Starting phenix.real_space_refine on Sun May 3 00:27:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uhb_64161/05_2026/9uhb_64161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uhb_64161/05_2026/9uhb_64161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uhb_64161/05_2026/9uhb_64161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uhb_64161/05_2026/9uhb_64161.map" model { file = "/net/cci-nas-00/data/ceres_data/9uhb_64161/05_2026/9uhb_64161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uhb_64161/05_2026/9uhb_64161.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 5753 2.51 5 N 1605 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 9168 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: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1906 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {' MG': 1, 'ANP': 1, 'BTN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 2.03, per 1000 atoms: 0.22 Number of scatterers: 9168 At special positions: 0 Unit cell: (96.05, 99.45, 136.85, 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 1750 8.00 N 1605 7.00 C 5753 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: 0.72 Conformation dependent library (CDL) restraints added in 371.9 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: 48 helices and 11 sheets defined 39.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.629A pdb=" N ALA A 98 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A 99 " --> pdb=" O VAL A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 100 through 106 removed outlier: 3.540A pdb=" N LYS A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.714A pdb=" N ILE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.577A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 187 removed outlier: 3.717A pdb=" N LYS A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 removed outlier: 3.958A pdb=" N GLU A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 removed outlier: 4.080A pdb=" N ALA A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.787A pdb=" N THR A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.786A 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 385 through 389 removed outlier: 3.886A pdb=" N ILE A 389 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.768A pdb=" N ILE A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.584A pdb=" N ASP A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 641 through 647 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.915A pdb=" N THR B 304 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 324 removed outlier: 4.069A 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: 3.563A pdb=" N VAL B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 removed outlier: 4.062A pdb=" N GLU B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 421 removed outlier: 3.778A pdb=" N HIS B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.593A pdb=" N CYS B 448 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 481 through 490 Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.717A pdb=" N ARG B 499 " --> pdb=" O PRO B 495 " (cutoff:3.500A) 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 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 36 through 48 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.679A pdb=" N ASN F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) 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 186 removed outlier: 3.965A pdb=" N LEU F 173 " --> pdb=" O GLY F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 204 removed outlier: 3.606A pdb=" N ALA F 204 " --> pdb=" O ALA F 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 204' Processing helix chain 'F' and resid 205 through 210 removed outlier: 3.706A pdb=" N ALA F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.802A pdb=" N MET F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 276 removed outlier: 3.576A pdb=" N ALA F 267 " --> pdb=" O ASN F 263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111 removed outlier: 4.165A pdb=" N GLU A 108 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE A 66 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 92 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL A 68 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS A 65 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N HIS A 140 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 67 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 3.575A 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 removed outlier: 3.913A pdb=" N ALA A 232 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 216 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.963A pdb=" N GLU A 336 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N MET A 350 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 334 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N HIS A 269 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN A 273 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN A 286 " --> pdb=" O GLN A 273 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU A 275 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP A 284 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER A 291 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 300 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN A 293 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS A 298 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 14.300A pdb=" N GLN A 297 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 10.851A pdb=" N TYR A 401 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 450 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.690A pdb=" N GLY A 415 " --> pdb=" O ILE A 441 " (cutoff:3.500A) 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: 6.775A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 669 through 673 removed outlier: 7.317A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 331 removed outlier: 8.402A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 388 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL B 429 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR B 390 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR B 431 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL B 392 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS B 433 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU B 459 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG B 432 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA B 461 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 434 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 331 removed outlier: 8.402A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 388 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL B 429 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR B 390 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR B 431 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL B 392 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS B 433 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 451 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 454 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 80 through 82 removed outlier: 4.691A pdb=" N THR F 109 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ILE F 156 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR F 120 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU F 158 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE F 122 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE F 213 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F 217 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG F 259 " --> pdb=" O THR F 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 199 through 200 397 hydrogen bonds defined for protein. 1110 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: 1.65 Time building geometry restraints manager: 0.94 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: 2260 1.42 - 1.56: 5410 1.56 - 1.70: 19 1.70 - 1.84: 88 Bond restraints: 9336 Sorted by residual: bond pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sigma weight residual 2.250 1.645 0.605 2.00e-02 2.50e+03 9.15e+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=" C1' ANP A 802 " pdb=" C2' ANP A 802 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP A 802 " pdb=" O4' ANP A 802 " ideal model delta sigma weight residual 1.394 1.619 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " ideal model delta sigma weight residual 1.682 1.468 0.214 2.00e-02 2.50e+03 1.14e+02 ... (remaining 9331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.20: 12629 11.20 - 22.39: 9 22.39 - 33.59: 3 33.59 - 44.79: 0 44.79 - 55.99: 1 Bond angle restraints: 12642 Sorted by residual: angle pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " pdb=" O15 1VU F5601 " ideal model delta sigma weight residual 53.72 109.71 -55.99 3.00e+00 1.11e-01 3.48e+02 angle pdb=" O8 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 140.21 109.00 31.21 3.00e+00 1.11e-01 1.08e+02 angle pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 78.74 109.31 -30.57 3.00e+00 1.11e-01 1.04e+02 angle pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O7 1VU F5601 " ideal model delta sigma weight residual 85.76 109.59 -23.83 3.00e+00 1.11e-01 6.31e+01 angle pdb=" P 1VU F5601 " pdb=" O7 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sigma weight residual 143.93 123.99 19.94 3.00e+00 1.11e-01 4.42e+01 ... (remaining 12637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 5576 35.37 - 70.73: 120 70.73 - 106.10: 15 106.10 - 141.47: 0 141.47 - 176.83: 5 Dihedral angle restraints: 5716 sinusoidal: 2333 harmonic: 3383 Sorted by residual: dihedral pdb=" O6 1VU F5601 " pdb=" O7 1VU F5601 " pdb=" P 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sinusoidal sigma weight residual -98.95 77.88 -176.83 1 3.00e+01 1.11e-03 2.13e+01 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 49.85 -173.73 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 -129.97 -172.63 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1414 0.122 - 0.243: 12 0.243 - 0.365: 1 0.365 - 0.486: 0 0.486 - 0.608: 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 -2.38 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" C2' ANP A 802 " pdb=" C1' ANP A 802 " pdb=" C3' ANP A 802 " pdb=" O2' ANP A 802 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.79e+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 2.47 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1425 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 537 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 538 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 538 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 538 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 446 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO A 447 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 447 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 447 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 398 " -0.036 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO B 399 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 399 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 399 " -0.029 5.00e-02 4.00e+02 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 73 2.61 - 3.18: 7856 3.18 - 3.75: 13380 3.75 - 4.33: 18238 4.33 - 4.90: 31097 Nonbonded interactions: 70644 Sorted by model distance: nonbonded pdb=" N3B ANP A 802 " pdb="MG MG A 803 " model vdw 2.037 2.250 nonbonded pdb=" OE1 GLU A 349 " pdb="MG MG A 803 " model vdw 2.124 2.170 nonbonded pdb=" O2A ANP A 802 " pdb="MG MG A 803 " model vdw 2.197 2.170 nonbonded pdb=" OD1 ASP F 266 " pdb=" ND2 ASN F 270 " model vdw 2.241 3.120 nonbonded pdb=" O VAL F 217 " pdb=" OG SER F 221 " model vdw 2.266 3.040 ... (remaining 70639 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: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 0.605 9337 Z= 0.576 Angle : 1.038 55.986 12642 Z= 0.406 Chirality : 0.048 0.608 1428 Planarity : 0.004 0.061 1639 Dihedral : 15.743 176.833 3540 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.45 (0.26), residues: 1175 helix: 1.21 (0.27), residues: 407 sheet: 1.43 (0.36), residues: 222 loop : -0.91 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 207 TYR 0.008 0.001 TYR B 435 PHE 0.009 0.001 PHE B 490 TRP 0.010 0.001 TRP A 394 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.01128 ( 9336) covalent geometry : angle 1.03783 (12642) hydrogen bonds : bond 0.18787 ( 385) hydrogen bonds : angle 6.60722 ( 1110) Misc. bond : bond 0.12894 ( 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 138 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.348 Fit side-chains REVERT: A 195 PHE cc_start: 0.7966 (t80) cc_final: 0.7455 (t80) REVERT: A 271 GLU cc_start: 0.7147 (tp30) cc_final: 0.6617 (tp30) REVERT: A 336 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7503 (mp0) REVERT: B 451 THR cc_start: 0.8977 (p) cc_final: 0.8742 (p) REVERT: B 518 ASP cc_start: 0.7847 (m-30) cc_final: 0.7574 (m-30) REVERT: F 239 VAL cc_start: 0.9215 (p) cc_final: 0.8973 (p) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0984 time to fit residues: 19.0324 Evaluate side-chains 107 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN A 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.130604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.087948 restraints weight = 17276.235| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.69 r_work: 0.2924 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9337 Z= 0.198 Angle : 0.607 11.821 12642 Z= 0.311 Chirality : 0.047 0.179 1428 Planarity : 0.004 0.057 1639 Dihedral : 13.622 164.512 1391 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.51 % Allowed : 6.33 % Favored : 93.16 % 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: 0.28 (0.25), residues: 1175 helix: 0.88 (0.26), residues: 430 sheet: 1.10 (0.34), residues: 237 loop : -0.84 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 243 TYR 0.013 0.002 TYR A 473 PHE 0.015 0.001 PHE A 629 TRP 0.010 0.001 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9336) covalent geometry : angle 0.60665 (12642) hydrogen bonds : bond 0.04914 ( 385) hydrogen bonds : angle 4.84164 ( 1110) Misc. bond : bond 0.00018 ( 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 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.372 Fit side-chains REVERT: A 128 MET cc_start: 0.8863 (mmm) cc_final: 0.8621 (mmm) REVERT: A 195 PHE cc_start: 0.8025 (t80) cc_final: 0.7461 (t80) REVERT: A 271 GLU cc_start: 0.7886 (tp30) cc_final: 0.7146 (tp30) REVERT: A 336 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8037 (mp0) REVERT: B 451 THR cc_start: 0.8743 (p) cc_final: 0.8458 (p) REVERT: B 459 GLU cc_start: 0.8455 (pp20) cc_final: 0.8129 (pp20) REVERT: B 486 TYR cc_start: 0.7847 (t80) cc_final: 0.7326 (t80) REVERT: B 488 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8893 (pp20) REVERT: F 61 ARG cc_start: 0.8693 (mtm180) cc_final: 0.8473 (mtm180) REVERT: F 253 MET cc_start: 0.8388 (ppp) cc_final: 0.7533 (ppp) outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.1029 time to fit residues: 15.1861 Evaluate side-chains 96 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain F residue 72 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.084386 restraints weight = 17254.726| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.53 r_work: 0.2860 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 9337 Z= 0.283 Angle : 0.638 11.167 12642 Z= 0.333 Chirality : 0.048 0.153 1428 Planarity : 0.005 0.055 1639 Dihedral : 12.016 148.796 1391 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.63 % Allowed : 8.58 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1175 helix: 0.74 (0.26), residues: 428 sheet: 0.90 (0.34), residues: 228 loop : -1.08 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 243 TYR 0.034 0.002 TYR A 473 PHE 0.019 0.002 PHE A 629 TRP 0.011 0.001 TRP A 394 HIS 0.008 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00665 ( 9336) covalent geometry : angle 0.63779 (12642) hydrogen bonds : bond 0.05626 ( 385) hydrogen bonds : angle 4.75341 ( 1110) Misc. bond : bond 0.00043 ( 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 118 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8971 (mt) cc_final: 0.8656 (mt) REVERT: A 195 PHE cc_start: 0.8282 (t80) cc_final: 0.7715 (t80) REVERT: B 451 THR cc_start: 0.8853 (p) cc_final: 0.8624 (p) REVERT: B 488 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8962 (pp20) REVERT: F 196 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9123 (mp) REVERT: F 197 MET cc_start: 0.9297 (mtt) cc_final: 0.9062 (mtt) REVERT: F 242 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8321 (tm-30) REVERT: F 253 MET cc_start: 0.8684 (ppp) cc_final: 0.8167 (ppp) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 0.0962 time to fit residues: 15.5475 Evaluate side-chains 96 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 196 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 chunk 41 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 78 optimal weight: 0.0270 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088145 restraints weight = 17270.016| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.32 r_work: 0.2951 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9337 Z= 0.103 Angle : 0.516 10.915 12642 Z= 0.267 Chirality : 0.044 0.162 1428 Planarity : 0.004 0.054 1639 Dihedral : 10.665 137.615 1391 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.12 % Allowed : 10.42 % Favored : 88.46 % 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: 0.30 (0.25), residues: 1175 helix: 1.06 (0.26), residues: 426 sheet: 1.05 (0.34), residues: 231 loop : -0.93 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 135 TYR 0.016 0.001 TYR A 473 PHE 0.021 0.001 PHE B 490 TRP 0.006 0.001 TRP A 284 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9336) covalent geometry : angle 0.51581 (12642) hydrogen bonds : bond 0.03599 ( 385) hydrogen bonds : angle 4.31423 ( 1110) Misc. bond : bond 0.00004 ( 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 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.416 Fit side-chains REVERT: A 156 LEU cc_start: 0.8863 (mt) cc_final: 0.8537 (mt) REVERT: A 195 PHE cc_start: 0.8252 (t80) cc_final: 0.7654 (t80) REVERT: A 336 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7950 (mt-10) REVERT: A 699 MET cc_start: 0.8570 (ppp) cc_final: 0.7943 (ppp) REVERT: B 451 THR cc_start: 0.8752 (p) cc_final: 0.8486 (p) REVERT: B 459 GLU cc_start: 0.8377 (pp20) cc_final: 0.8057 (pp20) outliers start: 11 outliers final: 7 residues processed: 111 average time/residue: 0.0943 time to fit residues: 14.8260 Evaluate side-chains 97 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.086367 restraints weight = 17359.413| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.48 r_work: 0.2902 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9337 Z= 0.181 Angle : 0.552 10.720 12642 Z= 0.286 Chirality : 0.046 0.178 1428 Planarity : 0.004 0.057 1639 Dihedral : 10.063 131.488 1391 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.63 % Allowed : 11.64 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1175 helix: 1.04 (0.26), residues: 428 sheet: 1.19 (0.34), residues: 216 loop : -0.98 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 268 TYR 0.022 0.001 TYR A 473 PHE 0.016 0.001 PHE B 490 TRP 0.006 0.001 TRP B 531 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9336) covalent geometry : angle 0.55245 (12642) hydrogen bonds : bond 0.04453 ( 385) hydrogen bonds : angle 4.38206 ( 1110) Misc. bond : bond 0.00005 ( 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 113 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.346 Fit side-chains REVERT: A 156 LEU cc_start: 0.9010 (mt) cc_final: 0.8668 (mt) REVERT: A 195 PHE cc_start: 0.8297 (t80) cc_final: 0.7675 (t80) REVERT: A 217 MET cc_start: 0.8359 (tpp) cc_final: 0.8117 (tpp) REVERT: A 699 MET cc_start: 0.8543 (ppp) cc_final: 0.7956 (ppp) REVERT: B 451 THR cc_start: 0.8874 (p) cc_final: 0.8613 (p) REVERT: B 488 GLU cc_start: 0.9305 (tm-30) cc_final: 0.8920 (pp20) REVERT: F 197 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.9003 (mtt) REVERT: F 242 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8238 (tm-30) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.1013 time to fit residues: 15.5250 Evaluate side-chains 99 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 197 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 696 GLN A 697 ASN B 321 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.128090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.085771 restraints weight = 17257.472| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.44 r_work: 0.2885 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9337 Z= 0.197 Angle : 0.564 10.609 12642 Z= 0.293 Chirality : 0.046 0.170 1428 Planarity : 0.004 0.057 1639 Dihedral : 9.803 129.912 1391 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.33 % Allowed : 13.38 % 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: 0.15 (0.25), residues: 1175 helix: 1.01 (0.26), residues: 427 sheet: 0.93 (0.33), residues: 227 loop : -1.05 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 38 TYR 0.028 0.002 TYR A 473 PHE 0.013 0.001 PHE A 629 TRP 0.007 0.001 TRP A 394 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9336) covalent geometry : angle 0.56424 (12642) hydrogen bonds : bond 0.04513 ( 385) hydrogen bonds : angle 4.39789 ( 1110) Misc. bond : bond 0.00002 ( 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 102 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.385 Fit side-chains REVERT: A 156 LEU cc_start: 0.9061 (mt) cc_final: 0.8715 (mt) REVERT: A 195 PHE cc_start: 0.8335 (t80) cc_final: 0.7781 (t80) REVERT: A 217 MET cc_start: 0.8395 (tpp) cc_final: 0.8081 (tpp) REVERT: A 699 MET cc_start: 0.8506 (ppp) cc_final: 0.7951 (ppp) REVERT: B 451 THR cc_start: 0.8911 (p) cc_final: 0.8641 (p) REVERT: B 463 MET cc_start: 0.8178 (ppp) cc_final: 0.7860 (ppp) REVERT: B 488 GLU cc_start: 0.9333 (tm-30) cc_final: 0.8932 (pp20) REVERT: F 196 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9061 (mp) REVERT: F 197 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9052 (mtt) REVERT: F 242 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8246 (tm-30) REVERT: F 253 MET cc_start: 0.8437 (ppp) cc_final: 0.7793 (ppp) outliers start: 13 outliers final: 9 residues processed: 99 average time/residue: 0.0994 time to fit residues: 13.9921 Evaluate side-chains 104 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 197 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 66 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 64 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN A 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.128633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.086174 restraints weight = 17254.908| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.48 r_work: 0.2890 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9337 Z= 0.163 Angle : 0.534 10.346 12642 Z= 0.277 Chirality : 0.045 0.151 1428 Planarity : 0.004 0.056 1639 Dihedral : 9.530 129.558 1391 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.23 % Allowed : 13.99 % Favored : 84.78 % 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: 0.21 (0.25), residues: 1175 helix: 1.07 (0.26), residues: 428 sheet: 1.13 (0.34), residues: 213 loop : -1.07 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.019 0.001 TYR A 473 PHE 0.012 0.001 PHE B 490 TRP 0.006 0.001 TRP B 531 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9336) covalent geometry : angle 0.53390 (12642) hydrogen bonds : bond 0.04158 ( 385) hydrogen bonds : angle 4.26168 ( 1110) Misc. bond : bond 0.00001 ( 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 111 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.398 Fit side-chains REVERT: A 156 LEU cc_start: 0.9038 (mt) cc_final: 0.8794 (mt) REVERT: A 195 PHE cc_start: 0.8342 (t80) cc_final: 0.7778 (t80) REVERT: A 217 MET cc_start: 0.8360 (tpp) cc_final: 0.8038 (tpp) REVERT: A 699 MET cc_start: 0.8501 (ppp) cc_final: 0.7955 (ppp) REVERT: B 463 MET cc_start: 0.8184 (ppp) cc_final: 0.7832 (ppp) REVERT: B 488 GLU cc_start: 0.9326 (tm-30) cc_final: 0.8928 (pp20) REVERT: F 196 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9050 (mp) outliers start: 12 outliers final: 11 residues processed: 108 average time/residue: 0.1002 time to fit residues: 15.2439 Evaluate side-chains 98 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 696 GLN Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.126947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.085129 restraints weight = 17264.292| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.45 r_work: 0.2881 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9337 Z= 0.197 Angle : 0.562 10.257 12642 Z= 0.291 Chirality : 0.046 0.147 1428 Planarity : 0.004 0.056 1639 Dihedral : 9.465 129.268 1391 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.53 % Allowed : 14.91 % 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: 0.16 (0.25), residues: 1175 helix: 1.06 (0.26), residues: 428 sheet: 1.06 (0.34), residues: 213 loop : -1.10 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 154 TYR 0.022 0.002 TYR A 473 PHE 0.013 0.001 PHE B 490 TRP 0.006 0.001 TRP A 394 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 9336) covalent geometry : angle 0.56162 (12642) hydrogen bonds : bond 0.04441 ( 385) hydrogen bonds : angle 4.31211 ( 1110) Misc. bond : bond 0.00010 ( 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 102 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.367 Fit side-chains REVERT: A 156 LEU cc_start: 0.9066 (mt) cc_final: 0.8759 (mt) REVERT: A 195 PHE cc_start: 0.8390 (t80) cc_final: 0.7836 (t80) REVERT: A 217 MET cc_start: 0.8350 (tpp) cc_final: 0.8051 (tpp) REVERT: A 699 MET cc_start: 0.8516 (ppp) cc_final: 0.7938 (ppp) REVERT: B 463 MET cc_start: 0.8175 (ppp) cc_final: 0.7763 (ppp) REVERT: B 488 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8908 (pp20) REVERT: F 196 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9057 (mp) REVERT: F 197 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.9010 (mtt) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.0975 time to fit residues: 13.7268 Evaluate side-chains 100 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 696 GLN Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 82 optimal weight: 0.0030 chunk 85 optimal weight: 0.0470 chunk 7 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.3888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.130064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.087830 restraints weight = 17246.764| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.62 r_work: 0.2930 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9337 Z= 0.100 Angle : 0.520 10.001 12642 Z= 0.268 Chirality : 0.044 0.147 1428 Planarity : 0.004 0.056 1639 Dihedral : 9.282 128.870 1391 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.02 % Allowed : 15.32 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1175 helix: 1.29 (0.27), residues: 422 sheet: 1.17 (0.35), residues: 210 loop : -0.97 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 154 TYR 0.013 0.001 TYR A 473 PHE 0.012 0.001 PHE B 490 TRP 0.007 0.001 TRP A 284 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9336) covalent geometry : angle 0.52033 (12642) hydrogen bonds : bond 0.03401 ( 385) hydrogen bonds : angle 4.14654 ( 1110) Misc. bond : bond 0.00015 ( 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 108 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.454 Fit side-chains REVERT: A 124 MET cc_start: 0.8313 (mmt) cc_final: 0.8054 (mmt) REVERT: A 195 PHE cc_start: 0.8354 (t80) cc_final: 0.7807 (t80) REVERT: A 217 MET cc_start: 0.8250 (tpp) cc_final: 0.7951 (tpp) REVERT: A 336 GLU cc_start: 0.8603 (mp0) cc_final: 0.8216 (mp0) REVERT: A 696 GLN cc_start: 0.6823 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: B 488 GLU cc_start: 0.9325 (tm-30) cc_final: 0.8912 (pp20) REVERT: F 196 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9032 (mp) REVERT: F 197 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8959 (mtt) outliers start: 10 outliers final: 6 residues processed: 104 average time/residue: 0.1043 time to fit residues: 15.3388 Evaluate side-chains 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 696 GLN Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 197 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 64 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 76 optimal weight: 0.0570 chunk 91 optimal weight: 10.0000 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN F 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.129930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087410 restraints weight = 17270.281| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.76 r_work: 0.2919 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9337 Z= 0.109 Angle : 0.535 9.918 12642 Z= 0.274 Chirality : 0.045 0.174 1428 Planarity : 0.004 0.059 1639 Dihedral : 9.201 128.415 1391 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.12 % Allowed : 15.22 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1175 helix: 1.26 (0.27), residues: 428 sheet: 1.17 (0.35), residues: 212 loop : -0.97 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 243 TYR 0.012 0.001 TYR A 473 PHE 0.012 0.001 PHE B 490 TRP 0.006 0.001 TRP A 284 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9336) covalent geometry : angle 0.53544 (12642) hydrogen bonds : bond 0.03412 ( 385) hydrogen bonds : angle 4.11510 ( 1110) Misc. bond : bond 0.00004 ( 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 120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.354 Fit side-chains REVERT: A 124 MET cc_start: 0.8401 (mmt) cc_final: 0.8141 (mmt) REVERT: A 195 PHE cc_start: 0.8325 (t80) cc_final: 0.7778 (t80) REVERT: A 217 MET cc_start: 0.8251 (tpp) cc_final: 0.7935 (tpp) REVERT: A 336 GLU cc_start: 0.8613 (mp0) cc_final: 0.8240 (mp0) REVERT: B 459 GLU cc_start: 0.8362 (pp20) cc_final: 0.8097 (pp20) REVERT: B 488 GLU cc_start: 0.9325 (tm-30) cc_final: 0.8904 (pp20) REVERT: F 196 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9029 (mp) REVERT: F 197 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8946 (mtt) outliers start: 11 outliers final: 9 residues processed: 115 average time/residue: 0.0981 time to fit residues: 15.9144 Evaluate side-chains 118 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 696 GLN Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 197 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.0370 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.130401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.087764 restraints weight = 16970.170| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.60 r_work: 0.2930 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9337 Z= 0.106 Angle : 0.550 9.830 12642 Z= 0.280 Chirality : 0.045 0.202 1428 Planarity : 0.004 0.057 1639 Dihedral : 9.125 128.038 1391 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.43 % Allowed : 15.12 % Favored : 83.45 % 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: 0.45 (0.25), residues: 1175 helix: 1.32 (0.27), residues: 422 sheet: 1.21 (0.35), residues: 212 loop : -0.92 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 243 TYR 0.011 0.001 TYR A 473 PHE 0.011 0.001 PHE B 490 TRP 0.006 0.001 TRP A 284 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9336) covalent geometry : angle 0.54966 (12642) hydrogen bonds : bond 0.03285 ( 385) hydrogen bonds : angle 4.12970 ( 1110) Misc. bond : bond 0.00036 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.93 seconds wall clock time: 42 minutes 38.51 seconds (2558.51 seconds total)