Starting phenix.real_space_refine on Thu Mar 13 19:42:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ffc_4256/03_2025/6ffc_4256.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ffc_4256/03_2025/6ffc_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_4256/03_2025/6ffc_4256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ffc_4256/03_2025/6ffc_4256.map" model { file = "/net/cci-nas-00/data/ceres_data/6ffc_4256/03_2025/6ffc_4256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ffc_4256/03_2025/6ffc_4256.cif" } resolution = 3.56 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= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.63, per 1000 atoms: 0.63 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.90 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: 2.34 Time building geometry restraints manager: 2.71 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 - 27.16: 5389 27.16 - 54.33: 72 54.33 - 81.49: 6 81.49 - 108.65: 2 108.65 - 135.82: 6 Dihedral angle restraints: 5475 sinusoidal: 2183 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 5472 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: 0.04 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: 2.110 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.960 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 9168 Z= 0.614 Angle : 1.091 14.446 12416 Z= 0.585 Chirality : 0.057 0.376 1432 Planarity : 0.010 0.220 1540 Dihedral : 11.436 135.815 3354 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 (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: -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 TRP 0.019 0.003 TRP A 624 HIS 0.015 0.002 HIS A 583 PHE 0.031 0.004 PHE A 489 TYR 0.021 0.002 TYR B 342 ARG 0.012 0.001 ARG B 383 *********************** 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 : 1.061 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: 0.2264 time to fit residues: 67.2171 Evaluate side-chains 112 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120936 restraints weight = 10620.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124264 restraints weight = 6407.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126302 restraints weight = 4673.768| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9168 Z= 0.204 Angle : 0.639 8.543 12416 Z= 0.320 Chirality : 0.041 0.164 1432 Planarity : 0.004 0.046 1540 Dihedral : 11.621 140.441 1310 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.16 % Allowed : 8.52 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -1.30 (0.24), residues: 1128 helix: -0.13 (0.19), residues: 674 sheet: -0.37 (0.69), residues: 48 loop : -2.09 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 379 HIS 0.006 0.001 HIS A 583 PHE 0.022 0.002 PHE B 293 TYR 0.013 0.001 TYR A 342 ARG 0.004 0.001 ARG A 246 *********************** 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 154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7940 (t70) cc_final: 0.7607 (t0) REVERT: B 331 LYS cc_start: 0.8086 (tttm) cc_final: 0.7877 (mptt) outliers start: 21 outliers final: 13 residues processed: 146 average time/residue: 0.2049 time to fit residues: 43.0609 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 51 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 120 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119819 restraints weight = 10947.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123158 restraints weight = 6565.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125317 restraints weight = 4782.765| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9168 Z= 0.209 Angle : 0.595 8.077 12416 Z= 0.297 Chirality : 0.042 0.174 1432 Planarity : 0.004 0.041 1540 Dihedral : 11.156 140.310 1310 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.05 % Allowed : 11.40 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -0.17 (0.25), residues: 1128 helix: 0.89 (0.20), residues: 666 sheet: 0.02 (0.73), residues: 48 loop : -1.80 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.006 0.001 HIS A 583 PHE 0.012 0.001 PHE B 142 TYR 0.011 0.001 TYR A 342 ARG 0.003 0.000 ARG B 246 *********************** 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 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6394 (mmt) REVERT: A 296 ASP cc_start: 0.7982 (t70) cc_final: 0.7680 (t0) REVERT: A 585 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7399 (tp30) REVERT: B 292 ASP cc_start: 0.9085 (m-30) cc_final: 0.8849 (m-30) REVERT: B 331 LYS cc_start: 0.8059 (tttm) cc_final: 0.7842 (mptt) outliers start: 20 outliers final: 12 residues processed: 140 average time/residue: 0.1660 time to fit residues: 34.7885 Evaluate side-chains 125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 0.5980 chunk 83 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS B 120 ASN 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 = 0.152327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123058 restraints weight = 10831.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124324 restraints weight = 7257.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125297 restraints weight = 6397.294| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9168 Z= 0.219 Angle : 0.593 8.968 12416 Z= 0.295 Chirality : 0.042 0.184 1432 Planarity : 0.003 0.035 1540 Dihedral : 10.901 141.151 1310 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.67 % Allowed : 11.91 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: 0.36 (0.26), residues: 1128 helix: 1.35 (0.21), residues: 666 sheet: 0.27 (0.73), residues: 48 loop : -1.66 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.005 0.001 HIS A 583 PHE 0.025 0.001 PHE A 293 TYR 0.009 0.001 TYR A 342 ARG 0.002 0.000 ARG B 160 *********************** 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: 26 poor density : 119 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.7225 (t) REVERT: A 296 ASP cc_start: 0.7937 (t70) cc_final: 0.7698 (t0) REVERT: B 71 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7193 (mmt) REVERT: B 331 LYS cc_start: 0.8051 (tttm) cc_final: 0.7822 (mptt) REVERT: B 541 MET cc_start: 0.8215 (tpp) cc_final: 0.8008 (tpp) outliers start: 26 outliers final: 16 residues processed: 137 average time/residue: 0.1663 time to fit residues: 34.4142 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 : 1.060 ------------------------------------------------------------------------------- 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 153 THR 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 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 71 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 113 optimal weight: 0.0270 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 617 GLN B 424 GLN B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123389 restraints weight = 10888.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123387 restraints weight = 7791.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124440 restraints weight = 6358.849| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9168 Z= 0.203 Angle : 0.580 7.991 12416 Z= 0.289 Chirality : 0.042 0.155 1432 Planarity : 0.003 0.036 1540 Dihedral : 10.613 142.316 1310 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.95 % Allowed : 13.76 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: 0.58 (0.26), residues: 1128 helix: 1.51 (0.21), residues: 666 sheet: 0.50 (0.76), residues: 48 loop : -1.54 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.002 0.001 HIS A 267 PHE 0.027 0.001 PHE B 293 TYR 0.014 0.001 TYR A 463 ARG 0.002 0.000 ARG B 163 *********************** 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 132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.891 Fit side-chains REVERT: A 71 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6422 (mmt) REVERT: A 296 ASP cc_start: 0.7902 (t70) cc_final: 0.7698 (t0) REVERT: A 339 SER cc_start: 0.8252 (p) cc_final: 0.8026 (m) REVERT: A 463 TYR cc_start: 0.9372 (m-80) cc_final: 0.9041 (m-80) REVERT: B 71 MET cc_start: 0.7451 (mtt) cc_final: 0.7187 (mmt) REVERT: B 331 LYS cc_start: 0.8129 (tttm) cc_final: 0.7861 (mptt) outliers start: 19 outliers final: 15 residues processed: 127 average time/residue: 0.1779 time to fit residues: 33.5554 Evaluate side-chains 118 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 150 THR 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 108 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 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 424 GLN B 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123805 restraints weight = 10768.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123766 restraints weight = 7677.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124145 restraints weight = 6219.599| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9168 Z= 0.196 Angle : 0.583 9.735 12416 Z= 0.289 Chirality : 0.041 0.180 1432 Planarity : 0.003 0.034 1540 Dihedral : 10.351 145.474 1310 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.85 % Allowed : 14.37 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.74 (0.26), residues: 1128 helix: 1.58 (0.21), residues: 670 sheet: 0.58 (0.62), residues: 66 loop : -1.49 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.002 0.001 HIS A 243 PHE 0.014 0.001 PHE B 578 TYR 0.012 0.001 TYR A 463 ARG 0.003 0.000 ARG B 246 *********************** 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: 18 poor density : 111 time to evaluate : 0.911 Fit side-chains REVERT: A 287 TYR cc_start: 0.5659 (m-80) cc_final: 0.5448 (m-80) REVERT: A 585 GLU cc_start: 0.7668 (tp30) cc_final: 0.7377 (tp30) REVERT: B 71 MET cc_start: 0.7472 (mtt) cc_final: 0.7156 (mmt) REVERT: B 331 LYS cc_start: 0.8084 (tttm) cc_final: 0.7713 (mptt) outliers start: 18 outliers final: 15 residues processed: 125 average time/residue: 0.1772 time to fit residues: 32.7197 Evaluate side-chains 116 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 176 SER 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 532 SER Chi-restraints excluded: chain B residue 108 ILE 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 20 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120705 restraints weight = 10926.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123984 restraints weight = 6579.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126053 restraints weight = 4779.784| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9168 Z= 0.200 Angle : 0.589 10.002 12416 Z= 0.290 Chirality : 0.041 0.162 1432 Planarity : 0.003 0.034 1540 Dihedral : 10.275 146.344 1310 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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 (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: 0.84 (0.26), residues: 1128 helix: 1.65 (0.21), residues: 670 sheet: 0.71 (0.63), residues: 66 loop : -1.43 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS A 267 PHE 0.011 0.001 PHE B 578 TYR 0.012 0.001 TYR A 463 ARG 0.002 0.000 ARG B 246 *********************** 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 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 463 TYR cc_start: 0.9361 (m-80) cc_final: 0.8962 (m-80) REVERT: A 585 GLU cc_start: 0.7707 (tp30) cc_final: 0.7421 (tp30) outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.1693 time to fit residues: 30.0431 Evaluate side-chains 114 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 108 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 483 MET 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 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.146564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114346 restraints weight = 11336.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117303 restraints weight = 7089.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119213 restraints weight = 5305.796| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9168 Z= 0.400 Angle : 0.697 11.903 12416 Z= 0.339 Chirality : 0.046 0.155 1432 Planarity : 0.003 0.033 1540 Dihedral : 10.328 146.105 1310 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.67 % Allowed : 13.86 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.26), residues: 1128 helix: 1.59 (0.20), residues: 646 sheet: 0.35 (0.63), residues: 68 loop : -1.59 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 379 HIS 0.003 0.001 HIS A 243 PHE 0.017 0.002 PHE B 240 TYR 0.016 0.002 TYR A 463 ARG 0.002 0.000 ARG A 193 *********************** 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 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.999 Fit side-chains REVERT: B 476 SER cc_start: 0.9123 (t) cc_final: 0.8920 (t) outliers start: 26 outliers final: 22 residues processed: 129 average time/residue: 0.1757 time to fit residues: 33.4120 Evaluate side-chains 118 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain A residue 214 THR 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 A residue 532 SER Chi-restraints excluded: chain A residue 540 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3760 r_free = 0.3760 target = 0.153776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120502 restraints weight = 11094.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123745 restraints weight = 6811.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125926 restraints weight = 5008.050| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9168 Z= 0.192 Angle : 0.608 10.167 12416 Z= 0.296 Chirality : 0.041 0.149 1432 Planarity : 0.003 0.034 1540 Dihedral : 10.378 147.910 1310 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.75 % Allowed : 14.89 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.26), residues: 1128 helix: 1.77 (0.20), residues: 658 sheet: 0.90 (0.66), residues: 62 loop : -1.61 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS B 350 PHE 0.025 0.001 PHE A 293 TYR 0.012 0.001 TYR A 463 ARG 0.003 0.000 ARG B 246 *********************** 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: 17 poor density : 104 time to evaluate : 0.930 Fit side-chains REVERT: A 463 TYR cc_start: 0.9379 (m-80) cc_final: 0.9030 (m-80) REVERT: A 585 GLU cc_start: 0.7636 (tp30) cc_final: 0.7384 (tp30) outliers start: 17 outliers final: 15 residues processed: 117 average time/residue: 0.1795 time to fit residues: 31.1132 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 : 1.031 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER 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 489 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 49 optimal weight: 0.0270 chunk 91 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3808 r_free = 0.3808 target = 0.157552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126153 restraints weight = 10948.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129573 restraints weight = 6466.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131871 restraints weight = 4638.384| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9168 Z= 0.174 Angle : 0.601 8.857 12416 Z= 0.290 Chirality : 0.040 0.143 1432 Planarity : 0.003 0.034 1540 Dihedral : 10.207 144.773 1310 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.54 % Allowed : 14.58 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.26), residues: 1128 helix: 1.95 (0.20), residues: 660 sheet: 1.04 (0.65), residues: 62 loop : -1.58 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS B 267 PHE 0.025 0.001 PHE B 293 TYR 0.012 0.001 TYR A 463 ARG 0.002 0.000 ARG B 246 ********************** 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 125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.933 Fit side-chains REVERT: A 463 TYR cc_start: 0.9364 (m-80) cc_final: 0.9056 (m-80) REVERT: A 541 MET cc_start: 0.8187 (tpp) cc_final: 0.7867 (mmm) REVERT: A 585 GLU cc_start: 0.7667 (tp30) cc_final: 0.7424 (tp30) REVERT: B 71 MET cc_start: 0.7411 (mtt) cc_final: 0.7181 (mmt) REVERT: B 152 MET cc_start: 0.7701 (ttt) cc_final: 0.7341 (ttt) REVERT: B 541 MET cc_start: 0.8229 (tpp) cc_final: 0.7866 (mmm) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.1826 time to fit residues: 32.6806 Evaluate side-chains 113 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 237 THR Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain B residue 38 SER 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 489 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126784 restraints weight = 10945.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130288 restraints weight = 6430.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132500 restraints weight = 4607.002| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9168 Z= 0.169 Angle : 0.599 11.809 12416 Z= 0.291 Chirality : 0.040 0.144 1432 Planarity : 0.003 0.034 1540 Dihedral : 10.148 143.576 1310 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.13 % Allowed : 15.30 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.26), residues: 1128 helix: 2.05 (0.21), residues: 660 sheet: 1.07 (0.64), residues: 62 loop : -1.53 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS B 267 PHE 0.022 0.001 PHE B 578 TYR 0.012 0.001 TYR A 463 ARG 0.002 0.000 ARG B 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.80 seconds wall clock time: 46 minutes 38.76 seconds (2798.76 seconds total)