109 (m-80) cc_final: 0.2629 (m-10) REVERT: H 162 CYS cc_start: 0.7168 (t) cc_final: 0.6581 (p) REVERT: H 227 LEU cc_start: 0.7119 (tt) cc_final: 0.6910 (tt) outliers start: 98 outliers final: 75 residues processed: 397 average time/residue: 0.1259 time to fit residues: 76.7162 Evaluate side-chains 391 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 308 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 239 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.0040 chunk 149 optimal weight: 1.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN E 71 HIS E 194 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.202205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.159274 restraints weight = 29702.716| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.84 r_work: 0.3865 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20853 Z= 0.139 Angle : 0.621 11.191 28223 Z= 0.310 Chirality : 0.043 0.219 3292 Planarity : 0.005 0.066 3607 Dihedral : 6.303 63.073 2872 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.27 % Allowed : 27.01 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.17), residues: 2577 helix: 0.79 (0.15), residues: 1201 sheet: 0.18 (0.23), residues: 534 loop : -0.38 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 854 TYR 0.024 0.001 TYR G 249 PHE 0.022 0.001 PHE G 2 TRP 0.021 0.002 TRP E 4 HIS 0.007 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00328 (20853) covalent geometry : angle 0.62135 (28223) hydrogen bonds : bond 0.03377 ( 1119) hydrogen bonds : angle 4.72937 ( 3231) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 309 time to evaluate : 0.704 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 482 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6612 (tt) REVERT: A 483 MET cc_start: 0.7163 (tpp) cc_final: 0.6727 (tpp) REVERT: A 531 MET cc_start: 0.4347 (tpp) cc_final: 0.3763 (ttt) REVERT: B 127 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7552 (ttpt) REVERT: B 136 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7506 (mtmt) REVERT: B 145 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7759 (m) REVERT: B 216 ASP cc_start: 0.5708 (p0) cc_final: 0.5162 (p0) REVERT: B 325 MET cc_start: 0.7884 (mtm) cc_final: 0.7376 (mpp) REVERT: C 51 ASP cc_start: 0.6525 (t0) cc_final: 0.5964 (t0) REVERT: C 85 SER cc_start: 0.7431 (m) cc_final: 0.7220 (p) REVERT: C 225 MET cc_start: 0.7976 (tmm) cc_final: 0.7755 (tmm) REVERT: D 272 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8132 (pt0) REVERT: E 104 ASP cc_start: 0.8380 (p0) cc_final: 0.8125 (p0) REVERT: E 127 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6614 (ttt90) REVERT: E 214 ARG cc_start: 0.6641 (mtp85) cc_final: 0.6437 (mtp85) REVERT: E 227 LEU cc_start: 0.7567 (mm) cc_final: 0.7325 (mp) REVERT: F 8 GLN cc_start: 0.7259 (tp-100) cc_final: 0.6997 (tp-100) REVERT: F 72 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8099 (mt) REVERT: F 243 ASP cc_start: 0.7518 (p0) cc_final: 0.7271 (p0) REVERT: G 27 CYS cc_start: 0.7619 (m) cc_final: 0.7032 (t) REVERT: H 8 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7143 (tm-30) REVERT: H 68 MET cc_start: 0.7198 (mtm) cc_final: 0.6767 (pmm) REVERT: H 91 ARG cc_start: 0.7776 (tmt170) cc_final: 0.7298 (tmt170) REVERT: H 133 TYR cc_start: 0.4241 (m-80) cc_final: 0.2848 (m-10) REVERT: H 162 CYS cc_start: 0.7216 (t) cc_final: 0.6589 (p) REVERT: H 207 PHE cc_start: 0.7586 (m-80) cc_final: 0.7030 (m-80) outliers start: 97 outliers final: 80 residues processed: 385 average time/residue: 0.1317 time to fit residues: 77.4129 Evaluate side-chains 392 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 305 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 97 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 241 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 347 GLN E 71 HIS E 213 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.202859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.160915 restraints weight = 29738.067| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.87 r_work: 0.3867 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20853 Z= 0.126 Angle : 0.616 10.260 28223 Z= 0.306 Chirality : 0.042 0.200 3292 Planarity : 0.004 0.064 3607 Dihedral : 6.246 62.692 2872 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.83 % Allowed : 27.32 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.38 (0.17), residues: 2577 helix: 0.83 (0.15), residues: 1209 sheet: 0.19 (0.23), residues: 536 loop : -0.35 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 854 TYR 0.020 0.001 TYR G 249 PHE 0.021 0.001 PHE B 223 TRP 0.019 0.002 TRP E 4 HIS 0.011 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00295 (20853) covalent geometry : angle 0.61558 (28223) hydrogen bonds : bond 0.03291 ( 1119) hydrogen bonds : angle 4.69107 ( 3231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4533.81 seconds wall clock time: 78 minutes 38.86 seconds (4718.86 seconds total)