Starting phenix.real_space_refine on Mon Nov 17 23:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ffc_4256/11_2025/6ffc_4256.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ffc_4256/11_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_4256/11_2025/6ffc_4256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ffc_4256/11_2025/6ffc_4256.map" model { file = "/net/cci-nas-00/data/ceres_data/6ffc_4256/11_2025/6ffc_4256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ffc_4256/11_2025/6ffc_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-2.0-5881/lib/python3.9/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: 2.10, per 1000 atoms: 0.23 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: 0.68 Conformation dependent library (CDL) restraints added in 354.3 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: 0.34 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: 1.71 Time building geometry restraints manager: 0.86 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: 0.02 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.770 Find NCS groups from input model: 0.070 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.640 ------------------------------------------------------------------------------- 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 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 : 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 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 covalent geometry : bond 0.00938 ( 9168) covalent geometry : angle 1.09125 (12416) SS BOND : bond 0.00834 ( 3) SS BOND : angle 3.65847 ( 6) hydrogen bonds : bond 0.15705 ( 504) hydrogen bonds : angle 6.74332 ( 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 : 0.352 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: 0.1012 time to fit residues: 30.1385 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 : 0.328 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3760 r_free = 0.3760 target = 0.153493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120381 restraints weight = 10748.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123776 restraints weight = 6477.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125921 restraints weight = 4713.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127052 restraints weight = 3874.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127619 restraints weight = 3459.061| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9171 Z= 0.146 Angle : 0.642 8.798 12422 Z= 0.321 Chirality : 0.042 0.156 1432 Planarity : 0.004 0.043 1540 Dihedral : 11.566 141.106 1310 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.16 % Allowed : 8.42 % Favored : 89.43 % 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: -1.23 (0.24), residues: 1128 helix: -0.08 (0.19), residues: 674 sheet: -0.33 (0.69), residues: 48 loop : -2.07 (0.29), residues: 406 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 0.022 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 covalent geometry : bond 0.00338 ( 9168) covalent geometry : angle 0.64069 (12416) SS BOND : bond 0.00621 ( 3) SS BOND : angle 1.86244 ( 6) hydrogen bonds : bond 0.03929 ( 504) hydrogen bonds : angle 4.56266 ( 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 159 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7945 (t70) cc_final: 0.7622 (t0) outliers start: 21 outliers final: 13 residues processed: 151 average time/residue: 0.0778 time to fit residues: 17.3684 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: 0.7980 chunk 36 optimal weight: 0.0470 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** 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 = 0.3721 r_free = 0.3721 target = 0.150074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116983 restraints weight = 10921.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120264 restraints weight = 6636.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122363 restraints weight = 4861.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123362 restraints weight = 4020.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124370 restraints weight = 3609.947| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9171 Z= 0.178 Angle : 0.628 8.494 12422 Z= 0.315 Chirality : 0.043 0.171 1432 Planarity : 0.004 0.038 1540 Dihedral : 11.246 140.482 1310 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.36 % Allowed : 11.19 % Favored : 86.45 % 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: -0.30 (0.25), residues: 1128 helix: 0.71 (0.20), residues: 676 sheet: -0.01 (0.74), residues: 48 loop : -1.76 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 163 TYR 0.012 0.001 TYR A 342 PHE 0.017 0.002 PHE B 578 TRP 0.010 0.001 TRP B 379 HIS 0.006 0.001 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9168) covalent geometry : angle 0.62727 (12416) SS BOND : bond 0.00662 ( 3) SS BOND : angle 1.54752 ( 6) hydrogen bonds : bond 0.03943 ( 504) hydrogen bonds : angle 4.28112 ( 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 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7974 (t70) cc_final: 0.7656 (t0) REVERT: B 71 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6739 (mmt) outliers start: 23 outliers final: 18 residues processed: 142 average time/residue: 0.0737 time to fit residues: 15.8484 Evaluate side-chains 126 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 186 VAL 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: 4.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 81 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 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 = 0.3764 r_free = 0.3764 target = 0.153680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124384 restraints weight = 10965.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124977 restraints weight = 7406.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126109 restraints weight = 6886.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126433 restraints weight = 5311.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.126784 restraints weight = 4683.298| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3236 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= 0.125 Angle : 0.571 8.809 12422 Z= 0.287 Chirality : 0.041 0.186 1432 Planarity : 0.003 0.037 1540 Dihedral : 10.973 142.133 1310 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.95 % Allowed : 13.45 % 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: 0.33 (0.26), residues: 1128 helix: 1.31 (0.21), residues: 668 sheet: 0.29 (0.74), residues: 48 loop : -1.65 (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 0.026 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 covalent geometry : bond 0.00289 ( 9168) covalent geometry : angle 0.57024 (12416) SS BOND : bond 0.00688 ( 3) SS BOND : angle 1.33614 ( 6) hydrogen bonds : bond 0.03377 ( 504) hydrogen bonds : angle 4.04101 ( 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 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7925 (t70) cc_final: 0.7682 (t0) outliers start: 19 outliers final: 14 residues processed: 133 average time/residue: 0.0730 time to fit residues: 14.8191 Evaluate side-chains 118 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.153144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123625 restraints weight = 10919.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124412 restraints weight = 7407.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126201 restraints weight = 6101.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126374 restraints weight = 4903.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126454 restraints weight = 4533.587| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3483 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= 0.137 Angle : 0.582 6.622 12422 Z= 0.290 Chirality : 0.042 0.180 1432 Planarity : 0.003 0.035 1540 Dihedral : 10.644 140.851 1310 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.26 % Allowed : 13.86 % Favored : 83.88 % 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: 0.60 (0.26), residues: 1128 helix: 1.51 (0.21), residues: 668 sheet: 0.53 (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 0.009 0.001 TYR A 463 PHE 0.027 0.001 PHE A 293 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9168) covalent geometry : angle 0.58115 (12416) SS BOND : bond 0.00625 ( 3) SS BOND : angle 1.17591 ( 6) hydrogen bonds : bond 0.03449 ( 504) hydrogen bonds : angle 3.97748 ( 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: 22 poor density : 113 time to evaluate : 0.303 Fit side-chains REVERT: A 296 ASP cc_start: 0.7889 (t70) cc_final: 0.7677 (t0) REVERT: B 71 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6635 (mmt) outliers start: 22 outliers final: 16 residues processed: 129 average time/residue: 0.0720 time to fit residues: 14.2163 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 71 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.152345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120388 restraints weight = 10927.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123723 restraints weight = 6524.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125906 restraints weight = 4691.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127209 restraints weight = 3835.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127814 restraints weight = 3400.894| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9171 Z= 0.142 Angle : 0.583 8.656 12422 Z= 0.289 Chirality : 0.042 0.187 1432 Planarity : 0.003 0.035 1540 Dihedral : 10.417 144.309 1310 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.16 % Allowed : 14.37 % Favored : 83.47 % 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: 0.69 (0.26), residues: 1128 helix: 1.59 (0.21), residues: 666 sheet: 0.56 (0.61), residues: 66 loop : -1.57 (0.33), residues: 396 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 0.013 0.001 PHE B 293 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9168) covalent geometry : angle 0.58114 (12416) SS BOND : bond 0.00542 ( 3) SS BOND : angle 1.98447 ( 6) hydrogen bonds : bond 0.03441 ( 504) hydrogen bonds : angle 3.92525 ( 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 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.361 Fit side-chains REVERT: A 296 ASP cc_start: 0.7824 (t70) cc_final: 0.7609 (t0) REVERT: A 585 GLU cc_start: 0.7699 (tp30) cc_final: 0.7424 (tp30) REVERT: B 71 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6833 (mmt) outliers start: 21 outliers final: 17 residues processed: 126 average time/residue: 0.0799 time to fit residues: 15.0117 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 MET 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 483 MET 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: 2.9990 chunk 29 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.154023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122099 restraints weight = 10927.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125413 restraints weight = 6511.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127543 restraints weight = 4698.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128914 restraints weight = 3859.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129502 restraints weight = 3418.142| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9171 Z= 0.118 Angle : 0.573 9.290 12422 Z= 0.280 Chirality : 0.041 0.163 1432 Planarity : 0.003 0.036 1540 Dihedral : 10.278 146.135 1310 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.95 % Allowed : 15.30 % Favored : 82.75 % 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: 0.90 (0.27), residues: 1128 helix: 1.73 (0.21), residues: 670 sheet: 0.74 (0.62), residues: 66 loop : -1.49 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.012 0.001 TYR A 463 PHE 0.017 0.001 PHE B 578 TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9168) covalent geometry : angle 0.56982 (12416) SS BOND : bond 0.00376 ( 3) SS BOND : angle 2.59929 ( 6) hydrogen bonds : bond 0.03249 ( 504) hydrogen bonds : angle 3.82935 ( 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 129 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.360 Fit side-chains REVERT: A 296 ASP cc_start: 0.7743 (t70) cc_final: 0.7541 (t0) REVERT: A 585 GLU cc_start: 0.7678 (tp30) cc_final: 0.7390 (tp30) REVERT: B 475 LEU cc_start: 0.8861 (tt) cc_final: 0.8604 (tp) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 0.0871 time to fit residues: 16.0671 Evaluate side-chains 113 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU 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 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 442 VAL Chi-restraints excluded: chain B residue 483 MET 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: 0.9980 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 108 optimal weight: 0.0270 chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.153517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121458 restraints weight = 10806.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124725 restraints weight = 6512.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126913 restraints weight = 4784.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128198 restraints weight = 3931.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129000 restraints weight = 3500.310| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3915 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= 0.126 Angle : 0.581 9.359 12422 Z= 0.283 Chirality : 0.041 0.151 1432 Planarity : 0.003 0.035 1540 Dihedral : 10.200 144.558 1310 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.95 % Allowed : 14.89 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1128 helix: 1.89 (0.21), residues: 658 sheet: 0.85 (0.62), residues: 66 loop : -1.64 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.009 0.001 TYR A 463 PHE 0.024 0.001 PHE A 293 TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9168) covalent geometry : angle 0.57962 (12416) SS BOND : bond 0.00061 ( 3) SS BOND : angle 2.04715 ( 6) hydrogen bonds : bond 0.03312 ( 504) hydrogen bonds : angle 3.78791 ( 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 124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.376 Fit side-chains REVERT: A 351 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 585 GLU cc_start: 0.7738 (tp30) cc_final: 0.7430 (tp30) REVERT: B 71 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7153 (mmt) outliers start: 19 outliers final: 15 residues processed: 118 average time/residue: 0.0878 time to fit residues: 15.2445 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 : 0.343 ------------------------------------------------------------------------------- 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 214 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 A residue 532 SER Chi-restraints excluded: chain B residue 71 MET 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 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 81 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.151238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119198 restraints weight = 10949.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122405 restraints weight = 6605.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124573 restraints weight = 4822.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125832 restraints weight = 3967.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126428 restraints weight = 3536.050| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9171 Z= 0.161 Angle : 0.604 10.325 12422 Z= 0.295 Chirality : 0.042 0.152 1432 Planarity : 0.003 0.034 1540 Dihedral : 10.200 144.407 1310 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.95 % Allowed : 15.20 % Favored : 82.85 % 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: 0.93 (0.26), residues: 1128 helix: 1.87 (0.20), residues: 658 sheet: 0.86 (0.63), residues: 66 loop : -1.64 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.009 0.001 TYR B 463 PHE 0.013 0.001 PHE B 293 TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9168) covalent geometry : angle 0.60294 (12416) SS BOND : bond 0.00295 ( 3) SS BOND : angle 1.96816 ( 6) hydrogen bonds : bond 0.03542 ( 504) hydrogen bonds : angle 3.83267 ( 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 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.363 Fit side-chains REVERT: A 585 GLU cc_start: 0.7733 (tp30) cc_final: 0.7495 (tp30) REVERT: B 71 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7203 (mmt) REVERT: B 585 GLU cc_start: 0.7612 (tp30) cc_final: 0.7274 (tp30) outliers start: 19 outliers final: 17 residues processed: 119 average time/residue: 0.0856 time to fit residues: 15.0354 Evaluate side-chains 113 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 486 SER 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 71 MET 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 486 SER 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: 1.9990 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 70 optimal weight: 0.0050 chunk 108 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3739 r_free = 0.3739 target = 0.151605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119912 restraints weight = 10925.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123075 restraints weight = 6769.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.125035 restraints weight = 5021.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126263 restraints weight = 4190.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126815 restraints weight = 3748.998| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9171 Z= 0.152 Angle : 0.611 10.425 12422 Z= 0.300 Chirality : 0.042 0.149 1432 Planarity : 0.003 0.036 1540 Dihedral : 10.232 144.656 1310 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.16 % Allowed : 15.50 % Favored : 82.34 % 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: 0.95 (0.26), residues: 1128 helix: 1.92 (0.20), residues: 658 sheet: 0.83 (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 0.009 0.001 TYR B 463 PHE 0.011 0.001 PHE B 578 TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9168) covalent geometry : angle 0.60986 (12416) SS BOND : bond 0.00336 ( 3) SS BOND : angle 1.93816 ( 6) hydrogen bonds : bond 0.03505 ( 504) hydrogen bonds : angle 3.84726 ( 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 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.400 Fit side-chains REVERT: A 585 GLU cc_start: 0.7735 (tp30) cc_final: 0.7493 (tp30) REVERT: B 71 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7117 (mmt) REVERT: B 585 GLU cc_start: 0.7639 (tp30) cc_final: 0.7268 (tp30) outliers start: 21 outliers final: 20 residues processed: 113 average time/residue: 0.0830 time to fit residues: 13.9719 Evaluate side-chains 115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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 A residue 532 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 71 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.0870 chunk 92 optimal weight: 0.7980 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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** B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126002 restraints weight = 10826.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129424 restraints weight = 6413.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131616 restraints weight = 4622.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.132618 restraints weight = 3775.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133488 restraints weight = 3380.289| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4169 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= 0.121 Angle : 0.579 8.631 12422 Z= 0.284 Chirality : 0.041 0.150 1432 Planarity : 0.003 0.035 1540 Dihedral : 10.220 144.143 1310 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.85 % Allowed : 15.81 % Favored : 82.34 % 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: 1.11 (0.26), residues: 1128 helix: 2.01 (0.20), residues: 658 sheet: 1.19 (0.65), residues: 62 loop : -1.56 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.011 0.001 TYR B 605 PHE 0.027 0.001 PHE A 293 TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9168) covalent geometry : angle 0.57852 (12416) SS BOND : bond 0.00321 ( 3) SS BOND : angle 1.53925 ( 6) hydrogen bonds : bond 0.03269 ( 504) hydrogen bonds : angle 3.77572 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1471.40 seconds wall clock time: 26 minutes 18.06 seconds (1578.06 seconds total)