Starting phenix.real_space_refine on Sun May 3 00:28:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zv6_60509/05_2026/8zv6_60509.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zv6_60509/05_2026/8zv6_60509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zv6_60509/05_2026/8zv6_60509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zv6_60509/05_2026/8zv6_60509.map" model { file = "/net/cci-nas-00/data/ceres_data/8zv6_60509/05_2026/8zv6_60509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zv6_60509/05_2026/8zv6_60509.cif" } resolution = 2.9 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= 0.001 sd= 0.015 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 6 5.49 5 Mg 1 5.21 5 S 53 5.16 5 C 5759 2.51 5 N 1604 2.21 5 O 1753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9176 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5190 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 24, 'TRANS': 648} Chain: "B" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1910 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "F" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1973 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {' MG': 1, 'ATP': 1, 'BCT': 1, 'BTN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'1VU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.52, per 1000 atoms: 0.27 Number of scatterers: 9176 At special positions: 0 Unit cell: (97.44, 99.12, 136.92, 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 53 16.00 P 6 15.00 Mg 1 11.99 O 1753 8.00 N 1604 7.00 C 5759 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 314.9 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 40.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 95 through 99 removed outlier: 4.477A pdb=" N SER A 99 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.327A pdb=" N ASP A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.989A pdb=" N GLU A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 252 Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 357 through 366 removed outlier: 4.480A pdb=" N THR A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'B' and resid 299 through 305 removed outlier: 4.186A pdb=" N THR B 304 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 305 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.942A pdb=" N ILE B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 328 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 384 removed outlier: 3.595A pdb=" N ARG B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.633A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 4.324A pdb=" N TYR B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.506A pdb=" N LEU B 447 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 478 through 490 removed outlier: 4.106A pdb=" N ALA B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 510 through 522 removed outlier: 3.783A pdb=" N CYS B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'F' and resid 33 through 48 removed outlier: 4.328A pdb=" N GLU F 37 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 61 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 134 through 152 Processing helix chain 'F' and resid 169 through 187 removed outlier: 3.938A pdb=" N LEU F 173 " --> pdb=" O GLY F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 211 removed outlier: 3.577A pdb=" N ALA F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 263 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.495A pdb=" N THR A 89 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL A 110 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA A 91 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 92 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 139 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 351 removed outlier: 6.783A pdb=" N PHE A 347 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 338 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 349 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N HIS A 269 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU A 289 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU A 271 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU A 287 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 283 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 291 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL A 300 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN A 293 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS A 298 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA5, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 565 removed outlier: 6.315A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 696 through 700 removed outlier: 6.152A pdb=" N ASN A 697 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 689 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET A 699 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ILE A 687 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL A 673 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 716 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 681 removed outlier: 3.589A pdb=" N VAL A 681 " --> pdb=" O GLY A 705 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.585A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.585A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 451 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 82 removed outlier: 4.401A pdb=" N THR F 109 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE F 156 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR F 120 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU F 158 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE F 122 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ASP F 160 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLN F 124 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET F 197 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN F 159 " --> pdb=" O MET F 197 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA F 201 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR F 222 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY F 198 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N PHE F 224 " --> pdb=" O GLY F 198 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS F 200 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 80 through 82 removed outlier: 4.401A pdb=" N THR F 109 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE F 156 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR F 120 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU F 158 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE F 122 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ASP F 160 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLN F 124 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET F 197 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN F 159 " --> pdb=" O MET F 197 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA F 201 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY F 198 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG F 259 " --> pdb=" O THR F 214 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1559 1.28 - 1.42: 2266 1.42 - 1.56: 5414 1.56 - 1.70: 20 1.70 - 1.84: 85 Bond restraints: 9344 Sorted by residual: bond pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sigma weight residual 2.250 1.643 0.607 2.00e-02 2.50e+03 9.21e+02 bond pdb=" C2 BTN A 801 " pdb=" S1 BTN A 801 " ideal model delta sigma weight residual 1.824 1.437 0.387 2.00e-02 2.50e+03 3.74e+02 bond pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " ideal model delta sigma weight residual 1.682 1.467 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C16 1VU F5601 " pdb=" C22 1VU F5601 " ideal model delta sigma weight residual 1.560 1.360 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C3 BTN A 801 " pdb=" N2 BTN A 801 " ideal model delta sigma weight residual 1.362 1.556 -0.194 2.00e-02 2.50e+03 9.38e+01 ... (remaining 9339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.19: 12641 11.19 - 22.38: 7 22.38 - 33.58: 3 33.58 - 44.77: 0 44.77 - 55.96: 1 Bond angle restraints: 12652 Sorted by residual: angle pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " pdb=" O15 1VU F5601 " ideal model delta sigma weight residual 53.72 109.68 -55.96 3.00e+00 1.11e-01 3.48e+02 angle pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 78.74 109.67 -30.93 3.00e+00 1.11e-01 1.06e+02 angle pdb=" O8 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 140.21 109.70 30.51 3.00e+00 1.11e-01 1.03e+02 angle pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O7 1VU F5601 " ideal model delta sigma weight residual 85.76 108.78 -23.02 3.00e+00 1.11e-01 5.89e+01 angle pdb=" P 1VU F5601 " pdb=" O7 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sigma weight residual 143.93 123.61 20.32 3.00e+00 1.11e-01 4.59e+01 ... (remaining 12647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 5623 35.89 - 71.78: 85 71.78 - 107.66: 6 107.66 - 143.55: 0 143.55 - 179.44: 5 Dihedral angle restraints: 5719 sinusoidal: 2335 harmonic: 3384 Sorted by residual: dihedral pdb=" C 1VU F5601 " pdb=" C1 1VU F5601 " pdb=" C2 1VU F5601 " pdb=" O 1VU F5601 " ideal model delta sinusoidal sigma weight residual -123.88 55.56 -179.44 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C 1VU F5601 " pdb=" C1 1VU F5601 " pdb=" C2 1VU F5601 " pdb=" S 1VU F5601 " ideal model delta sinusoidal sigma weight residual 57.40 -124.26 -178.34 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C15 1VU F5601 " pdb=" C23 1VU F5601 " pdb=" O13 1VU F5601 " pdb=" P2 1VU F5601 " ideal model delta sinusoidal sigma weight residual 86.09 -82.29 168.38 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 5716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1401 0.116 - 0.233: 26 0.233 - 0.349: 0 0.349 - 0.465: 0 0.465 - 0.582: 1 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C22 1VU F5601 " pdb=" C16 1VU F5601 " pdb=" C23 1VU F5601 " pdb=" O12 1VU F5601 " both_signs ideal model delta sigma weight residual False -2.99 -2.41 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" C16 1VU F5601 " pdb=" C22 1VU F5601 " pdb=" N2 1VU F5601 " pdb=" O11 1VU F5601 " both_signs ideal model delta sigma weight residual False 2.69 2.46 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE B 537 " pdb=" CA ILE B 537 " pdb=" CG1 ILE B 537 " pdb=" CG2 ILE B 537 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 1425 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 537 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO B 538 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 538 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 538 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 207 " 0.149 9.50e-02 1.11e+02 6.71e-02 3.53e+00 pdb=" NE ARG A 207 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 207 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 207 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 207 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 664 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 665 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 665 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 665 " -0.026 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 89 2.59 - 3.17: 7877 3.17 - 3.75: 14106 3.75 - 4.32: 19889 4.32 - 4.90: 32969 Nonbonded interactions: 74930 Sorted by model distance: nonbonded pdb=" O1A ATP A 802 " pdb="MG MG A 803 " model vdw 2.013 2.170 nonbonded pdb=" O3B ATP A 802 " pdb="MG MG A 803 " model vdw 2.030 2.170 nonbonded pdb=" O2G ATP A 802 " pdb="MG MG A 803 " model vdw 2.149 2.170 nonbonded pdb=" OE1 GLU A 349 " pdb="MG MG A 803 " model vdw 2.153 2.170 nonbonded pdb=" OE1 GLU A 203 " pdb=" NH1 ARG A 207 " model vdw 2.165 3.120 ... (remaining 74925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.220 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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 : 0.011 0.607 9345 Z= 0.547 Angle : 0.999 55.960 12652 Z= 0.412 Chirality : 0.048 0.582 1428 Planarity : 0.004 0.067 1640 Dihedral : 14.531 179.438 3543 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1175 helix: 0.46 (0.26), residues: 418 sheet: 0.55 (0.34), residues: 219 loop : -0.85 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 207 TYR 0.018 0.001 TYR A 473 PHE 0.018 0.001 PHE A 307 TRP 0.010 0.001 TRP A 233 HIS 0.007 0.001 HIS B 446 Details of bonding type rmsd covalent geometry : bond 0.01069 ( 9344) covalent geometry : angle 0.99943 (12652) hydrogen bonds : bond 0.14497 ( 424) hydrogen bonds : angle 6.16118 ( 1251) Misc. bond : bond 0.13001 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: F 100 ASN cc_start: 0.8611 (m110) cc_final: 0.8351 (m110) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.7650 time to fit residues: 98.9797 Evaluate side-chains 88 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 169 HIS A 190 ASN A 344 ASN ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN B 452 ASN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN F 192 GLN F 241 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.133091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.081770 restraints weight = 15738.739| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.45 r_work: 0.2848 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9345 Z= 0.267 Angle : 0.661 9.410 12652 Z= 0.340 Chirality : 0.049 0.188 1428 Planarity : 0.005 0.060 1640 Dihedral : 13.631 174.532 1394 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.82 % Allowed : 10.32 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1175 helix: 0.59 (0.25), residues: 428 sheet: 0.57 (0.34), residues: 217 loop : -0.94 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 239 TYR 0.024 0.002 TYR A 473 PHE 0.023 0.002 PHE F 122 TRP 0.012 0.002 TRP A 233 HIS 0.005 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 9344) covalent geometry : angle 0.66081 (12652) hydrogen bonds : bond 0.05306 ( 424) hydrogen bonds : angle 4.93164 ( 1251) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.7028 (tmm) cc_final: 0.6728 (tmm) REVERT: A 448 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8269 (ttt) REVERT: A 466 MET cc_start: 0.8762 (tpt) cc_final: 0.8331 (tpp) REVERT: B 485 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8915 (tm-30) REVERT: F 100 ASN cc_start: 0.8795 (m110) cc_final: 0.8570 (m110) REVERT: F 290 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7450 (pp20) outliers start: 8 outliers final: 0 residues processed: 94 average time/residue: 0.7217 time to fit residues: 72.0348 Evaluate side-chains 86 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 45 optimal weight: 0.0570 chunk 91 optimal weight: 8.9990 chunk 114 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.085129 restraints weight = 15761.296| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.48 r_work: 0.2913 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9345 Z= 0.115 Angle : 0.566 10.744 12652 Z= 0.288 Chirality : 0.045 0.202 1428 Planarity : 0.004 0.064 1640 Dihedral : 13.391 173.388 1394 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.53 % Allowed : 11.44 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1175 helix: 0.82 (0.25), residues: 422 sheet: 0.12 (0.33), residues: 245 loop : -0.70 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 230 TYR 0.016 0.001 TYR A 473 PHE 0.011 0.001 PHE A 347 TRP 0.012 0.001 TRP A 233 HIS 0.006 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9344) covalent geometry : angle 0.56589 (12652) hydrogen bonds : bond 0.03783 ( 424) hydrogen bonds : angle 4.54859 ( 1251) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.7040 (tmm) cc_final: 0.6756 (tmm) REVERT: B 485 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8702 (tm-30) REVERT: F 38 ARG cc_start: 0.2990 (OUTLIER) cc_final: 0.0389 (ttt180) REVERT: F 100 ASN cc_start: 0.8750 (m110) cc_final: 0.8542 (m110) REVERT: F 237 GLU cc_start: 0.8739 (tt0) cc_final: 0.8127 (pt0) outliers start: 15 outliers final: 2 residues processed: 99 average time/residue: 0.6665 time to fit residues: 70.3243 Evaluate side-chains 83 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain F residue 38 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 108 optimal weight: 0.0470 chunk 45 optimal weight: 0.0170 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.0270 chunk 89 optimal weight: 2.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** B 492 ASN ** 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 = 0.3878 r_free = 0.3878 target = 0.135907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084997 restraints weight = 15830.825| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.47 r_work: 0.2919 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9345 Z= 0.123 Angle : 0.563 10.794 12652 Z= 0.285 Chirality : 0.045 0.165 1428 Planarity : 0.004 0.064 1640 Dihedral : 13.089 169.318 1394 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.53 % Allowed : 13.18 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1175 helix: 0.97 (0.25), residues: 422 sheet: 0.32 (0.33), residues: 235 loop : -0.74 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.015 0.001 TYR A 473 PHE 0.013 0.001 PHE F 122 TRP 0.012 0.001 TRP A 233 HIS 0.006 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9344) covalent geometry : angle 0.56306 (12652) hydrogen bonds : bond 0.03740 ( 424) hydrogen bonds : angle 4.43057 ( 1251) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 212 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8912 (pp) REVERT: A 217 MET cc_start: 0.7075 (tmm) cc_final: 0.6807 (tmm) REVERT: B 485 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8729 (tm-30) REVERT: F 38 ARG cc_start: 0.2911 (OUTLIER) cc_final: 0.0316 (ttt180) REVERT: F 95 MET cc_start: 0.9005 (tpp) cc_final: 0.8195 (mmm) REVERT: F 100 ASN cc_start: 0.8738 (m110) cc_final: 0.8511 (m110) REVERT: F 237 GLU cc_start: 0.8720 (tt0) cc_final: 0.8147 (pt0) REVERT: F 290 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7018 (pp20) outliers start: 15 outliers final: 2 residues processed: 96 average time/residue: 0.6224 time to fit residues: 63.7998 Evaluate side-chains 87 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** 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 = 0.3824 r_free = 0.3824 target = 0.131768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.079912 restraints weight = 15800.712| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.45 r_work: 0.2816 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 9345 Z= 0.353 Angle : 0.680 11.411 12652 Z= 0.353 Chirality : 0.051 0.178 1428 Planarity : 0.005 0.058 1640 Dihedral : 13.062 164.184 1394 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 13.28 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1175 helix: 0.58 (0.25), residues: 428 sheet: 0.46 (0.34), residues: 219 loop : -0.99 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 113 TYR 0.035 0.002 TYR A 473 PHE 0.028 0.002 PHE F 122 TRP 0.014 0.002 TRP A 233 HIS 0.011 0.002 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00849 ( 9344) covalent geometry : angle 0.68020 (12652) hydrogen bonds : bond 0.05663 ( 424) hydrogen bonds : angle 4.75848 ( 1251) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8941 (pp) REVERT: A 217 MET cc_start: 0.7114 (tmm) cc_final: 0.6578 (tmm) REVERT: B 328 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8476 (tp30) REVERT: B 485 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8794 (tm-30) REVERT: F 38 ARG cc_start: 0.2936 (OUTLIER) cc_final: 0.0300 (ttt180) REVERT: F 100 ASN cc_start: 0.8781 (m110) cc_final: 0.8556 (m110) REVERT: F 237 GLU cc_start: 0.8805 (tt0) cc_final: 0.8157 (pt0) REVERT: F 290 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7097 (pp20) outliers start: 20 outliers final: 8 residues processed: 95 average time/residue: 0.6359 time to fit residues: 64.5590 Evaluate side-chains 92 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 25 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 115 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** 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 = 0.3870 r_free = 0.3870 target = 0.135512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084402 restraints weight = 15732.478| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.48 r_work: 0.2912 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9345 Z= 0.110 Angle : 0.580 14.073 12652 Z= 0.295 Chirality : 0.045 0.176 1428 Planarity : 0.004 0.066 1640 Dihedral : 12.524 168.181 1394 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.33 % Allowed : 15.12 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1175 helix: 0.88 (0.25), residues: 424 sheet: 0.24 (0.33), residues: 235 loop : -0.74 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.014 0.001 TYR A 473 PHE 0.009 0.001 PHE F 122 TRP 0.014 0.001 TRP A 233 HIS 0.006 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9344) covalent geometry : angle 0.58025 (12652) hydrogen bonds : bond 0.03646 ( 424) hydrogen bonds : angle 4.45882 ( 1251) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8890 (pp) REVERT: A 217 MET cc_start: 0.7095 (tmm) cc_final: 0.6553 (tmm) REVERT: A 316 MET cc_start: 0.8549 (mmm) cc_final: 0.8218 (mmm) REVERT: A 693 MET cc_start: 0.6766 (ppp) cc_final: 0.6160 (ptm) REVERT: B 485 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8809 (tm-30) REVERT: F 38 ARG cc_start: 0.3025 (tmt170) cc_final: 0.2815 (tmt170) REVERT: F 95 MET cc_start: 0.9008 (tpp) cc_final: 0.8564 (mmm) REVERT: F 237 GLU cc_start: 0.8753 (tt0) cc_final: 0.8149 (pt0) REVERT: F 290 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6924 (pp20) outliers start: 13 outliers final: 4 residues processed: 94 average time/residue: 0.6116 time to fit residues: 61.6707 Evaluate side-chains 97 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.084128 restraints weight = 15844.808| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.48 r_work: 0.2885 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9345 Z= 0.139 Angle : 0.572 11.985 12652 Z= 0.292 Chirality : 0.045 0.168 1428 Planarity : 0.004 0.065 1640 Dihedral : 12.205 173.735 1394 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.74 % Allowed : 15.73 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.07 (0.25), residues: 1175 helix: 0.94 (0.25), residues: 422 sheet: 0.26 (0.33), residues: 235 loop : -0.74 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 230 TYR 0.014 0.001 TYR A 473 PHE 0.015 0.001 PHE F 122 TRP 0.014 0.001 TRP A 233 HIS 0.006 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9344) covalent geometry : angle 0.57189 (12652) hydrogen bonds : bond 0.03914 ( 424) hydrogen bonds : angle 4.41329 ( 1251) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8607 (mpp) REVERT: A 156 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8855 (mp) REVERT: A 212 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8893 (pp) REVERT: A 699 MET cc_start: 0.6560 (ttt) cc_final: 0.6286 (ttp) REVERT: B 485 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8829 (tm-30) REVERT: F 237 GLU cc_start: 0.8754 (tt0) cc_final: 0.8144 (pt0) REVERT: F 290 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6920 (pp20) outliers start: 17 outliers final: 5 residues processed: 94 average time/residue: 0.5953 time to fit residues: 60.1235 Evaluate side-chains 91 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.079878 restraints weight = 15775.244| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.50 r_work: 0.2835 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 9345 Z= 0.317 Angle : 0.681 16.022 12652 Z= 0.349 Chirality : 0.050 0.171 1428 Planarity : 0.005 0.062 1640 Dihedral : 11.940 175.035 1394 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.74 % Allowed : 15.93 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1175 helix: 0.57 (0.25), residues: 429 sheet: 0.49 (0.34), residues: 219 loop : -0.95 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 113 TYR 0.029 0.002 TYR A 473 PHE 0.028 0.002 PHE F 122 TRP 0.014 0.002 TRP A 233 HIS 0.009 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00760 ( 9344) covalent geometry : angle 0.68109 (12652) hydrogen bonds : bond 0.05368 ( 424) hydrogen bonds : angle 4.68072 ( 1251) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8551 (mpp) REVERT: A 212 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8921 (pp) REVERT: A 693 MET cc_start: 0.6805 (ppp) cc_final: 0.6346 (ptm) REVERT: B 328 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8506 (tp30) REVERT: B 463 MET cc_start: 0.8043 (ptm) cc_final: 0.7533 (pp-130) REVERT: B 485 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8813 (tm-30) REVERT: F 237 GLU cc_start: 0.8794 (tt0) cc_final: 0.8143 (pt0) REVERT: F 290 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6945 (pp20) outliers start: 17 outliers final: 7 residues processed: 97 average time/residue: 0.6328 time to fit residues: 65.5642 Evaluate side-chains 95 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 64 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 85 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 266 ASN ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084667 restraints weight = 15557.898| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.45 r_work: 0.2912 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9345 Z= 0.114 Angle : 0.619 16.289 12652 Z= 0.306 Chirality : 0.046 0.179 1428 Planarity : 0.004 0.066 1640 Dihedral : 11.124 171.173 1394 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.43 % Allowed : 16.96 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1175 helix: 0.90 (0.26), residues: 421 sheet: 0.31 (0.33), residues: 235 loop : -0.78 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 239 TYR 0.013 0.001 TYR A 473 PHE 0.008 0.001 PHE A 533 TRP 0.016 0.001 TRP A 233 HIS 0.007 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9344) covalent geometry : angle 0.61946 (12652) hydrogen bonds : bond 0.03614 ( 424) hydrogen bonds : angle 4.41786 ( 1251) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8896 (pp) REVERT: A 217 MET cc_start: 0.7033 (tmm) cc_final: 0.6787 (tmm) REVERT: A 693 MET cc_start: 0.6974 (ppp) cc_final: 0.6225 (ptm) REVERT: B 485 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8821 (tm-30) REVERT: F 237 GLU cc_start: 0.8765 (tt0) cc_final: 0.8143 (pt0) REVERT: F 290 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6869 (pp20) outliers start: 14 outliers final: 6 residues processed: 104 average time/residue: 0.6084 time to fit residues: 67.6650 Evaluate side-chains 92 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 62 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082972 restraints weight = 15695.905| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.44 r_work: 0.2886 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9345 Z= 0.167 Angle : 0.651 14.125 12652 Z= 0.327 Chirality : 0.047 0.184 1428 Planarity : 0.004 0.066 1640 Dihedral : 10.806 168.205 1394 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.02 % Allowed : 18.08 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1175 helix: 0.81 (0.25), residues: 422 sheet: 0.58 (0.35), residues: 211 loop : -0.80 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.016 0.001 TYR B 486 PHE 0.044 0.001 PHE A 152 TRP 0.016 0.001 TRP A 233 HIS 0.007 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9344) covalent geometry : angle 0.65136 (12652) hydrogen bonds : bond 0.04184 ( 424) hydrogen bonds : angle 4.42510 ( 1251) Misc. bond : bond 0.00014 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8780 (pp) REVERT: A 217 MET cc_start: 0.7016 (tmm) cc_final: 0.6681 (tmm) REVERT: A 693 MET cc_start: 0.7016 (ppp) cc_final: 0.6329 (ptm) REVERT: B 463 MET cc_start: 0.7944 (pp-130) cc_final: 0.7339 (pp-130) REVERT: B 485 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8824 (tm-30) REVERT: F 237 GLU cc_start: 0.8685 (tt0) cc_final: 0.8121 (pt0) REVERT: F 290 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6864 (pp20) outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 0.6329 time to fit residues: 67.0108 Evaluate side-chains 90 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 113 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 116 optimal weight: 0.3980 overall best weight: 2.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 169 HIS ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.081369 restraints weight = 15461.923| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.45 r_work: 0.2855 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9345 Z= 0.258 Angle : 0.699 14.025 12652 Z= 0.356 Chirality : 0.049 0.186 1428 Planarity : 0.005 0.064 1640 Dihedral : 10.654 164.180 1394 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.23 % Allowed : 18.08 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1175 helix: 0.64 (0.25), residues: 426 sheet: 0.53 (0.34), residues: 211 loop : -0.89 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 53 TYR 0.023 0.002 TYR A 473 PHE 0.036 0.002 PHE A 152 TRP 0.019 0.002 TRP A 233 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 9344) covalent geometry : angle 0.69949 (12652) hydrogen bonds : bond 0.04964 ( 424) hydrogen bonds : angle 4.58663 ( 1251) Misc. bond : bond 0.00012 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.55 seconds wall clock time: 69 minutes 47.56 seconds (4187.56 seconds total)