Starting phenix.real_space_refine on Thu Mar 13 14:56:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p27_17358/03_2025/8p27_17358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p27_17358/03_2025/8p27_17358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p27_17358/03_2025/8p27_17358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p27_17358/03_2025/8p27_17358.map" model { file = "/net/cci-nas-00/data/ceres_data/8p27_17358/03_2025/8p27_17358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p27_17358/03_2025/8p27_17358.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.014 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 2 5.21 5 S 54 5.16 5 C 5564 2.51 5 N 1517 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8810 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4372 Classifications: {'peptide': 544} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 523} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4376 Classifications: {'peptide': 545} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.96, per 1000 atoms: 0.79 Number of scatterers: 8810 At special positions: 0 Unit cell: (101.509, 104.112, 96.3036, 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 54 16.00 P 6 15.00 Mg 2 11.99 O 1667 8.00 N 1517 7.00 C 5564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2032 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 6 sheets defined 50.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 121 through 142 removed outlier: 3.714A pdb=" N MET A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.768A pdb=" N ALA A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 175 through 182 removed outlier: 4.140A pdb=" N ILE A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 223 through 247 Proline residue: A 230 - end of helix removed outlier: 3.763A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 322 through 334 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.945A pdb=" N GLN A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 339' Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.833A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.703A pdb=" N GLU A 410 " --> pdb=" O TYR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 4.123A pdb=" N LEU A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 486 removed outlier: 3.698A pdb=" N ARG A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 516 through 520 removed outlier: 4.030A pdb=" N HIS A 519 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 removed outlier: 3.515A pdb=" N CYS A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.608A pdb=" N LEU A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 570 removed outlier: 3.772A pdb=" N THR A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 596 removed outlier: 3.726A pdb=" N LYS A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 629 removed outlier: 3.724A pdb=" N LYS A 624 " --> pdb=" O THR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.384A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.560A pdb=" N TYR A 666 " --> pdb=" O MET A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 142 removed outlier: 3.671A pdb=" N PHE B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix removed outlier: 3.528A pdb=" N ASP B 140 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.789A pdb=" N MET B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.553A pdb=" N TYR B 163 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.698A pdb=" N HIS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 212 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 223 through 229 removed outlier: 3.634A pdb=" N LEU B 228 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 241 removed outlier: 3.810A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 299 removed outlier: 3.833A pdb=" N LEU B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.572A pdb=" N ILE B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.660A pdb=" N GLN B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 339' Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.515A pdb=" N ALA B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.702A pdb=" N GLU B 410 " --> pdb=" O TYR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 4.097A pdb=" N LEU B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 486 removed outlier: 3.669A pdb=" N ARG B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.639A pdb=" N PHE B 493 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.892A pdb=" N HIS B 519 " --> pdb=" O VAL B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 534 removed outlier: 3.523A pdb=" N CYS B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 570 removed outlier: 3.567A pdb=" N LEU B 552 " --> pdb=" O GLN B 548 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N MET B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 593 removed outlier: 3.597A pdb=" N LYS B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 629 removed outlier: 3.812A pdb=" N ILE B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 4.329A pdb=" N LEU B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 removed outlier: 4.289A pdb=" N VAL B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 666 " --> pdb=" O MET B 662 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158 removed outlier: 5.152A pdb=" N ASN A 435 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N GLY A 523 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 437 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLY A 525 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER A 439 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 526 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 removed outlier: 3.658A pdb=" N CYS A 171 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 172 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN A 219 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN A 316 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 221 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER A 313 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ILE A 352 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A 315 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LYS A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR A 317 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLN A 351 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU A 387 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP A 353 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158 removed outlier: 7.896A pdb=" N GLY B 523 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE B 438 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.663A pdb=" N CYS B 171 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 172 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 316 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER B 313 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE B 352 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 315 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS B 354 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR B 317 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN B 351 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU B 387 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP B 353 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL B 643 " --> pdb=" O ASN B 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 186 315 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2901 1.34 - 1.46: 1587 1.46 - 1.57: 4420 1.57 - 1.69: 10 1.69 - 1.81: 90 Bond restraints: 9008 Sorted by residual: bond pdb=" CA SER B 304 " pdb=" C SER B 304 " ideal model delta sigma weight residual 1.528 1.516 0.011 1.37e-02 5.33e+03 6.93e-01 bond pdb=" C4' DTP B 801 " pdb=" O4' DTP B 801 " ideal model delta sigma weight residual 1.444 1.436 0.008 1.10e-02 8.26e+03 5.41e-01 bond pdb=" CB GLU A 277 " pdb=" CG GLU A 277 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.84e-01 bond pdb=" CG PRO B 175 " pdb=" CD PRO B 175 " ideal model delta sigma weight residual 1.503 1.480 0.023 3.40e-02 8.65e+02 4.72e-01 bond pdb=" CA LYS A 135 " pdb=" C LYS A 135 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 4.36e-01 ... (remaining 9003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 11889 1.43 - 2.86: 230 2.86 - 4.28: 39 4.28 - 5.71: 20 5.71 - 7.14: 1 Bond angle restraints: 12179 Sorted by residual: angle pdb=" N GLU A 514 " pdb=" CA GLU A 514 " pdb=" C GLU A 514 " ideal model delta sigma weight residual 114.75 110.29 4.46 1.26e+00 6.30e-01 1.25e+01 angle pdb=" N ALA A 535 " pdb=" CA ALA A 535 " pdb=" C ALA A 535 " ideal model delta sigma weight residual 114.16 110.17 3.99 1.48e+00 4.57e-01 7.26e+00 angle pdb=" CA GLU A 514 " pdb=" C GLU A 514 " pdb=" N SER A 515 " ideal model delta sigma weight residual 119.80 116.34 3.46 1.34e+00 5.57e-01 6.67e+00 angle pdb=" C ALA A 391 " pdb=" N THR A 392 " pdb=" CA THR A 392 " ideal model delta sigma weight residual 121.54 125.85 -4.31 1.91e+00 2.74e-01 5.10e+00 angle pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " pdb=" CG TYR A 231 " ideal model delta sigma weight residual 113.90 109.85 4.05 1.80e+00 3.09e-01 5.07e+00 ... (remaining 12174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 4922 15.53 - 31.07: 358 31.07 - 46.60: 101 46.60 - 62.14: 33 62.14 - 77.67: 5 Dihedral angle restraints: 5419 sinusoidal: 2250 harmonic: 3169 Sorted by residual: dihedral pdb=" CA VAL A 534 " pdb=" C VAL A 534 " pdb=" N ALA A 535 " pdb=" CA ALA A 535 " ideal model delta harmonic sigma weight residual 180.00 152.85 27.15 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ASP B 390 " pdb=" C ASP B 390 " pdb=" N ALA B 391 " pdb=" CA ALA B 391 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA VAL B 534 " pdb=" C VAL B 534 " pdb=" N ALA B 535 " pdb=" CA ALA B 535 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 5416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 704 0.030 - 0.061: 392 0.061 - 0.091: 133 0.091 - 0.122: 59 0.122 - 0.152: 12 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ILE A 524 " pdb=" N ILE A 524 " pdb=" C ILE A 524 " pdb=" CB ILE A 524 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA VAL A 613 " pdb=" N VAL A 613 " pdb=" C VAL A 613 " pdb=" CB VAL A 613 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1297 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 495 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C LEU A 495 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU A 495 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 496 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 192 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 193 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 362 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 363 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 363 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 363 " 0.019 5.00e-02 4.00e+02 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 44 2.53 - 3.12: 6427 3.12 - 3.71: 12905 3.71 - 4.31: 18190 4.31 - 4.90: 31234 Nonbonded interactions: 68800 Sorted by model distance: nonbonded pdb=" O3B DTP A 801 " pdb="MG MG B 802 " model vdw 1.936 2.170 nonbonded pdb="MG MG A 802 " pdb=" O2B DTP B 801 " model vdw 1.985 2.170 nonbonded pdb="MG MG A 802 " pdb=" O3B DTP B 801 " model vdw 1.985 2.170 nonbonded pdb=" O2B DTP A 801 " pdb="MG MG B 802 " model vdw 2.135 2.170 nonbonded pdb=" O2A DTP A 801 " pdb="MG MG B 802 " model vdw 2.156 2.170 ... (remaining 68795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 120 through 304 or resid 311 through 675 or resid 801 thro \ ugh 802)) } 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: 12.670 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.120 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.060 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:15.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.004 0.031 9008 Z= 0.237 Angle : 0.551 7.141 12179 Z= 0.298 Chirality : 0.045 0.152 1300 Planarity : 0.004 0.035 1573 Dihedral : 12.492 77.670 3387 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.43 % Allowed : 6.70 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.25), residues: 1077 helix: -0.91 (0.23), residues: 504 sheet: 1.09 (0.51), residues: 108 loop : -2.50 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.005 0.001 HIS A 279 PHE 0.015 0.002 PHE A 224 TYR 0.017 0.002 TYR A 231 ARG 0.002 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 293 GLU cc_start: 0.7909 (tt0) cc_final: 0.7629 (tt0) REVERT: A 330 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7342 (ttp-110) REVERT: A 451 MET cc_start: 0.7642 (mtm) cc_final: 0.7387 (mtp) REVERT: A 540 HIS cc_start: 0.7885 (p-80) cc_final: 0.7437 (p90) REVERT: A 564 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: B 249 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.5327 (mp0) REVERT: B 277 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6110 (mm-30) REVERT: B 278 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5919 (tm-30) REVERT: B 424 ARG cc_start: 0.7491 (mtt90) cc_final: 0.7206 (mtt-85) REVERT: B 478 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6776 (mt) REVERT: B 534 VAL cc_start: 0.8319 (t) cc_final: 0.8109 (p) REVERT: B 545 GLU cc_start: 0.6883 (tp30) cc_final: 0.6506 (tp30) REVERT: B 560 ASP cc_start: 0.7821 (m-30) cc_final: 0.7604 (m-30) outliers start: 51 outliers final: 25 residues processed: 276 average time/residue: 1.1114 time to fit residues: 329.9504 Evaluate side-chains 236 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.0030 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 367 ASN A 609 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 367 ASN B 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.139956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131039 restraints weight = 12023.466| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.62 r_work: 0.3692 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9008 Z= 0.249 Angle : 0.599 6.601 12179 Z= 0.325 Chirality : 0.047 0.140 1300 Planarity : 0.005 0.048 1573 Dihedral : 9.908 70.395 1308 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 5.85 % Allowed : 13.40 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 1077 helix: -0.48 (0.23), residues: 506 sheet: 1.33 (0.49), residues: 107 loop : -2.56 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 399 HIS 0.008 0.001 HIS A 279 PHE 0.018 0.002 PHE A 184 TYR 0.020 0.002 TYR A 231 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.7440 (mt) cc_final: 0.7136 (mt) REVERT: A 283 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8114 (mtpp) REVERT: A 330 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7660 (ttp-110) REVERT: A 451 MET cc_start: 0.7768 (mtm) cc_final: 0.7491 (mtp) REVERT: B 120 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7011 (m-30) REVERT: B 169 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7752 (mt) REVERT: B 277 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5918 (mm-30) REVERT: B 278 GLN cc_start: 0.6207 (OUTLIER) cc_final: 0.5713 (tp-100) REVERT: B 424 ARG cc_start: 0.7735 (mtt90) cc_final: 0.7446 (mtt-85) REVERT: B 478 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6924 (mt) REVERT: B 489 MET cc_start: 0.7857 (mmt) cc_final: 0.7201 (mmt) REVERT: B 560 ASP cc_start: 0.7756 (m-30) cc_final: 0.7445 (m-30) REVERT: B 657 GLU cc_start: 0.7532 (tt0) cc_final: 0.7331 (mt-10) outliers start: 55 outliers final: 22 residues processed: 245 average time/residue: 1.0964 time to fit residues: 287.8963 Evaluate side-chains 228 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 385 ASN A 395 GLN A 609 ASN A 652 ASN B 297 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.137081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.128573 restraints weight = 11956.075| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.51 r_work: 0.3680 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9008 Z= 0.386 Angle : 0.680 9.826 12179 Z= 0.365 Chirality : 0.050 0.146 1300 Planarity : 0.005 0.051 1573 Dihedral : 9.609 74.703 1290 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 7.66 % Allowed : 15.11 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.24), residues: 1077 helix: -0.42 (0.23), residues: 500 sheet: 1.38 (0.53), residues: 90 loop : -2.65 (0.24), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 399 HIS 0.010 0.001 HIS A 279 PHE 0.019 0.002 PHE A 184 TYR 0.019 0.002 TYR A 231 ARG 0.003 0.001 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 198 time to evaluate : 1.021 Fit side-chains REVERT: A 126 MET cc_start: 0.8288 (mmm) cc_final: 0.7830 (mmt) REVERT: A 142 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7172 (mt) REVERT: A 241 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6856 (mtmm) REVERT: A 278 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: A 283 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8253 (mtpp) REVERT: A 431 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7898 (mm) REVERT: A 451 MET cc_start: 0.7945 (mtm) cc_final: 0.7686 (mtp) REVERT: A 505 GLU cc_start: 0.7209 (pp20) cc_final: 0.6777 (pp20) REVERT: B 241 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7222 (mmtm) REVERT: B 277 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6205 (mm-30) REVERT: B 278 GLN cc_start: 0.6270 (OUTLIER) cc_final: 0.5876 (tp-100) REVERT: B 424 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7493 (mtt-85) REVERT: B 560 ASP cc_start: 0.7820 (m-30) cc_final: 0.7359 (m-30) REVERT: B 564 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: B 657 GLU cc_start: 0.7609 (tt0) cc_final: 0.7407 (mt-10) outliers start: 72 outliers final: 33 residues processed: 241 average time/residue: 1.1120 time to fit residues: 286.7489 Evaluate side-chains 235 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 609 ASN A 652 ASN B 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129858 restraints weight = 11926.466| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.56 r_work: 0.3703 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9008 Z= 0.276 Angle : 0.612 9.716 12179 Z= 0.329 Chirality : 0.047 0.142 1300 Planarity : 0.005 0.052 1573 Dihedral : 9.368 75.447 1286 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 6.38 % Allowed : 18.40 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.25), residues: 1077 helix: -0.32 (0.23), residues: 506 sheet: 1.37 (0.54), residues: 91 loop : -2.59 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 399 HIS 0.008 0.001 HIS A 279 PHE 0.018 0.002 PHE A 184 TYR 0.018 0.002 TYR A 231 ARG 0.007 0.001 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 126 MET cc_start: 0.8255 (mmm) cc_final: 0.7898 (mmt) REVERT: A 142 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7169 (mt) REVERT: A 283 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8225 (mtpp) REVERT: A 451 MET cc_start: 0.7834 (mtm) cc_final: 0.7601 (mtp) REVERT: A 505 GLU cc_start: 0.7163 (pp20) cc_final: 0.6746 (pp20) REVERT: B 244 GLU cc_start: 0.4964 (OUTLIER) cc_final: 0.4656 (pp20) REVERT: B 277 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6357 (mm-30) REVERT: B 278 GLN cc_start: 0.6362 (OUTLIER) cc_final: 0.4958 (tm-30) REVERT: B 424 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7486 (mtt-85) REVERT: B 560 ASP cc_start: 0.7853 (m-30) cc_final: 0.7086 (m-30) REVERT: B 564 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7423 (mp0) outliers start: 60 outliers final: 36 residues processed: 236 average time/residue: 1.1508 time to fit residues: 290.2029 Evaluate side-chains 234 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 609 ASN A 652 ASN B 188 HIS B 626 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.137474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.128890 restraints weight = 11927.470| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.54 r_work: 0.3688 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9008 Z= 0.303 Angle : 0.618 6.685 12179 Z= 0.333 Chirality : 0.048 0.141 1300 Planarity : 0.005 0.052 1573 Dihedral : 9.431 77.303 1286 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 6.81 % Allowed : 18.94 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.25), residues: 1077 helix: -0.24 (0.24), residues: 502 sheet: 1.31 (0.54), residues: 91 loop : -2.59 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 399 HIS 0.008 0.001 HIS A 279 PHE 0.019 0.002 PHE A 184 TYR 0.019 0.002 TYR A 231 ARG 0.005 0.001 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7154 (mt) REVERT: A 283 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8255 (mtpp) REVERT: A 342 ASN cc_start: 0.7638 (t0) cc_final: 0.7346 (t0) REVERT: A 451 MET cc_start: 0.7888 (mtm) cc_final: 0.7684 (mtp) REVERT: A 505 GLU cc_start: 0.7264 (pp20) cc_final: 0.6854 (pp20) REVERT: B 249 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.4114 (mp0) REVERT: B 254 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7240 (mt) REVERT: B 277 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5662 (mp0) REVERT: B 278 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.4818 (tm-30) REVERT: B 564 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7486 (mp0) outliers start: 64 outliers final: 39 residues processed: 239 average time/residue: 1.1106 time to fit residues: 283.7841 Evaluate side-chains 239 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 0.0040 chunk 49 optimal weight: 0.7980 chunk 83 optimal weight: 0.0030 chunk 93 optimal weight: 0.3980 chunk 43 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 105 optimal weight: 0.0870 overall best weight: 0.1178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 395 GLN ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 188 HIS B 626 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.142712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134131 restraints weight = 12053.571| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.56 r_work: 0.3760 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9008 Z= 0.142 Angle : 0.521 8.146 12179 Z= 0.278 Chirality : 0.043 0.136 1300 Planarity : 0.004 0.050 1573 Dihedral : 8.794 73.097 1286 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 5.43 % Allowed : 20.32 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.25), residues: 1077 helix: 0.09 (0.24), residues: 512 sheet: 1.70 (0.48), residues: 107 loop : -2.65 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 399 HIS 0.004 0.001 HIS B 188 PHE 0.019 0.001 PHE A 184 TYR 0.014 0.001 TYR A 231 ARG 0.006 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7015 (mt) REVERT: A 219 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7949 (mm-40) REVERT: A 241 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6861 (mtmm) REVERT: A 268 ASP cc_start: 0.7304 (t70) cc_final: 0.7091 (t0) REVERT: A 283 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8188 (mtpp) REVERT: A 451 MET cc_start: 0.7691 (mtm) cc_final: 0.7483 (mtp) REVERT: A 505 GLU cc_start: 0.7076 (pp20) cc_final: 0.6689 (pp20) REVERT: B 244 GLU cc_start: 0.4804 (OUTLIER) cc_final: 0.4433 (pp20) REVERT: B 254 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7224 (mt) REVERT: B 277 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5674 (mp0) REVERT: B 478 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6925 (mt) REVERT: B 564 GLU cc_start: 0.7769 (mp0) cc_final: 0.7541 (mp0) outliers start: 51 outliers final: 22 residues processed: 234 average time/residue: 1.4622 time to fit residues: 366.0771 Evaluate side-chains 223 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 0.0370 chunk 33 optimal weight: 0.1980 chunk 101 optimal weight: 0.0170 chunk 98 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 395 GLN A 609 ASN A 639 HIS A 652 ASN B 213 ASN B 278 GLN B 351 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.141668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.133036 restraints weight = 12227.647| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.58 r_work: 0.3744 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9008 Z= 0.167 Angle : 0.529 6.361 12179 Z= 0.284 Chirality : 0.044 0.170 1300 Planarity : 0.004 0.048 1573 Dihedral : 8.031 73.629 1273 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.64 % Allowed : 21.91 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1077 helix: 0.26 (0.24), residues: 510 sheet: 1.70 (0.53), residues: 88 loop : -2.46 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.004 0.001 HIS A 279 PHE 0.019 0.001 PHE A 184 TYR 0.016 0.001 TYR A 164 ARG 0.004 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7011 (mt) REVERT: A 268 ASP cc_start: 0.7272 (t70) cc_final: 0.7060 (t0) REVERT: A 283 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8201 (mtpp) REVERT: A 342 ASN cc_start: 0.7552 (t0) cc_final: 0.7226 (t0) REVERT: A 451 MET cc_start: 0.7717 (mtm) cc_final: 0.7468 (mtp) REVERT: A 505 GLU cc_start: 0.7102 (pp20) cc_final: 0.6738 (pp20) REVERT: B 152 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.6686 (pmm) REVERT: B 244 GLU cc_start: 0.4828 (OUTLIER) cc_final: 0.4469 (pp20) REVERT: B 254 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7222 (mt) REVERT: B 277 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5748 (mp0) REVERT: B 329 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6366 (mmm) REVERT: B 564 GLU cc_start: 0.7762 (mp0) cc_final: 0.7429 (mp0) REVERT: B 576 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8269 (tp) outliers start: 53 outliers final: 28 residues processed: 230 average time/residue: 1.2148 time to fit residues: 299.2797 Evaluate side-chains 230 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 0.6980 chunk 98 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 388 ASN A 609 ASN A 639 HIS A 652 ASN B 278 GLN B 334 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.140081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131466 restraints weight = 12198.822| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.57 r_work: 0.3720 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9008 Z= 0.246 Angle : 0.571 6.526 12179 Z= 0.308 Chirality : 0.046 0.160 1300 Planarity : 0.004 0.047 1573 Dihedral : 8.165 74.504 1273 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 5.96 % Allowed : 22.55 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1077 helix: 0.17 (0.24), residues: 514 sheet: 1.66 (0.53), residues: 88 loop : -2.44 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 399 HIS 0.006 0.001 HIS A 279 PHE 0.019 0.002 PHE A 184 TYR 0.018 0.001 TYR A 231 ARG 0.004 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7085 (mt) REVERT: A 219 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7994 (mm-40) REVERT: A 268 ASP cc_start: 0.7253 (t70) cc_final: 0.7039 (t0) REVERT: A 278 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6227 (tm-30) REVERT: A 283 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8221 (mtpp) REVERT: A 342 ASN cc_start: 0.7593 (t0) cc_final: 0.7264 (t0) REVERT: A 451 MET cc_start: 0.7786 (mtm) cc_final: 0.7535 (mtp) REVERT: A 505 GLU cc_start: 0.7160 (pp20) cc_final: 0.6768 (pp20) REVERT: A 657 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7433 (mt-10) REVERT: B 152 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6701 (pmm) REVERT: B 169 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7659 (mp) REVERT: B 254 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7267 (mt) REVERT: B 277 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5771 (mp0) REVERT: B 329 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.6409 (mmm) REVERT: B 560 ASP cc_start: 0.7905 (m-30) cc_final: 0.7235 (m-30) REVERT: B 564 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: B 576 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8293 (tp) outliers start: 56 outliers final: 31 residues processed: 233 average time/residue: 1.1593 time to fit residues: 288.8830 Evaluate side-chains 241 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 609 ASN A 652 ASN B 278 GLN B 626 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.138217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.129563 restraints weight = 12090.623| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.56 r_work: 0.3693 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9008 Z= 0.333 Angle : 0.635 6.973 12179 Z= 0.342 Chirality : 0.049 0.197 1300 Planarity : 0.005 0.048 1573 Dihedral : 8.426 76.868 1273 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.96 % Allowed : 22.66 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.25), residues: 1077 helix: 0.02 (0.24), residues: 512 sheet: 1.69 (0.54), residues: 87 loop : -2.54 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 399 HIS 0.007 0.001 HIS A 639 PHE 0.017 0.002 PHE A 184 TYR 0.019 0.002 TYR A 231 ARG 0.006 0.001 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8053 (mm-40) REVERT: A 268 ASP cc_start: 0.7246 (t70) cc_final: 0.7033 (t0) REVERT: A 342 ASN cc_start: 0.7623 (t0) cc_final: 0.7295 (t0) REVERT: A 451 MET cc_start: 0.7834 (mtm) cc_final: 0.7581 (mtp) REVERT: A 505 GLU cc_start: 0.7269 (pp20) cc_final: 0.6844 (pp20) REVERT: A 657 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7453 (mt-10) REVERT: B 152 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6558 (pmm) REVERT: B 254 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7225 (mt) REVERT: B 277 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5812 (mp0) REVERT: B 329 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.6709 (mtm) REVERT: B 576 LEU cc_start: 0.8528 (tp) cc_final: 0.8322 (tp) outliers start: 56 outliers final: 34 residues processed: 233 average time/residue: 1.1980 time to fit residues: 298.3459 Evaluate side-chains 235 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.3980 chunk 106 optimal weight: 0.7980 chunk 73 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 609 ASN A 639 HIS A 652 ASN B 278 GLN B 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129810 restraints weight = 11996.757| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.57 r_work: 0.3699 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9008 Z= 0.318 Angle : 0.638 6.864 12179 Z= 0.343 Chirality : 0.049 0.220 1300 Planarity : 0.005 0.049 1573 Dihedral : 8.523 77.958 1273 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 5.21 % Allowed : 24.15 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.25), residues: 1077 helix: -0.07 (0.23), residues: 510 sheet: 1.56 (0.54), residues: 88 loop : -2.58 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 399 HIS 0.008 0.001 HIS A 279 PHE 0.015 0.002 PHE A 184 TYR 0.019 0.002 TYR A 231 ARG 0.006 0.001 ARG B 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.7477 (mt) cc_final: 0.7195 (mt) REVERT: A 219 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8086 (mm-40) REVERT: A 283 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8218 (mtpp) REVERT: A 342 ASN cc_start: 0.7654 (t0) cc_final: 0.7319 (t0) REVERT: A 451 MET cc_start: 0.7811 (mtm) cc_final: 0.7546 (mtp) REVERT: A 505 GLU cc_start: 0.7299 (pp20) cc_final: 0.6888 (pp20) REVERT: A 657 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7558 (mt-10) REVERT: B 152 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6521 (pmm) REVERT: B 249 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.4116 (mp0) REVERT: B 254 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7286 (mt) REVERT: B 277 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5586 (mp0) REVERT: B 329 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.6646 (mtm) outliers start: 49 outliers final: 34 residues processed: 228 average time/residue: 1.2001 time to fit residues: 293.0894 Evaluate side-chains 236 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 9 optimal weight: 0.0870 chunk 43 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 96 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 0.0270 chunk 44 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 609 ASN A 639 HIS A 652 ASN B 278 GLN B 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.140908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132197 restraints weight = 12083.516| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.56 r_work: 0.3730 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9008 Z= 0.178 Angle : 0.582 6.538 12179 Z= 0.313 Chirality : 0.045 0.195 1300 Planarity : 0.004 0.048 1573 Dihedral : 8.341 75.918 1273 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.36 % Allowed : 24.26 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.25), residues: 1077 helix: 0.10 (0.24), residues: 509 sheet: 1.55 (0.53), residues: 88 loop : -2.52 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 399 HIS 0.012 0.001 HIS A 639 PHE 0.015 0.001 PHE A 184 TYR 0.018 0.001 TYR A 231 ARG 0.004 0.000 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7622.51 seconds wall clock time: 133 minutes 33.53 seconds (8013.53 seconds total)