Starting phenix.real_space_refine on Fri Sep 11 11:35:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ffc_4256/09_2026/6ffc_4256.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ffc_4256/09_2026/6ffc_4256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ffc_4256/09_2026/6ffc_4256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ffc_4256/09_2026/6ffc_4256.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ffc_4256/09_2026/6ffc_4256.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ffc_4256/09_2026/6ffc_4256.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ffc_4256/09_2026/6ffc_4256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ffc_4256/09_2026/6ffc_4256.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5836 2.51 5 N 1472 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8974 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4449 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 19, 'TRANS': 552} Chain breaks: 3 Chain: "B" Number of atoms: 4449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4449 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 19, 'TRANS': 552} Chain breaks: 3 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'BWQ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'BWQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.19 Number of scatterers: 8974 At special positions: 0 Unit cell: (96.628, 84.448, 126.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1608 8.00 N 1472 7.00 C 5836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 431.3 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 62.8% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.577A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.663A pdb=" N GLY A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.927A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.415A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 329 through 338 removed outlier: 3.788A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.984A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 392 through 413 removed outlier: 4.519A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 441 Processing helix chain 'A' and resid 446 through 451 removed outlier: 3.863A pdb=" N GLU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 479 through 498 Proline residue: A 485 - end of helix removed outlier: 4.722A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 529 removed outlier: 3.734A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 549 Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.678A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.660A pdb=" N GLN A 569 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.570A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 605 removed outlier: 3.785A pdb=" N ASN A 604 " --> pdb=" O ASN A 601 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 605 " --> pdb=" O PRO A 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 601 through 605' Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.534A pdb=" N TYR A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 650 removed outlier: 4.974A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.577A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 removed outlier: 3.663A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 removed outlier: 3.928A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 271 through 281 removed outlier: 4.414A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.788A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.984A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 392 through 413 removed outlier: 4.520A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 441 Processing helix chain 'B' and resid 446 through 451 removed outlier: 3.863A pdb=" N GLU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 479 through 498 Proline residue: B 485 - end of helix removed outlier: 4.721A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 529 removed outlier: 3.734A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 549 Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.677A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.659A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.570A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.786A pdb=" N ASN B 604 " --> pdb=" O ASN B 601 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR B 605 " --> pdb=" O PRO B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 601 through 605' Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.535A pdb=" N TYR B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 removed outlier: 4.974A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 71 removed outlier: 7.087A pdb=" N LYS A 61 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS A 47 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 63 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG A 45 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER A 65 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS A 43 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.442A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 71 removed outlier: 7.087A pdb=" N LYS B 61 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS B 47 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 63 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG B 45 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER B 65 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 43 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.441A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1406 1.31 - 1.45: 2506 1.45 - 1.58: 5162 1.58 - 1.71: 0 1.71 - 1.84: 94 Bond restraints: 9168 Sorted by residual: bond pdb=" C36 BWQ B 701 " pdb=" O37 BWQ B 701 " ideal model delta sigma weight residual 1.220 1.393 -0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C36 BWQ A 701 " pdb=" O37 BWQ A 701 " ideal model delta sigma weight residual 1.220 1.393 -0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C23 BWQ B 701 " pdb=" O24 BWQ B 701 " ideal model delta sigma weight residual 1.222 1.390 -0.168 2.00e-02 2.50e+03 7.04e+01 bond pdb=" C23 BWQ A 701 " pdb=" O24 BWQ A 701 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 7.00e+01 bond pdb=" C19 BWQ A 701 " pdb=" C20 BWQ A 701 " ideal model delta sigma weight residual 1.431 1.566 -0.135 2.00e-02 2.50e+03 4.54e+01 ... (remaining 9163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 12109 2.89 - 5.78: 242 5.78 - 8.67: 56 8.67 - 11.56: 7 11.56 - 14.45: 2 Bond angle restraints: 12416 Sorted by residual: angle pdb=" C SER B 572 " pdb=" N ILE B 573 " pdb=" CA ILE B 573 " ideal model delta sigma weight residual 120.24 126.49 -6.25 6.30e-01 2.52e+00 9.84e+01 angle pdb=" C SER A 572 " pdb=" N ILE A 573 " pdb=" CA ILE A 573 " ideal model delta sigma weight residual 120.24 126.47 -6.23 6.30e-01 2.52e+00 9.77e+01 angle pdb=" C VAL A 445 " pdb=" N GLU A 446 " pdb=" CA GLU A 446 " ideal model delta sigma weight residual 120.38 127.88 -7.50 1.46e+00 4.69e-01 2.64e+01 angle pdb=" C VAL B 445 " pdb=" N GLU B 446 " pdb=" CA GLU B 446 " ideal model delta sigma weight residual 120.38 127.81 -7.43 1.46e+00 4.69e-01 2.59e+01 angle pdb=" C06 BWQ A 701 " pdb=" N07 BWQ A 701 " pdb=" C08 BWQ A 701 " ideal model delta sigma weight residual 109.00 123.45 -14.45 3.00e+00 1.11e-01 2.32e+01 ... (remaining 12411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 5097 14.28 - 28.55: 250 28.55 - 42.83: 46 42.83 - 57.10: 8 57.10 - 71.38: 2 Dihedral angle restraints: 5403 sinusoidal: 2111 harmonic: 3292 Sorted by residual: dihedral pdb=" CA ASN A 601 " pdb=" C ASN A 601 " pdb=" N PRO A 602 " pdb=" CA PRO A 602 " ideal model delta harmonic sigma weight residual -180.00 -130.70 -49.30 0 5.00e+00 4.00e-02 9.72e+01 dihedral pdb=" CA ASN B 601 " pdb=" C ASN B 601 " pdb=" N PRO B 602 " pdb=" CA PRO B 602 " ideal model delta harmonic sigma weight residual -180.00 -130.74 -49.26 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CA PRO B 602 " pdb=" C PRO B 602 " pdb=" N CYS B 603 " pdb=" CA CYS B 603 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1238 0.075 - 0.150: 164 0.150 - 0.226: 22 0.226 - 0.301: 6 0.301 - 0.376: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CB VAL B 173 " pdb=" CA VAL B 173 " pdb=" CG1 VAL B 173 " pdb=" CG2 VAL B 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB VAL A 173 " pdb=" CA VAL A 173 " pdb=" CG1 VAL A 173 " pdb=" CG2 VAL A 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C22 BWQ A 701 " pdb=" C21 BWQ A 701 " pdb=" C23 BWQ A 701 " pdb=" N38 BWQ A 701 " both_signs ideal model delta sigma weight residual False -2.33 -2.59 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1429 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 BWQ B 701 " -0.184 2.00e-02 2.50e+03 2.20e-01 7.24e+02 pdb=" C22 BWQ B 701 " 0.309 2.00e-02 2.50e+03 pdb=" C26 BWQ B 701 " -0.200 2.00e-02 2.50e+03 pdb=" C36 BWQ B 701 " -0.026 2.00e-02 2.50e+03 pdb=" N38 BWQ B 701 " -0.189 2.00e-02 2.50e+03 pdb=" O37 BWQ B 701 " 0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 BWQ B 701 " 0.032 2.00e-02 2.50e+03 2.14e-01 5.74e+02 pdb=" C23 BWQ B 701 " 0.063 2.00e-02 2.50e+03 pdb=" C26 BWQ B 701 " -0.264 2.00e-02 2.50e+03 pdb=" N25 BWQ B 701 " 0.349 2.00e-02 2.50e+03 pdb=" O24 BWQ B 701 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 BWQ A 701 " -0.046 2.00e-02 2.50e+03 8.93e-02 1.20e+02 pdb=" C22 BWQ A 701 " -0.097 2.00e-02 2.50e+03 pdb=" C26 BWQ A 701 " -0.010 2.00e-02 2.50e+03 pdb=" C36 BWQ A 701 " 0.038 2.00e-02 2.50e+03 pdb=" N38 BWQ A 701 " 0.176 2.00e-02 2.50e+03 pdb=" O37 BWQ A 701 " -0.060 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1823 2.77 - 3.30: 8297 3.30 - 3.83: 14537 3.83 - 4.37: 16989 4.37 - 4.90: 30383 Nonbonded interactions: 72029 Sorted by model distance: nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.236 3.040 nonbonded pdb=" NH1 ARG B 426 " pdb=" OE2 GLU B 585 " model vdw 2.341 3.120 nonbonded pdb=" NH1 ARG A 426 " pdb=" OE2 GLU A 585 " model vdw 2.341 3.120 nonbonded pdb=" OG SER A 218 " pdb=" ND2 ASN B 299 " model vdw 2.360 3.120 ... (remaining 72024 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.009 0.173 9171 Z= 0.422 Angle : 1.094 14.446 12422 Z= 0.586 Chirality : 0.057 0.376 1432 Planarity : 0.010 0.220 1540 Dihedral : 9.213 71.380 3282 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.90 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.20), residues: 1128 helix: -1.94 (0.16), residues: 658 sheet: -0.72 (0.66), residues: 48 loop : -2.52 (0.25), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 383 TYR 0.021 0.002 TYR B 342 PHE 0.031 0.004 PHE A 489 TRP 0.019 0.003 TRP A 624 HIS 0.015 0.002 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00938 / 0.42 ( 9168) covalent geometry : angle 1.09125 / 0.58 (12416) SS BOND : bond 0.00834 / 0.47 ( 3) SS BOND : angle 3.65847 / 1.94 ( 6) hydrogen bonds : bond 0.15705 / 10.27 ( 504) hydrogen bonds : angle 6.74332 / 4.72 ( 1476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 348 GLU cc_start: 0.7797 (tp30) cc_final: 0.7404 (tm-30) REVERT: A 385 PHE cc_start: 0.8823 (t80) cc_final: 0.8528 (t80) REVERT: B 331 LYS cc_start: 0.8247 (tttm) cc_final: 0.7986 (mptt) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.0947 time to fit residues: 28.5956 Evaluate side-chains 111 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 116 ASN A 425 ASN A 437 GLN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 299 ASN B 425 ASN B 437 GLN B 582 GLN ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120355 restraints weight = 10742.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123725 restraints weight = 6486.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125875 restraints weight = 4716.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127073 restraints weight = 3881.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127978 restraints weight = 3456.628| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9171 Z= 0.147 Angle : 0.640 8.690 12422 Z= 0.320 Chirality : 0.041 0.159 1432 Planarity : 0.004 0.046 1540 Dihedral : 5.981 75.820 1238 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.05 % Allowed : 8.42 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.24), residues: 1128 helix: -0.07 (0.19), residues: 672 sheet: -0.33 (0.69), residues: 48 loop : -2.03 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 246 TYR 0.013 0.001 TYR A 463 PHE 0.021 0.002 PHE B 293 TRP 0.012 0.002 TRP B 379 HIS 0.006 0.001 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9168) covalent geometry : angle 0.63913 / 0.32 (12416) SS BOND : bond 0.00616 / 0.34 ( 3) SS BOND : angle 1.84817 / 1.04 ( 6) hydrogen bonds : bond 0.03915 / 2.71 ( 504) hydrogen bonds : angle 4.55868 / 3.23 ( 1476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7919 (t70) cc_final: 0.7599 (t0) outliers start: 20 outliers final: 13 residues processed: 150 average time/residue: 0.0732 time to fit residues: 16.4155 Evaluate side-chains 127 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B 583 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115835 restraints weight = 10955.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118952 restraints weight = 6673.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121076 restraints weight = 4915.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122219 restraints weight = 4070.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.123051 restraints weight = 3652.159| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9171 Z= 0.198 Angle : 0.644 9.596 12422 Z= 0.322 Chirality : 0.044 0.170 1432 Planarity : 0.004 0.036 1540 Dihedral : 5.872 83.235 1238 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.57 % Allowed : 10.78 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1128 helix: 0.67 (0.20), residues: 674 sheet: -0.04 (0.74), residues: 48 loop : -1.77 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.012 0.001 TYR A 342 PHE 0.019 0.002 PHE B 578 TRP 0.010 0.001 TRP B 379 HIS 0.006 0.002 HIS B 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 9168) covalent geometry : angle 0.64325 / 0.32 (12416) SS BOND : bond 0.00621 / 0.34 ( 3) SS BOND : angle 1.56522 / 0.88 ( 6) hydrogen bonds : bond 0.04044 / 2.78 ( 504) hydrogen bonds : angle 4.29959 / 3.06 ( 1476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7965 (t70) cc_final: 0.7653 (t0) REVERT: B 71 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.6613 (mmt) outliers start: 25 outliers final: 17 residues processed: 144 average time/residue: 0.0637 time to fit residues: 14.0067 Evaluate side-chains 124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 chunk 81 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123784 restraints weight = 10983.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125222 restraints weight = 7426.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126370 restraints weight = 6242.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126687 restraints weight = 5028.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126892 restraints weight = 4489.595| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9171 Z= 0.130 Angle : 0.566 6.592 12422 Z= 0.287 Chirality : 0.041 0.184 1432 Planarity : 0.003 0.036 1540 Dihedral : 5.731 86.468 1238 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.36 % Allowed : 13.04 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 1128 helix: 1.29 (0.21), residues: 668 sheet: 0.21 (0.74), residues: 48 loop : -1.69 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.008 0.001 TYR A 463 PHE 0.027 0.001 PHE B 293 TRP 0.010 0.001 TRP B 379 HIS 0.004 0.001 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9168) covalent geometry : angle 0.56527 / 0.29 (12416) SS BOND : bond 0.00698 / 0.39 ( 3) SS BOND : angle 1.35992 / 0.77 ( 6) hydrogen bonds : bond 0.03441 / 2.37 ( 504) hydrogen bonds : angle 4.05397 / 2.90 ( 1476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7908 (t70) cc_final: 0.7652 (t0) REVERT: A 585 GLU cc_start: 0.7631 (tp30) cc_final: 0.7335 (tp30) outliers start: 23 outliers final: 16 residues processed: 138 average time/residue: 0.0656 time to fit residues: 13.8192 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN B 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120420 restraints weight = 11007.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123841 restraints weight = 6576.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125986 restraints weight = 4762.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127166 restraints weight = 3909.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128110 restraints weight = 3479.428| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9171 Z= 0.140 Angle : 0.582 6.394 12422 Z= 0.291 Chirality : 0.042 0.192 1432 Planarity : 0.003 0.037 1540 Dihedral : 5.688 85.511 1238 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.16 % Allowed : 14.07 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1128 helix: 1.45 (0.21), residues: 668 sheet: 0.46 (0.76), residues: 48 loop : -1.52 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.008 0.001 TYR A 463 PHE 0.025 0.001 PHE B 293 TRP 0.009 0.001 TRP B 379 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9168) covalent geometry : angle 0.58175 / 0.29 (12416) SS BOND : bond 0.00630 / 0.35 ( 3) SS BOND : angle 1.18099 / 0.67 ( 6) hydrogen bonds : bond 0.03501 / 2.41 ( 504) hydrogen bonds : angle 3.97761 / 2.83 ( 1476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.336 Fit side-chains REVERT: A 296 ASP cc_start: 0.7884 (t70) cc_final: 0.7672 (t0) REVERT: A 339 SER cc_start: 0.8161 (p) cc_final: 0.7948 (m) outliers start: 21 outliers final: 17 residues processed: 129 average time/residue: 0.0728 time to fit residues: 14.3311 Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN A 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118223 restraints weight = 11023.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121432 restraints weight = 6622.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123535 restraints weight = 4817.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124501 restraints weight = 3972.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125337 restraints weight = 3571.980| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9171 Z= 0.170 Angle : 0.609 10.822 12422 Z= 0.301 Chirality : 0.043 0.178 1432 Planarity : 0.003 0.035 1540 Dihedral : 5.828 87.146 1238 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.16 % Allowed : 14.48 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1128 helix: 1.50 (0.21), residues: 668 sheet: 0.51 (0.61), residues: 66 loop : -1.59 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.010 0.001 TYR A 463 PHE 0.012 0.001 PHE B 293 TRP 0.009 0.001 TRP B 379 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 9168) covalent geometry : angle 0.60793 / 0.30 (12416) SS BOND : bond 0.00564 / 0.31 ( 3) SS BOND : angle 1.60677 / 0.88 ( 6) hydrogen bonds : bond 0.03698 / 2.55 ( 504) hydrogen bonds : angle 3.97900 / 2.83 ( 1476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.347 Fit side-chains REVERT: A 585 GLU cc_start: 0.7683 (tp30) cc_final: 0.7421 (tp30) outliers start: 21 outliers final: 15 residues processed: 123 average time/residue: 0.0759 time to fit residues: 13.8943 Evaluate side-chains 113 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126307 restraints weight = 11230.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.125581 restraints weight = 7076.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126208 restraints weight = 6126.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126572 restraints weight = 5382.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126802 restraints weight = 5191.802| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9171 Z= 0.172 Angle : 0.606 8.411 12422 Z= 0.302 Chirality : 0.043 0.162 1432 Planarity : 0.003 0.035 1540 Dihedral : 5.867 87.583 1238 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.36 % Allowed : 14.58 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1128 helix: 1.54 (0.20), residues: 670 sheet: 0.58 (0.62), residues: 66 loop : -1.52 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.015 0.001 TYR A 463 PHE 0.014 0.001 PHE B 293 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 9168) covalent geometry : angle 0.60368 / 0.30 (12416) SS BOND : bond 0.00041 / 0.02 ( 3) SS BOND : angle 2.65875 / 1.50 ( 6) hydrogen bonds : bond 0.03680 / 2.54 ( 504) hydrogen bonds : angle 3.96974 / 2.82 ( 1476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.313 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 125 average time/residue: 0.0758 time to fit residues: 14.3399 Evaluate side-chains 116 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.6980 chunk 109 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.156358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128195 restraints weight = 10818.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127941 restraints weight = 7864.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129584 restraints weight = 6494.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129965 restraints weight = 5211.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130132 restraints weight = 4738.180| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9171 Z= 0.117 Angle : 0.582 10.433 12422 Z= 0.285 Chirality : 0.041 0.151 1432 Planarity : 0.003 0.035 1540 Dihedral : 5.747 87.280 1238 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.85 % Allowed : 15.20 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 1128 helix: 1.85 (0.21), residues: 658 sheet: 0.77 (0.63), residues: 66 loop : -1.66 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.008 0.001 TYR A 463 PHE 0.025 0.001 PHE A 293 TRP 0.009 0.001 TRP B 379 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9168) covalent geometry : angle 0.58028 / 0.28 (12416) SS BOND : bond 0.00416 / 0.23 ( 3) SS BOND : angle 1.97530 / 1.16 ( 6) hydrogen bonds : bond 0.03283 / 2.25 ( 504) hydrogen bonds : angle 3.86901 / 2.74 ( 1476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.335 Fit side-chains REVERT: A 585 GLU cc_start: 0.7625 (tp30) cc_final: 0.7338 (tp30) outliers start: 18 outliers final: 16 residues processed: 118 average time/residue: 0.0707 time to fit residues: 12.6550 Evaluate side-chains 115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 0.0270 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119541 restraints weight = 11081.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122894 restraints weight = 6580.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125035 restraints weight = 4759.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126159 restraints weight = 3906.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127075 restraints weight = 3489.170| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9171 Z= 0.213 Angle : 0.649 11.696 12422 Z= 0.318 Chirality : 0.044 0.157 1432 Planarity : 0.003 0.034 1540 Dihedral : 5.959 88.779 1238 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.05 % Allowed : 15.40 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1128 helix: 1.68 (0.20), residues: 658 sheet: 0.73 (0.66), residues: 64 loop : -1.68 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.013 0.001 TYR B 463 PHE 0.019 0.002 PHE A 293 TRP 0.008 0.001 TRP B 379 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.21 ( 9168) covalent geometry : angle 0.64791 / 0.32 (12416) SS BOND : bond 0.00202 / 0.11 ( 3) SS BOND : angle 2.01615 / 1.16 ( 6) hydrogen bonds : bond 0.03885 / 2.69 ( 504) hydrogen bonds : angle 4.01848 / 2.85 ( 1476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.448 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 118 average time/residue: 0.0849 time to fit residues: 14.8796 Evaluate side-chains 112 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 108 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122525 restraints weight = 10994.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125929 restraints weight = 6512.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128107 restraints weight = 4697.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129379 restraints weight = 3842.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129815 restraints weight = 3413.052| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9171 Z= 0.151 Angle : 0.629 11.337 12422 Z= 0.306 Chirality : 0.042 0.148 1432 Planarity : 0.004 0.083 1540 Dihedral : 5.914 89.114 1238 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.54 % Allowed : 16.53 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.26), residues: 1128 helix: 1.94 (0.20), residues: 646 sheet: 0.70 (0.65), residues: 64 loop : -1.52 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.010 0.001 TYR B 463 PHE 0.016 0.001 PHE B 578 TRP 0.009 0.001 TRP B 379 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 9168) covalent geometry : angle 0.62764 / 0.31 (12416) SS BOND : bond 0.00424 / 0.24 ( 3) SS BOND : angle 1.86159 / 1.09 ( 6) hydrogen bonds : bond 0.03491 / 2.42 ( 504) hydrogen bonds : angle 3.97084 / 2.82 ( 1476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.211 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 111 average time/residue: 0.0781 time to fit residues: 13.1048 Evaluate side-chains 108 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 108 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123191 restraints weight = 10910.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126489 restraints weight = 6450.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128680 restraints weight = 4644.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129827 restraints weight = 3795.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130784 restraints weight = 3378.096| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9171 Z= 0.139 Angle : 0.619 10.502 12422 Z= 0.299 Chirality : 0.041 0.148 1432 Planarity : 0.004 0.073 1540 Dihedral : 5.834 87.895 1238 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.54 % Allowed : 16.84 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1128 helix: 2.00 (0.20), residues: 646 sheet: 0.69 (0.64), residues: 64 loop : -1.50 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.020 0.001 TYR B 463 PHE 0.015 0.001 PHE B 578 TRP 0.009 0.001 TRP B 379 HIS 0.002 0.001 HIS B 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9168) covalent geometry : angle 0.61786 / 0.30 (12416) SS BOND : bond 0.00375 / 0.21 ( 3) SS BOND : angle 1.80750 / 1.06 ( 6) hydrogen bonds : bond 0.03405 / 2.36 ( 504) hydrogen bonds : angle 3.91174 / 2.77 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1389.86 seconds wall clock time: 24 minutes 58.52 seconds (1498.52 seconds total)