Starting phenix.real_space_refine on Thu Mar 5 00:12:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9h_49169/03_2026/9n9h_49169_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9h_49169/03_2026/9n9h_49169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n9h_49169/03_2026/9n9h_49169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9h_49169/03_2026/9n9h_49169.map" model { file = "/net/cci-nas-00/data/ceres_data/9n9h_49169/03_2026/9n9h_49169_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9h_49169/03_2026/9n9h_49169_neut.cif" } resolution = 3.31 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= 0.000 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 10 5.49 5 Mg 4 5.21 5 S 116 5.16 5 C 10654 2.51 5 N 2910 2.21 5 O 3264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16958 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3365 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3402 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Chain: "M" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3220 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 393} 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: "a" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3372 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "b" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {' MG': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {' MG': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.93, per 1000 atoms: 0.23 Number of scatterers: 16958 At special positions: 0 Unit cell: (107.141, 89.1072, 196.248, 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 116 16.00 P 10 15.00 Mg 4 11.99 O 3264 8.00 N 2910 7.00 C 10654 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: 1.51 Conformation dependent library (CDL) restraints added in 643.7 milliseconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3946 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 15 sheets defined 52.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.748A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.683A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.651A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.395A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.804A pdb=" N LYS A 112 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.810A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.205A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.829A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.537A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.030A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.560A pdb=" N CYS A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 removed outlier: 3.501A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.700A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.099A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.575A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.021A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.628A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.300A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.549A pdb=" N ALA B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 113' Processing helix chain 'B' and resid 114 through 128 removed outlier: 3.592A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.752A pdb=" N GLU B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.662A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.642A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.743A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 338 removed outlier: 3.532A pdb=" N GLN B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.737A pdb=" N PHE B 343 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 400 removed outlier: 4.185A pdb=" N LEU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 415 through 437 removed outlier: 3.798A pdb=" N THR B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 430 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 204 removed outlier: 3.519A pdb=" N VAL M 199 " --> pdb=" O LYS M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 223 removed outlier: 3.828A pdb=" N MET M 221 " --> pdb=" O TYR M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 231 Processing helix chain 'M' and resid 233 through 247 Processing helix chain 'M' and resid 273 through 280 Processing helix chain 'M' and resid 324 through 331 removed outlier: 3.847A pdb=" N PHE M 331 " --> pdb=" O VAL M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 340 Processing helix chain 'M' and resid 341 through 343 No H-bonds generated for 'chain 'M' and resid 341 through 343' Processing helix chain 'M' and resid 357 through 363 Processing helix chain 'M' and resid 376 through 390 removed outlier: 3.505A pdb=" N VAL M 385 " --> pdb=" O ALA M 381 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE M 386 " --> pdb=" O SER M 382 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP M 390 " --> pdb=" O PHE M 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 396 Processing helix chain 'M' and resid 445 through 461 Processing helix chain 'M' and resid 506 through 533 Processing helix chain 'M' and resid 542 through 545 removed outlier: 3.590A pdb=" N GLU M 545 " --> pdb=" O PRO M 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 542 through 545' Processing helix chain 'M' and resid 546 through 557 removed outlier: 5.005A pdb=" N ASP M 554 " --> pdb=" O GLN M 550 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER M 555 " --> pdb=" O ILE M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 572 through 574 No H-bonds generated for 'chain 'M' and resid 572 through 574' Processing helix chain 'M' and resid 575 through 591 removed outlier: 3.538A pdb=" N THR M 582 " --> pdb=" O TYR M 578 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL M 589 " --> pdb=" O TYR M 585 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS M 590 " --> pdb=" O ALA M 586 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 29 removed outlier: 3.603A pdb=" N ALA a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS a 25 " --> pdb=" O TRP a 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU a 26 " --> pdb=" O GLU a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 51 removed outlier: 3.961A pdb=" N THR a 51 " --> pdb=" O SER a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 79 removed outlier: 4.750A pdb=" N ILE a 75 " --> pdb=" O GLU a 71 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU a 77 " --> pdb=" O THR a 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL a 78 " --> pdb=" O VAL a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 90 No H-bonds generated for 'chain 'a' and resid 88 through 90' Processing helix chain 'a' and resid 102 through 108 Processing helix chain 'a' and resid 110 through 129 removed outlier: 4.091A pdb=" N ILE a 114 " --> pdb=" O ILE a 110 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP a 116 " --> pdb=" O LYS a 112 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU a 117 " --> pdb=" O GLU a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 161 removed outlier: 4.112A pdb=" N THR a 150 " --> pdb=" O GLY a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 190 Processing helix chain 'a' and resid 190 through 197 Processing helix chain 'a' and resid 206 through 217 Processing helix chain 'a' and resid 223 through 240 removed outlier: 3.651A pdb=" N LEU a 227 " --> pdb=" O THR a 223 " (cutoff:3.500A) Processing helix chain 'a' and resid 241 through 243 No H-bonds generated for 'chain 'a' and resid 241 through 243' Processing helix chain 'a' and resid 251 through 260 Processing helix chain 'a' and resid 287 through 295 removed outlier: 3.773A pdb=" N CYS a 295 " --> pdb=" O ILE a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 296 through 301 removed outlier: 6.120A pdb=" N ALA a 299 " --> pdb=" O PHE a 296 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN a 301 " --> pdb=" O PRO a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 324 through 337 removed outlier: 3.543A pdb=" N THR a 337 " --> pdb=" O ALA a 333 " (cutoff:3.500A) Processing helix chain 'a' and resid 384 through 400 removed outlier: 3.651A pdb=" N TRP a 388 " --> pdb=" O ILE a 384 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG a 390 " --> pdb=" O GLU a 386 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS a 393 " --> pdb=" O ALA a 389 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET a 398 " --> pdb=" O LYS a 394 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA a 400 " --> pdb=" O ASP a 396 " (cutoff:3.500A) Processing helix chain 'a' and resid 404 through 410 removed outlier: 3.938A pdb=" N TYR a 408 " --> pdb=" O PHE a 404 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 435 removed outlier: 4.326A pdb=" N PHE a 418 " --> pdb=" O GLU a 414 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER a 419 " --> pdb=" O GLU a 415 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS a 430 " --> pdb=" O ALA a 426 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL a 435 " --> pdb=" O ASP a 431 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 28 Processing helix chain 'b' and resid 41 through 48 removed outlier: 4.109A pdb=" N ARG b 48 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 51 No H-bonds generated for 'chain 'b' and resid 49 through 51' Processing helix chain 'b' and resid 71 through 80 removed outlier: 4.392A pdb=" N MET b 75 " --> pdb=" O GLU b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 90 No H-bonds generated for 'chain 'b' and resid 88 through 90' Processing helix chain 'b' and resid 102 through 108 Processing helix chain 'b' and resid 108 through 129 removed outlier: 3.692A pdb=" N GLU b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP b 116 " --> pdb=" O ALA b 112 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER b 117 " --> pdb=" O GLU b 113 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL b 118 " --> pdb=" O LEU b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 161 removed outlier: 3.591A pdb=" N GLY b 148 " --> pdb=" O GLY b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 198 removed outlier: 3.534A pdb=" N HIS b 192 " --> pdb=" O THR b 188 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN b 193 " --> pdb=" O LEU b 189 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU b 196 " --> pdb=" O HIS b 192 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN b 197 " --> pdb=" O GLN b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 216 Processing helix chain 'b' and resid 223 through 239 removed outlier: 3.885A pdb=" N LEU b 230 " --> pdb=" O ASP b 226 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL b 231 " --> pdb=" O LEU b 227 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR b 239 " --> pdb=" O MET b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 240 through 243 Processing helix chain 'b' and resid 251 through 260 Processing helix chain 'b' and resid 280 through 284 Processing helix chain 'b' and resid 287 through 297 Processing helix chain 'b' and resid 298 through 301 Processing helix chain 'b' and resid 306 through 310 Processing helix chain 'b' and resid 324 through 339 Processing helix chain 'b' and resid 340 through 343 removed outlier: 3.578A pdb=" N PHE b 343 " --> pdb=" O SER b 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 340 through 343' Processing helix chain 'b' and resid 383 through 402 removed outlier: 4.303A pdb=" N LEU b 387 " --> pdb=" O ALA b 383 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE b 388 " --> pdb=" O ILE b 384 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA b 397 " --> pdb=" O GLU b 393 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG b 401 " --> pdb=" O ALA b 397 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 410 Processing helix chain 'b' and resid 414 through 435 removed outlier: 3.561A pdb=" N PHE b 418 " --> pdb=" O ASP b 414 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.163A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.699A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.025A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU B 3 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN B 136 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 5 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR B 138 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 7 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N SER B 140 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ALA B 9 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'M' and resid 317 through 319 removed outlier: 6.150A pdb=" N VAL M 265 " --> pdb=" O PHE M 317 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE M 319 " --> pdb=" O VAL M 265 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL M 267 " --> pdb=" O PHE M 319 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS M 345 " --> pdb=" O ARG M 562 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N CYS M 564 " --> pdb=" O LYS M 345 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR M 347 " --> pdb=" O CYS M 564 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE M 566 " --> pdb=" O THR M 347 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE M 349 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET M 568 " --> pdb=" O PHE M 349 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR M 351 " --> pdb=" O MET M 568 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA M 346 " --> pdb=" O SER M 493 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL M 495 " --> pdb=" O ALA M 346 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS M 348 " --> pdb=" O VAL M 495 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU M 482 " --> pdb=" O HIS M 489 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS M 491 " --> pdb=" O ILE M 480 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE M 480 " --> pdb=" O LYS M 491 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER M 493 " --> pdb=" O LEU M 478 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU M 478 " --> pdb=" O SER M 493 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL M 495 " --> pdb=" O ALA M 476 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA M 476 " --> pdb=" O VAL M 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 317 through 319 removed outlier: 6.150A pdb=" N VAL M 265 " --> pdb=" O PHE M 317 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE M 319 " --> pdb=" O VAL M 265 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL M 267 " --> pdb=" O PHE M 319 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS M 345 " --> pdb=" O ARG M 562 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N CYS M 564 " --> pdb=" O LYS M 345 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR M 347 " --> pdb=" O CYS M 564 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE M 566 " --> pdb=" O THR M 347 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE M 349 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET M 568 " --> pdb=" O PHE M 349 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR M 351 " --> pdb=" O MET M 568 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA M 346 " --> pdb=" O SER M 493 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL M 495 " --> pdb=" O ALA M 346 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS M 348 " --> pdb=" O VAL M 495 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU M 482 " --> pdb=" O HIS M 489 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS M 491 " --> pdb=" O ILE M 480 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE M 480 " --> pdb=" O LYS M 491 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER M 493 " --> pdb=" O LEU M 478 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU M 478 " --> pdb=" O SER M 493 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL M 495 " --> pdb=" O ALA M 476 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA M 476 " --> pdb=" O VAL M 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 285 through 286 Processing sheet with id=AB1, first strand: chain 'M' and resid 424 through 427 removed outlier: 3.546A pdb=" N ARG M 424 " --> pdb=" O VAL M 436 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 92 through 94 removed outlier: 8.038A pdb=" N ILE a 93 " --> pdb=" O ALA a 65 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE a 67 " --> pdb=" O ILE a 93 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE a 5 " --> pdb=" O LEU a 136 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE a 138 " --> pdb=" O ILE a 5 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE a 7 " --> pdb=" O PHE a 138 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N SER a 140 " --> pdb=" O ILE a 7 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N VAL a 9 " --> pdb=" O SER a 140 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N PHE a 135 " --> pdb=" O LEU a 167 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE a 169 " --> pdb=" O PHE a 135 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL a 137 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE a 171 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N HIS a 139 " --> pdb=" O ILE a 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'a' and resid 269 through 273 removed outlier: 3.574A pdb=" N ALA a 314 " --> pdb=" O ASN a 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 92 through 94 removed outlier: 8.042A pdb=" N VAL b 93 " --> pdb=" O ALA b 65 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU b 67 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER b 140 " --> pdb=" O ALA b 9 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE b 135 " --> pdb=" O ASN b 167 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE b 169 " --> pdb=" O PHE b 135 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU b 137 " --> pdb=" O PHE b 169 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL b 171 " --> pdb=" O LEU b 137 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N HIS b 139 " --> pdb=" O VAL b 171 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR b 201 " --> pdb=" O PHE b 268 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N CYS b 203 " --> pdb=" O PRO b 270 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N PHE b 272 " --> pdb=" O CYS b 203 " (cutoff:3.500A) removed outlier: 13.814A pdb=" N ASP b 205 " --> pdb=" O PHE b 272 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE b 267 " --> pdb=" O SER b 381 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER b 381 " --> pdb=" O PHE b 267 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER b 374 " --> pdb=" O PHE b 319 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE b 319 " --> pdb=" O SER b 374 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR b 376 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA b 317 " --> pdb=" O THR b 376 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE b 378 " --> pdb=" O VAL b 315 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL b 315 " --> pdb=" O ILE b 378 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN b 380 " --> pdb=" O LEU b 313 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 53 through 56 790 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2878 1.31 - 1.44: 4623 1.44 - 1.56: 9618 1.56 - 1.69: 25 1.69 - 1.81: 183 Bond restraints: 17327 Sorted by residual: bond pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 1.524 1.300 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3' GTP a 501 " pdb=" C4' GTP a 501 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C4' GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sigma weight residual 1.410 1.619 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C4' GTP a 501 " pdb=" O4' GTP a 501 " ideal model delta sigma weight residual 1.410 1.618 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.533 -0.143 2.00e-02 2.50e+03 5.12e+01 ... (remaining 17322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 23135 2.45 - 4.90: 308 4.90 - 7.35: 33 7.35 - 9.80: 20 9.80 - 12.25: 5 Bond angle restraints: 23501 Sorted by residual: angle pdb=" OE1 GLN M 225 " pdb=" CD GLN M 225 " pdb=" NE2 GLN M 225 " ideal model delta sigma weight residual 122.60 118.05 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CA PHE M 236 " pdb=" CB PHE M 236 " pdb=" CG PHE M 236 " ideal model delta sigma weight residual 113.80 118.32 -4.52 1.00e+00 1.00e+00 2.05e+01 angle pdb=" OE1 GLN M 212 " pdb=" CD GLN M 212 " pdb=" NE2 GLN M 212 " ideal model delta sigma weight residual 122.60 118.34 4.26 1.00e+00 1.00e+00 1.82e+01 angle pdb=" N PHE M 236 " pdb=" CA PHE M 236 " pdb=" C PHE M 236 " ideal model delta sigma weight residual 113.01 107.98 5.03 1.20e+00 6.94e-01 1.76e+01 angle pdb=" C14 TA1 b 503 " pdb=" C11 TA1 b 503 " pdb=" O04 TA1 b 503 " ideal model delta sigma weight residual 119.42 107.17 12.25 3.00e+00 1.11e-01 1.67e+01 ... (remaining 23496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 10253 34.86 - 69.71: 226 69.71 - 104.57: 28 104.57 - 139.42: 8 139.42 - 174.28: 4 Dihedral angle restraints: 10519 sinusoidal: 4381 harmonic: 6138 Sorted by residual: dihedral pdb=" C8 GTP a 501 " pdb=" C1' GTP a 501 " pdb=" N9 GTP a 501 " pdb=" O4' GTP a 501 " ideal model delta sinusoidal sigma weight residual 104.59 -69.68 174.28 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -59.34 163.93 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual -68.92 73.07 -141.99 1 2.00e+01 2.50e-03 4.29e+01 ... (remaining 10516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2377 0.086 - 0.171: 182 0.171 - 0.257: 9 0.257 - 0.343: 0 0.343 - 0.429: 1 Chirality restraints: 2569 Sorted by residual: chirality pdb=" C18 TA1 b 503 " pdb=" C10 TA1 b 503 " pdb=" C17 TA1 b 503 " pdb=" C20 TA1 b 503 " both_signs ideal model delta sigma weight residual False -3.16 -2.73 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CA ILE M 263 " pdb=" N ILE M 263 " pdb=" C ILE M 263 " pdb=" CB ILE M 263 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA MET M 205 " pdb=" N MET M 205 " pdb=" C MET M 205 " pdb=" CB MET M 205 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2566 not shown) Planarity restraints: 3053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 b 503 " 0.039 2.00e-02 2.50e+03 3.22e-02 1.29e+01 pdb=" C30 TA1 b 503 " -0.005 2.00e-02 2.50e+03 pdb=" C31 TA1 b 503 " 0.028 2.00e-02 2.50e+03 pdb=" N01 TA1 b 503 " -0.052 2.00e-02 2.50e+03 pdb=" O14 TA1 b 503 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 262 " 0.263 9.50e-02 1.11e+02 1.18e-01 8.58e+00 pdb=" NE ARG M 262 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG M 262 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG M 262 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG M 262 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET M 205 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C MET M 205 " -0.043 2.00e-02 2.50e+03 pdb=" O MET M 205 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS M 206 " 0.015 2.00e-02 2.50e+03 ... (remaining 3050 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 118 2.56 - 3.15: 13598 3.15 - 3.73: 25894 3.73 - 4.32: 36541 4.32 - 4.90: 62587 Nonbonded interactions: 138738 Sorted by model distance: nonbonded pdb=" O2G GTP a 501 " pdb="MG MG a 502 " model vdw 1.977 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.992 2.170 nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 1.994 2.170 nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.002 2.170 nonbonded pdb=" O1B GTP a 501 " pdb="MG MG a 502 " model vdw 2.030 2.170 ... (remaining 138733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'a' and (resid 1 through 431 or (resid 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 436 or resid 501 through 503)) selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 0.224 17327 Z= 0.333 Angle : 0.723 12.251 23501 Z= 0.399 Chirality : 0.046 0.429 2569 Planarity : 0.005 0.118 3053 Dihedral : 15.801 174.277 6573 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.22 % Allowed : 7.64 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2108 helix: 0.48 (0.18), residues: 897 sheet: 0.47 (0.26), residues: 376 loop : -0.43 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 514 TYR 0.021 0.001 TYR M 217 PHE 0.015 0.001 PHE M 236 TRP 0.013 0.002 TRP b 346 HIS 0.003 0.001 HIS a 61 Details of bonding type rmsd covalent geometry : bond 0.00632 (17327) covalent geometry : angle 0.72305 (23501) hydrogen bonds : bond 0.17573 ( 773) hydrogen bonds : angle 6.68610 ( 2268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.660 Fit side-chains REVERT: A 377 MET cc_start: 0.8416 (ttm) cc_final: 0.7812 (ttp) REVERT: A 425 MET cc_start: 0.8620 (tpt) cc_final: 0.8309 (tpp) REVERT: B 1 MET cc_start: 0.9105 (ttm) cc_final: 0.8800 (ttt) REVERT: B 117 SER cc_start: 0.9216 (t) cc_final: 0.9014 (m) REVERT: B 259 MET cc_start: 0.9106 (tpp) cc_final: 0.7743 (mmt) REVERT: B 301 MET cc_start: 0.9198 (mmp) cc_final: 0.8973 (mmp) REVERT: B 325 MET cc_start: 0.8583 (mmm) cc_final: 0.7956 (mmm) REVERT: B 332 MET cc_start: 0.8745 (mmp) cc_final: 0.8372 (mmp) REVERT: M 236 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.6489 (t80) REVERT: M 550 GLN cc_start: 0.7901 (tp40) cc_final: 0.7661 (tp40) REVERT: M 578 TYR cc_start: 0.8363 (m-80) cc_final: 0.7999 (m-80) REVERT: a 154 MET cc_start: 0.8409 (mmt) cc_final: 0.8200 (mmm) REVERT: a 398 MET cc_start: 0.8467 (mtm) cc_final: 0.8058 (mtp) REVERT: b 75 MET cc_start: 0.7378 (mmp) cc_final: 0.6802 (mmt) outliers start: 4 outliers final: 0 residues processed: 135 average time/residue: 0.1400 time to fit residues: 28.5903 Evaluate side-chains 90 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 236 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN B 350 ASN M 189 ASN M 225 GLN M 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.093125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.074867 restraints weight = 31492.046| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.33 r_work: 0.3015 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17327 Z= 0.126 Angle : 0.539 8.097 23501 Z= 0.270 Chirality : 0.043 0.204 2569 Planarity : 0.004 0.043 3053 Dihedral : 10.710 157.413 2575 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.82 % Allowed : 8.35 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 2108 helix: 1.03 (0.17), residues: 902 sheet: 0.55 (0.27), residues: 367 loop : -0.35 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 322 TYR 0.015 0.001 TYR A 282 PHE 0.020 0.001 PHE M 236 TRP 0.018 0.002 TRP A 388 HIS 0.005 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00284 (17327) covalent geometry : angle 0.53882 (23501) hydrogen bonds : bond 0.04094 ( 773) hydrogen bonds : angle 4.49421 ( 2268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 193 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 166 MET cc_start: 0.9155 (tpt) cc_final: 0.8685 (tpt) REVERT: B 235 MET cc_start: 0.8815 (mtp) cc_final: 0.8560 (mtm) REVERT: B 325 MET cc_start: 0.9156 (mmm) cc_final: 0.8774 (mmm) REVERT: B 398 MET cc_start: 0.9099 (mtp) cc_final: 0.8787 (mtp) REVERT: a 117 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8357 (tt) REVERT: b 75 MET cc_start: 0.8777 (mmp) cc_final: 0.7970 (mmt) outliers start: 15 outliers final: 7 residues processed: 104 average time/residue: 0.1219 time to fit residues: 20.3487 Evaluate side-chains 92 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain M residue 373 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 193 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 259 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 72 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** M 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075286 restraints weight = 31929.524| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.21 r_work: 0.2977 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17327 Z= 0.127 Angle : 0.508 9.272 23501 Z= 0.252 Chirality : 0.043 0.204 2569 Planarity : 0.004 0.042 3053 Dihedral : 10.009 170.120 2573 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.43 % Allowed : 8.63 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2108 helix: 1.18 (0.17), residues: 918 sheet: 0.51 (0.27), residues: 368 loop : -0.46 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 322 TYR 0.015 0.001 TYR M 409 PHE 0.020 0.001 PHE M 236 TRP 0.014 0.001 TRP A 346 HIS 0.003 0.001 HIS a 61 Details of bonding type rmsd covalent geometry : bond 0.00291 (17327) covalent geometry : angle 0.50797 (23501) hydrogen bonds : bond 0.03918 ( 773) hydrogen bonds : angle 4.26523 ( 2268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 114 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 313 MET cc_start: 0.9298 (mtm) cc_final: 0.9058 (mtt) REVERT: A 332 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8550 (mt) REVERT: B 3 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8566 (mt-10) REVERT: B 166 MET cc_start: 0.9157 (tpt) cc_final: 0.8633 (tpt) REVERT: B 235 MET cc_start: 0.8822 (mtp) cc_final: 0.8547 (mtm) REVERT: B 325 MET cc_start: 0.9110 (mmm) cc_final: 0.8778 (mmm) REVERT: B 398 MET cc_start: 0.9119 (mtp) cc_final: 0.8821 (mtp) REVERT: M 424 ARG cc_start: 0.7293 (mmm-85) cc_final: 0.7022 (mmm-85) REVERT: a 398 MET cc_start: 0.9085 (mtp) cc_final: 0.8809 (mtp) REVERT: b 75 MET cc_start: 0.8872 (mmp) cc_final: 0.8198 (mmt) outliers start: 26 outliers final: 13 residues processed: 106 average time/residue: 0.1278 time to fit residues: 21.5155 Evaluate side-chains 98 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain M residue 322 THR Chi-restraints excluded: chain M residue 373 VAL Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 550 GLN Chi-restraints excluded: chain M residue 557 ILE Chi-restraints excluded: chain a residue 363 VAL Chi-restraints excluded: chain b residue 145 THR Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 12 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 159 optimal weight: 0.0050 chunk 114 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 0.0170 chunk 193 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 8 GLN a 101 ASN a 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.091018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.073791 restraints weight = 31952.652| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.16 r_work: 0.2980 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17327 Z= 0.146 Angle : 0.521 10.269 23501 Z= 0.256 Chirality : 0.044 0.205 2569 Planarity : 0.004 0.041 3053 Dihedral : 9.645 176.565 2573 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 8.63 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2108 helix: 1.13 (0.17), residues: 916 sheet: 0.50 (0.27), residues: 368 loop : -0.50 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 484 TYR 0.011 0.001 TYR A 103 PHE 0.015 0.001 PHE M 236 TRP 0.013 0.001 TRP A 346 HIS 0.004 0.001 HIS a 61 Details of bonding type rmsd covalent geometry : bond 0.00348 (17327) covalent geometry : angle 0.52071 (23501) hydrogen bonds : bond 0.03877 ( 773) hydrogen bonds : angle 4.25552 ( 2268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.741 Fit side-chains REVERT: A 114 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8504 (mt) REVERT: A 332 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8567 (mt) REVERT: B 3 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8724 (mt-10) REVERT: B 166 MET cc_start: 0.9155 (tpt) cc_final: 0.8638 (tpt) REVERT: B 193 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: B 259 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7589 (mpp) REVERT: B 325 MET cc_start: 0.9030 (mmm) cc_final: 0.8786 (mmm) REVERT: B 398 MET cc_start: 0.9199 (mtp) cc_final: 0.8891 (mtp) REVERT: M 260 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7216 (mm-30) REVERT: a 117 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8408 (tt) REVERT: a 398 MET cc_start: 0.9061 (mtp) cc_final: 0.8844 (mtm) REVERT: b 75 MET cc_start: 0.8834 (mmp) cc_final: 0.8197 (mmt) outliers start: 32 outliers final: 18 residues processed: 111 average time/residue: 0.1191 time to fit residues: 21.3320 Evaluate side-chains 103 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain M residue 322 THR Chi-restraints excluded: chain M residue 373 VAL Chi-restraints excluded: chain M residue 481 ILE Chi-restraints excluded: chain M residue 550 GLN Chi-restraints excluded: chain a residue 101 ASN Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 193 THR Chi-restraints excluded: chain a residue 363 VAL Chi-restraints excluded: chain b residue 145 THR Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 276 THR Chi-restraints excluded: chain b residue 287 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 130 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS B 8 GLN ** M 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074979 restraints weight = 31430.326| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.22 r_work: 0.3019 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17327 Z= 0.094 Angle : 0.476 9.633 23501 Z= 0.233 Chirality : 0.042 0.195 2569 Planarity : 0.003 0.040 3053 Dihedral : 9.220 179.657 2573 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.54 % Allowed : 9.51 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 2108 helix: 1.36 (0.17), residues: 903 sheet: 0.56 (0.28), residues: 368 loop : -0.40 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 322 TYR 0.008 0.001 TYR b 312 PHE 0.015 0.001 PHE M 236 TRP 0.012 0.001 TRP A 21 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00205 (17327) covalent geometry : angle 0.47592 (23501) hydrogen bonds : bond 0.03223 ( 773) hydrogen bonds : angle 4.07170 ( 2268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.613 Fit side-chains REVERT: A 114 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 332 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8543 (mt) REVERT: A 425 MET cc_start: 0.8711 (tpp) cc_final: 0.7877 (tpp) REVERT: B 3 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8659 (mt-10) REVERT: B 166 MET cc_start: 0.9134 (tpt) cc_final: 0.8569 (tpt) REVERT: B 193 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: B 235 MET cc_start: 0.8846 (mtp) cc_final: 0.8596 (mtm) REVERT: B 325 MET cc_start: 0.9004 (mmm) cc_final: 0.8702 (mmm) REVERT: B 398 MET cc_start: 0.9137 (mtp) cc_final: 0.8843 (mtp) REVERT: M 260 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7170 (mm-30) REVERT: a 117 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8354 (tt) REVERT: a 302 MET cc_start: 0.9160 (mtp) cc_final: 0.8879 (mtt) REVERT: a 398 MET cc_start: 0.9053 (mtp) cc_final: 0.8755 (mtm) REVERT: b 55 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: b 75 MET cc_start: 0.8801 (mmp) cc_final: 0.8209 (mmt) REVERT: b 113 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7807 (mt-10) outliers start: 28 outliers final: 16 residues processed: 109 average time/residue: 0.1154 time to fit residues: 20.6381 Evaluate side-chains 102 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain M residue 322 THR Chi-restraints excluded: chain M residue 373 VAL Chi-restraints excluded: chain M residue 550 GLN Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 193 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 145 THR Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 276 THR Chi-restraints excluded: chain b residue 287 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 186 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN ** M 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071786 restraints weight = 31917.739| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.24 r_work: 0.2955 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17327 Z= 0.175 Angle : 0.534 11.028 23501 Z= 0.264 Chirality : 0.044 0.206 2569 Planarity : 0.004 0.040 3053 Dihedral : 9.353 175.955 2573 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 9.78 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2108 helix: 1.16 (0.17), residues: 905 sheet: 0.39 (0.27), residues: 374 loop : -0.56 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 322 TYR 0.014 0.001 TYR A 103 PHE 0.018 0.002 PHE A 255 TRP 0.011 0.001 TRP A 346 HIS 0.004 0.001 HIS a 61 Details of bonding type rmsd covalent geometry : bond 0.00421 (17327) covalent geometry : angle 0.53446 (23501) hydrogen bonds : bond 0.04127 ( 773) hydrogen bonds : angle 4.26607 ( 2268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.653 Fit side-chains REVERT: A 114 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8584 (mt) REVERT: A 168 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: A 332 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8541 (mt) REVERT: A 425 MET cc_start: 0.8757 (tpp) cc_final: 0.8518 (tpp) REVERT: B 3 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8746 (mt-10) REVERT: B 166 MET cc_start: 0.9189 (tpt) cc_final: 0.8720 (tpt) REVERT: B 193 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: B 259 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7648 (mpp) REVERT: B 398 MET cc_start: 0.9201 (mtp) cc_final: 0.8896 (mtp) REVERT: M 537 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.8014 (t0) REVERT: a 117 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8378 (tt) REVERT: a 398 MET cc_start: 0.9109 (mtp) cc_final: 0.8866 (mtm) REVERT: b 55 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: b 75 MET cc_start: 0.8824 (mmp) cc_final: 0.8210 (mmt) outliers start: 35 outliers final: 21 residues processed: 112 average time/residue: 0.1166 time to fit residues: 21.5880 Evaluate side-chains 108 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain M residue 322 THR Chi-restraints excluded: chain M residue 373 VAL Chi-restraints excluded: chain M residue 525 LEU Chi-restraints excluded: chain M residue 537 ASN Chi-restraints excluded: chain M residue 550 GLN Chi-restraints excluded: chain a residue 68 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 193 THR Chi-restraints excluded: chain a residue 363 VAL Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 145 THR Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 276 THR Chi-restraints excluded: chain b residue 287 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 96 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 161 optimal weight: 0.3980 chunk 135 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.074342 restraints weight = 31449.218| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.23 r_work: 0.3048 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17327 Z= 0.100 Angle : 0.473 9.451 23501 Z= 0.232 Chirality : 0.042 0.192 2569 Planarity : 0.003 0.041 3053 Dihedral : 8.932 170.699 2573 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.70 % Allowed : 10.38 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 2108 helix: 1.32 (0.17), residues: 903 sheet: 0.51 (0.28), residues: 364 loop : -0.47 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 322 TYR 0.008 0.001 TYR b 312 PHE 0.013 0.001 PHE M 236 TRP 0.013 0.001 TRP A 21 HIS 0.002 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00227 (17327) covalent geometry : angle 0.47309 (23501) hydrogen bonds : bond 0.03240 ( 773) hydrogen bonds : angle 4.04475 ( 2268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.625 Fit side-chains REVERT: A 114 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8578 (mt) REVERT: A 332 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8572 (mt) REVERT: A 425 MET cc_start: 0.8656 (tpp) cc_final: 0.8456 (tpp) REVERT: B 3 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8689 (mt-10) REVERT: B 166 MET cc_start: 0.9147 (tpt) cc_final: 0.8589 (tpt) REVERT: B 193 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: B 235 MET cc_start: 0.8886 (mtp) cc_final: 0.8637 (mtm) REVERT: B 259 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7601 (mpp) REVERT: B 398 MET cc_start: 0.9182 (mtp) cc_final: 0.8906 (mtp) REVERT: M 537 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7937 (t0) REVERT: a 117 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8378 (tt) REVERT: a 133 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: a 302 MET cc_start: 0.9160 (mtp) cc_final: 0.8929 (mtt) REVERT: a 398 MET cc_start: 0.9080 (mtp) cc_final: 0.8861 (mtm) REVERT: b 55 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8436 (tt0) outliers start: 31 outliers final: 18 residues processed: 113 average time/residue: 0.1245 time to fit residues: 22.8240 Evaluate side-chains 106 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain M residue 322 THR Chi-restraints excluded: chain M residue 373 VAL Chi-restraints excluded: chain M residue 431 GLN Chi-restraints excluded: chain M residue 481 ILE Chi-restraints excluded: chain M residue 525 LEU Chi-restraints excluded: chain M residue 537 ASN Chi-restraints excluded: chain M residue 550 GLN Chi-restraints excluded: chain a residue 68 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 133 GLN Chi-restraints excluded: chain a residue 193 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 145 THR Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 276 THR Chi-restraints excluded: chain b residue 287 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 67 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN ** M 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.074882 restraints weight = 31741.905| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.22 r_work: 0.3006 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17327 Z= 0.095 Angle : 0.470 9.211 23501 Z= 0.229 Chirality : 0.042 0.197 2569 Planarity : 0.003 0.042 3053 Dihedral : 8.645 164.593 2573 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.65 % Allowed : 10.38 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 2108 helix: 1.46 (0.18), residues: 898 sheet: 0.35 (0.27), residues: 382 loop : -0.43 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 322 TYR 0.008 0.001 TYR b 312 PHE 0.018 0.001 PHE M 236 TRP 0.012 0.001 TRP A 21 HIS 0.002 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00215 (17327) covalent geometry : angle 0.47041 (23501) hydrogen bonds : bond 0.03152 ( 773) hydrogen bonds : angle 3.97327 ( 2268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.675 Fit side-chains REVERT: A 114 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8573 (mt) REVERT: A 332 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8513 (mt) REVERT: A 425 MET cc_start: 0.8698 (tpp) cc_final: 0.7829 (tpp) REVERT: B 3 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: B 166 MET cc_start: 0.9139 (tpt) cc_final: 0.8604 (tpt) REVERT: B 193 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: B 235 MET cc_start: 0.8876 (mtp) cc_final: 0.8620 (mtm) REVERT: B 259 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7678 (mpp) REVERT: B 398 MET cc_start: 0.9159 (mtp) cc_final: 0.8878 (mtp) REVERT: M 537 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7862 (t0) REVERT: a 117 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8363 (tt) REVERT: a 133 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: a 302 MET cc_start: 0.9151 (mtp) cc_final: 0.8930 (mtt) REVERT: a 398 MET cc_start: 0.9062 (mtp) cc_final: 0.8840 (mtm) REVERT: b 55 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: b 373 MET cc_start: 0.7831 (mtp) cc_final: 0.7570 (mmt) outliers start: 30 outliers final: 16 residues processed: 108 average time/residue: 0.1192 time to fit residues: 21.1515 Evaluate side-chains 102 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain M residue 322 THR Chi-restraints excluded: chain M residue 373 VAL Chi-restraints excluded: chain M residue 481 ILE Chi-restraints excluded: chain M residue 525 LEU Chi-restraints excluded: chain M residue 537 ASN Chi-restraints excluded: chain a residue 68 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 133 GLN Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 145 THR Chi-restraints excluded: chain b residue 276 THR Chi-restraints excluded: chain b residue 287 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 180 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 159 optimal weight: 0.0070 chunk 182 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN ** M 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072431 restraints weight = 31620.478| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.24 r_work: 0.2968 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17327 Z= 0.153 Angle : 0.518 10.897 23501 Z= 0.254 Chirality : 0.043 0.204 2569 Planarity : 0.004 0.041 3053 Dihedral : 8.782 162.141 2573 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.70 % Allowed : 10.22 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2108 helix: 1.32 (0.18), residues: 892 sheet: 0.43 (0.27), residues: 364 loop : -0.53 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 215 TYR 0.012 0.001 TYR A 103 PHE 0.019 0.001 PHE M 236 TRP 0.011 0.001 TRP A 346 HIS 0.003 0.001 HIS a 61 Details of bonding type rmsd covalent geometry : bond 0.00365 (17327) covalent geometry : angle 0.51792 (23501) hydrogen bonds : bond 0.03856 ( 773) hydrogen bonds : angle 4.16509 ( 2268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.643 Fit side-chains REVERT: A 114 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 168 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7865 (pt0) REVERT: A 332 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8546 (mt) REVERT: A 425 MET cc_start: 0.8746 (tpp) cc_final: 0.8512 (tpp) REVERT: B 3 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8729 (mt-10) REVERT: B 166 MET cc_start: 0.9183 (tpt) cc_final: 0.8705 (tpt) REVERT: B 193 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: B 259 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.7750 (mpp) REVERT: B 398 MET cc_start: 0.9160 (mtp) cc_final: 0.8874 (mtp) REVERT: M 537 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7903 (t0) REVERT: a 117 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8415 (tt) REVERT: a 133 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: a 302 MET cc_start: 0.9210 (mtp) cc_final: 0.8964 (mtt) REVERT: b 55 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: b 373 MET cc_start: 0.8211 (mtp) cc_final: 0.7962 (mmt) outliers start: 31 outliers final: 17 residues processed: 105 average time/residue: 0.1153 time to fit residues: 20.1984 Evaluate side-chains 105 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain M residue 322 THR Chi-restraints excluded: chain M residue 373 VAL Chi-restraints excluded: chain M residue 481 ILE Chi-restraints excluded: chain M residue 525 LEU Chi-restraints excluded: chain M residue 537 ASN Chi-restraints excluded: chain a residue 68 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 133 GLN Chi-restraints excluded: chain a residue 193 THR Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 145 THR Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 276 THR Chi-restraints excluded: chain b residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 144 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.074166 restraints weight = 31489.266| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.21 r_work: 0.2991 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17327 Z= 0.104 Angle : 0.482 9.886 23501 Z= 0.235 Chirality : 0.042 0.195 2569 Planarity : 0.003 0.042 3053 Dihedral : 8.468 156.126 2573 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.70 % Allowed : 10.27 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2108 helix: 1.37 (0.17), residues: 906 sheet: 0.45 (0.28), residues: 362 loop : -0.46 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 322 TYR 0.009 0.001 TYR b 312 PHE 0.019 0.001 PHE M 236 TRP 0.012 0.001 TRP A 21 HIS 0.002 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00239 (17327) covalent geometry : angle 0.48151 (23501) hydrogen bonds : bond 0.03322 ( 773) hydrogen bonds : angle 4.03392 ( 2268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.642 Fit side-chains REVERT: A 114 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8578 (mt) REVERT: A 168 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: A 332 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8528 (mt) REVERT: A 425 MET cc_start: 0.8697 (tpp) cc_final: 0.7840 (tpp) REVERT: B 3 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8725 (mt-10) REVERT: B 166 MET cc_start: 0.9154 (tpt) cc_final: 0.8609 (tpt) REVERT: B 259 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7687 (mpp) REVERT: B 398 MET cc_start: 0.9156 (mtp) cc_final: 0.8848 (mtp) REVERT: M 537 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7882 (t0) REVERT: a 62 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8905 (m) REVERT: a 117 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8372 (tt) REVERT: a 133 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: a 302 MET cc_start: 0.9182 (mtp) cc_final: 0.8945 (mtt) REVERT: b 1 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7881 (ptp) REVERT: b 55 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: b 235 MET cc_start: 0.8272 (mmm) cc_final: 0.7774 (mtp) outliers start: 31 outliers final: 17 residues processed: 105 average time/residue: 0.1198 time to fit residues: 20.5987 Evaluate side-chains 107 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain M residue 322 THR Chi-restraints excluded: chain M residue 481 ILE Chi-restraints excluded: chain M residue 525 LEU Chi-restraints excluded: chain M residue 537 ASN Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 68 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 133 GLN Chi-restraints excluded: chain a residue 193 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 145 THR Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 276 THR Chi-restraints excluded: chain b residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 202 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 141 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.074628 restraints weight = 31436.936| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.22 r_work: 0.3002 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17327 Z= 0.100 Angle : 0.477 9.299 23501 Z= 0.232 Chirality : 0.042 0.196 2569 Planarity : 0.003 0.042 3053 Dihedral : 8.093 145.539 2573 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.48 % Allowed : 10.77 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 2108 helix: 1.44 (0.17), residues: 906 sheet: 0.47 (0.28), residues: 362 loop : -0.43 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 322 TYR 0.009 0.001 TYR b 312 PHE 0.018 0.001 PHE M 236 TRP 0.012 0.001 TRP A 21 HIS 0.002 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00229 (17327) covalent geometry : angle 0.47710 (23501) hydrogen bonds : bond 0.03200 ( 773) hydrogen bonds : angle 3.98981 ( 2268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3501.89 seconds wall clock time: 61 minutes 1.64 seconds (3661.64 seconds total)