Starting phenix.real_space_refine on Thu Jul 2 23:41:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bc0_15958/07_2026/8bc0_15958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc0_15958/07_2026/8bc0_15958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bc0_15958/07_2026/8bc0_15958.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bc0_15958/07_2026/8bc0_15958.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bc0_15958/07_2026/8bc0_15958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc0_15958/07_2026/8bc0_15958.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bc0_15958/07_2026/8bc0_15958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc0_15958/07_2026/8bc0_15958.map" } resolution = 3.09 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= -0.001 sd= 0.019 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 71 5.16 5 C 7160 2.51 5 N 1749 2.21 5 O 1875 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10861 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5611 Classifications: {'peptide': 680} Link IDs: {'PTRANS': 30, 'TRANS': 649} Chain breaks: 9 Chain: "B" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5244 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 27, 'TRANS': 608} Chain breaks: 9 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.20, per 1000 atoms: 0.20 Number of scatterers: 10861 At special positions: 0 Unit cell: (75.516, 113.274, 127.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 71 16.00 O 1875 8.00 N 1749 7.00 C 7160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 271.0 milliseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 66.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 328 removed outlier: 3.600A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.945A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.845A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 487 removed outlier: 4.405A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 539 removed outlier: 3.724A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 4.578A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 639 Proline residue: A 628 - end of helix removed outlier: 3.692A pdb=" N ARG A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.566A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.663A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.991A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.528A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.695A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.287A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.864A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'B' and resid 92 through 109 removed outlier: 3.530A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.577A pdb=" N ARG B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.610A pdb=" N SER B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.719A pdb=" N ILE B 279 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 361 through 375 removed outlier: 4.069A pdb=" N LYS B 369 " --> pdb=" O CYS B 365 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.728A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 475 Processing helix chain 'B' and resid 510 through 537 removed outlier: 3.922A pdb=" N ASN B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 543 through 573 removed outlier: 4.923A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.944A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 681 removed outlier: 3.819A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.952A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.654A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.559A pdb=" N ASN B 779 " --> pdb=" O GLY B 775 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.646A pdb=" N PHE B 73 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.393A pdb=" N MET B 348 " --> pdb=" O TRP B 359 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 673 hydrogen bonds defined for protein. 1992 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: 1.59 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3284 1.34 - 1.46: 2919 1.46 - 1.58: 4841 1.58 - 1.70: 1 1.70 - 1.82: 108 Bond restraints: 11153 Sorted by residual: bond pdb=" CA ASP A 375 " pdb=" CB ASP A 375 " ideal model delta sigma weight residual 1.528 1.589 -0.060 2.61e-02 1.47e+03 5.33e+00 bond pdb=" C ASP A 583 " pdb=" O ASP A 583 " ideal model delta sigma weight residual 1.235 1.246 -0.011 4.70e-03 4.53e+04 5.25e+00 bond pdb=" CB VAL B 702 " pdb=" CG1 VAL B 702 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.26e+00 bond pdb=" CG LEU B 836 " pdb=" CD1 LEU B 836 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CA LYS B 835 " pdb=" C LYS B 835 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.35e-02 5.49e+03 1.25e+00 ... (remaining 11148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 14870 1.82 - 3.64: 209 3.64 - 5.47: 25 5.47 - 7.29: 10 7.29 - 9.11: 2 Bond angle restraints: 15116 Sorted by residual: angle pdb=" N ALA B 834 " pdb=" CA ALA B 834 " pdb=" C ALA B 834 " ideal model delta sigma weight residual 111.07 118.18 -7.11 1.07e+00 8.73e-01 4.41e+01 angle pdb=" N LEU B 836 " pdb=" CA LEU B 836 " pdb=" CB LEU B 836 " ideal model delta sigma weight residual 110.30 119.41 -9.11 1.54e+00 4.22e-01 3.50e+01 angle pdb=" N LYS B 835 " pdb=" CA LYS B 835 " pdb=" C LYS B 835 " ideal model delta sigma weight residual 111.82 117.11 -5.29 1.16e+00 7.43e-01 2.08e+01 angle pdb=" N LEU B 836 " pdb=" CA LEU B 836 " pdb=" C LEU B 836 " ideal model delta sigma weight residual 112.23 106.55 5.68 1.26e+00 6.30e-01 2.03e+01 angle pdb=" C LYS B 835 " pdb=" CA LYS B 835 " pdb=" CB LYS B 835 " ideal model delta sigma weight residual 110.67 103.41 7.26 1.92e+00 2.71e-01 1.43e+01 ... (remaining 15111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 5948 16.50 - 33.01: 439 33.01 - 49.51: 129 49.51 - 66.02: 30 66.02 - 82.52: 2 Dihedral angle restraints: 6548 sinusoidal: 2662 harmonic: 3886 Sorted by residual: dihedral pdb=" N LEU B 836 " pdb=" C LEU B 836 " pdb=" CA LEU B 836 " pdb=" CB LEU B 836 " ideal model delta harmonic sigma weight residual 122.80 131.89 -9.09 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA ARG A 712 " pdb=" C ARG A 712 " pdb=" N ARG A 713 " pdb=" CA ARG A 713 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 121.55 -28.55 1 1.00e+01 1.00e-02 1.17e+01 ... (remaining 6545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1404 0.058 - 0.116: 243 0.116 - 0.173: 5 0.173 - 0.231: 1 0.231 - 0.289: 2 Chirality restraints: 1655 Sorted by residual: chirality pdb=" CA ALA B 834 " pdb=" N ALA B 834 " pdb=" C ALA B 834 " pdb=" CB ALA B 834 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LEU B 836 " pdb=" N LEU B 836 " pdb=" C LEU B 836 " pdb=" CB LEU B 836 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA PRO A 752 " pdb=" N PRO A 752 " pdb=" C PRO A 752 " pdb=" CB PRO A 752 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 1652 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 685 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 686 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 686 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 686 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 757 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C TYR B 757 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR B 757 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP B 758 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 246 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A 247 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.032 5.00e-02 4.00e+02 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 181 2.62 - 3.19: 10641 3.19 - 3.76: 18021 3.76 - 4.33: 24202 4.33 - 4.90: 38741 Nonbonded interactions: 91786 Sorted by model distance: nonbonded pdb=" OE2 GLU A 667 " pdb="CA CA A1002 " model vdw 2.052 2.510 nonbonded pdb=" O ILE B 743 " pdb=" OG1 THR B 747 " model vdw 2.127 3.040 nonbonded pdb=" OE2 GLU A 699 " pdb="CA CA A1001 " model vdw 2.195 2.510 nonbonded pdb=" O TYR A 291 " pdb=" NH2 ARG A 713 " model vdw 2.197 3.120 nonbonded pdb=" OD1 ASP A 703 " pdb="CA CA A1002 " model vdw 2.198 2.510 ... (remaining 91781 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 50 through 120 or resid 122 through 414 or resid 451 throu \ gh 475 or resid 509 through 638 or resid 645 through 788 or resid 805 through 10 \ 03)) selection = (chain 'B' and (resid 50 through 587 or resid 591 through 1003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 9.530 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11158 Z= 0.190 Angle : 0.586 9.111 15126 Z= 0.330 Chirality : 0.041 0.289 1655 Planarity : 0.005 0.061 1862 Dihedral : 13.165 82.524 4027 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 7.06 % Allowed : 9.01 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1276 helix: 1.08 (0.18), residues: 810 sheet: -1.10 (0.69), residues: 50 loop : -1.62 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.017 0.002 TYR B 580 PHE 0.015 0.002 PHE A 73 TRP 0.030 0.002 TRP A 397 HIS 0.004 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (11153) covalent geometry : angle 0.58614 / 0.33 (15116) SS BOND : bond 0.00369 / 0.24 ( 5) SS BOND : angle 0.81365 / 0.47 ( 10) hydrogen bonds : bond 0.13727 / 8.80 ( 673) hydrogen bonds : angle 6.38181 / 4.60 ( 1992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 298 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2962 (OUTLIER) cc_final: 0.1539 (t-90) REVERT: A 211 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.3202 (mmp80) REVERT: A 386 MET cc_start: 0.6159 (mmp) cc_final: 0.5912 (mmp) REVERT: A 403 GLU cc_start: 0.7143 (tt0) cc_final: 0.6640 (tp30) REVERT: A 478 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7939 (mtt180) REVERT: A 667 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6512 (mp0) REVERT: A 699 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6565 (mm-30) REVERT: A 701 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6458 (mmt90) REVERT: A 730 GLN cc_start: 0.8495 (mt0) cc_final: 0.8260 (mm-40) REVERT: A 809 TYR cc_start: 0.5893 (p90) cc_final: 0.4418 (t80) REVERT: A 810 ARG cc_start: 0.4234 (OUTLIER) cc_final: 0.3647 (ttp80) REVERT: A 843 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6648 (mt-10) REVERT: B 93 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7336 (tmtt) REVERT: B 205 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.6936 (m-40) REVERT: B 326 LEU cc_start: 0.7149 (mt) cc_final: 0.6800 (mt) REVERT: B 528 TYR cc_start: 0.7572 (m-10) cc_final: 0.7336 (m-10) REVERT: B 573 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: B 611 ILE cc_start: 0.8299 (mt) cc_final: 0.7939 (mt) REVERT: B 619 TRP cc_start: 0.6703 (m100) cc_final: 0.5700 (m100) REVERT: B 701 ARG cc_start: 0.5133 (OUTLIER) cc_final: 0.4873 (mmm160) REVERT: B 774 ASP cc_start: 0.6791 (t0) cc_final: 0.6434 (m-30) outliers start: 83 outliers final: 37 residues processed: 363 average time/residue: 0.0819 time to fit residues: 42.6298 Evaluate side-chains 270 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN A 674 GLN A 696 ASN A 730 GLN B 111 GLN B 328 GLN B 351 GLN B 401 GLN B 710 GLN B 730 GLN B 779 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.225214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.203392 restraints weight = 21629.175| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 3.04 r_work: 0.4490 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11158 Z= 0.180 Angle : 0.645 11.141 15126 Z= 0.343 Chirality : 0.042 0.159 1655 Planarity : 0.006 0.079 1862 Dihedral : 8.784 59.668 1538 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.04 % Allowed : 14.54 % Favored : 79.42 % 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: 0.12 (0.23), residues: 1276 helix: 1.01 (0.17), residues: 822 sheet: -1.21 (0.67), residues: 50 loop : -1.66 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 219 TYR 0.019 0.002 TYR B 666 PHE 0.025 0.002 PHE A 851 TRP 0.025 0.002 TRP A 397 HIS 0.009 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (11153) covalent geometry : angle 0.64157 / 0.34 (15116) SS BOND : bond 0.00565 / 0.39 ( 5) SS BOND : angle 2.78825 / 1.48 ( 10) hydrogen bonds : bond 0.05471 / 3.55 ( 673) hydrogen bonds : angle 5.50578 / 3.94 ( 1992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 247 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.3358 (OUTLIER) cc_final: 0.2218 (t-90) REVERT: A 211 ARG cc_start: 0.3486 (OUTLIER) cc_final: 0.2805 (mmp80) REVERT: A 234 ASN cc_start: 0.6565 (OUTLIER) cc_final: 0.6236 (p0) REVERT: A 403 GLU cc_start: 0.6958 (tt0) cc_final: 0.6548 (tp30) REVERT: A 608 GLN cc_start: 0.8505 (tp40) cc_final: 0.8201 (tp40) REVERT: A 667 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6365 (mp0) REVERT: A 699 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.5459 (tp30) REVERT: A 730 GLN cc_start: 0.8581 (mt0) cc_final: 0.8324 (mm-40) REVERT: A 773 MET cc_start: 0.7874 (mmm) cc_final: 0.7267 (mmm) REVERT: A 809 TYR cc_start: 0.5705 (p90) cc_final: 0.4238 (t80) REVERT: A 843 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6792 (mt-10) REVERT: B 93 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7432 (tmtt) REVERT: B 204 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.6103 (m-10) REVERT: B 528 TYR cc_start: 0.6818 (m-10) cc_final: 0.6615 (m-10) REVERT: B 572 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: B 573 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: B 611 ILE cc_start: 0.8144 (mt) cc_final: 0.7816 (mt) REVERT: B 619 TRP cc_start: 0.6762 (m100) cc_final: 0.5787 (m100) REVERT: B 701 ARG cc_start: 0.5485 (OUTLIER) cc_final: 0.5105 (mmm160) REVERT: B 734 ILE cc_start: 0.9064 (mt) cc_final: 0.8675 (pt) REVERT: B 774 ASP cc_start: 0.6830 (t0) cc_final: 0.6320 (m-30) REVERT: B 777 ILE cc_start: 0.6635 (mp) cc_final: 0.6329 (mp) outliers start: 71 outliers final: 39 residues processed: 298 average time/residue: 0.0854 time to fit residues: 36.6323 Evaluate side-chains 259 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 710 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.225312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.203572 restraints weight = 22066.916| |-----------------------------------------------------------------------------| r_work (start): 0.4612 rms_B_bonded: 3.04 r_work: 0.4501 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11158 Z= 0.164 Angle : 0.633 11.037 15126 Z= 0.334 Chirality : 0.043 0.235 1655 Planarity : 0.005 0.059 1862 Dihedral : 7.976 58.906 1508 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.53 % Allowed : 16.58 % Favored : 77.89 % 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: 0.04 (0.23), residues: 1276 helix: 0.98 (0.17), residues: 813 sheet: -1.04 (0.70), residues: 51 loop : -1.76 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 98 TYR 0.029 0.002 TYR A 423 PHE 0.032 0.002 PHE A 385 TRP 0.023 0.002 TRP A 397 HIS 0.005 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11153) covalent geometry : angle 0.63026 / 0.33 (15116) SS BOND : bond 0.00346 / 0.23 ( 5) SS BOND : angle 2.42251 / 1.28 ( 10) hydrogen bonds : bond 0.05242 / 3.41 ( 673) hydrogen bonds : angle 5.41647 / 3.87 ( 1992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2882 (OUTLIER) cc_final: 0.1623 (t-90) REVERT: A 211 ARG cc_start: 0.3247 (OUTLIER) cc_final: 0.2981 (mmp-170) REVERT: A 400 ARG cc_start: 0.6799 (tpt-90) cc_final: 0.6405 (mmm160) REVERT: A 403 GLU cc_start: 0.6574 (tt0) cc_final: 0.6107 (tp30) REVERT: A 595 GLU cc_start: 0.5319 (mp0) cc_final: 0.3166 (tt0) REVERT: A 604 GLU cc_start: 0.6989 (mp0) cc_final: 0.6725 (pm20) REVERT: A 608 GLN cc_start: 0.8474 (tp40) cc_final: 0.8265 (tp40) REVERT: A 656 LEU cc_start: 0.7396 (mt) cc_final: 0.6635 (mt) REVERT: A 667 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6482 (mp0) REVERT: A 699 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.5353 (tp30) REVERT: A 714 MET cc_start: 0.7492 (tpt) cc_final: 0.7093 (mmp) REVERT: A 730 GLN cc_start: 0.8406 (mt0) cc_final: 0.8187 (mm-40) REVERT: A 843 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6589 (mt-10) REVERT: A 851 PHE cc_start: 0.7887 (m-80) cc_final: 0.7445 (m-80) REVERT: B 93 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7410 (tmtt) REVERT: B 204 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.6397 (m-10) REVERT: B 381 ILE cc_start: 0.6974 (OUTLIER) cc_final: 0.6481 (mm) REVERT: B 396 PHE cc_start: 0.4637 (OUTLIER) cc_final: 0.4261 (m-80) REVERT: B 405 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6200 (mt-10) REVERT: B 524 LEU cc_start: 0.9315 (mp) cc_final: 0.8946 (mp) REVERT: B 528 TYR cc_start: 0.7104 (m-10) cc_final: 0.6666 (m-10) REVERT: B 572 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: B 573 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: B 611 ILE cc_start: 0.8122 (mt) cc_final: 0.7853 (mt) REVERT: B 619 TRP cc_start: 0.6729 (m100) cc_final: 0.5807 (m100) REVERT: B 662 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6645 (pp) REVERT: B 701 ARG cc_start: 0.5509 (OUTLIER) cc_final: 0.5219 (mmm160) REVERT: B 734 ILE cc_start: 0.9009 (mt) cc_final: 0.8770 (pt) REVERT: B 777 ILE cc_start: 0.6595 (mp) cc_final: 0.6239 (mp) outliers start: 65 outliers final: 36 residues processed: 287 average time/residue: 0.0790 time to fit residues: 33.0050 Evaluate side-chains 252 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 10 optimal weight: 0.1980 chunk 105 optimal weight: 0.2980 chunk 125 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 44 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** 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 = 0.4882 r_free = 0.4882 target = 0.227266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.205938 restraints weight = 22188.399| |-----------------------------------------------------------------------------| r_work (start): 0.4637 rms_B_bonded: 3.06 r_work: 0.4527 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11158 Z= 0.140 Angle : 0.610 10.634 15126 Z= 0.321 Chirality : 0.041 0.186 1655 Planarity : 0.005 0.057 1862 Dihedral : 7.689 58.567 1502 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.85 % Allowed : 17.77 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.23), residues: 1276 helix: 1.07 (0.17), residues: 817 sheet: -0.92 (0.71), residues: 51 loop : -1.73 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 98 TYR 0.016 0.001 TYR A 477 PHE 0.031 0.002 PHE B 851 TRP 0.020 0.001 TRP A 397 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (11153) covalent geometry : angle 0.60920 / 0.32 (15116) SS BOND : bond 0.00228 / 0.14 ( 5) SS BOND : angle 1.06307 / 0.57 ( 10) hydrogen bonds : bond 0.04938 / 3.23 ( 673) hydrogen bonds : angle 5.28371 / 3.78 ( 1992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2831 (OUTLIER) cc_final: 0.1478 (t-90) REVERT: A 211 ARG cc_start: 0.3328 (OUTLIER) cc_final: 0.2859 (mmp80) REVERT: A 348 MET cc_start: 0.6726 (mmm) cc_final: 0.6337 (mmm) REVERT: A 403 GLU cc_start: 0.6378 (tt0) cc_final: 0.5864 (tp30) REVERT: A 595 GLU cc_start: 0.5276 (mp0) cc_final: 0.3112 (tt0) REVERT: A 604 GLU cc_start: 0.7080 (mp0) cc_final: 0.6853 (pm20) REVERT: A 608 GLN cc_start: 0.8452 (tp40) cc_final: 0.8217 (tp40) REVERT: A 613 MET cc_start: 0.7680 (mtp) cc_final: 0.7299 (mtp) REVERT: A 667 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6530 (mp0) REVERT: A 730 GLN cc_start: 0.8482 (mt0) cc_final: 0.8256 (mm-40) REVERT: A 773 MET cc_start: 0.7324 (tpp) cc_final: 0.6725 (mmm) REVERT: A 851 PHE cc_start: 0.7852 (m-80) cc_final: 0.7557 (m-80) REVERT: B 93 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7399 (tmtt) REVERT: B 204 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.6428 (m-10) REVERT: B 405 GLU cc_start: 0.6425 (mt-10) cc_final: 0.6213 (mt-10) REVERT: B 528 TYR cc_start: 0.7284 (m-10) cc_final: 0.7004 (m-10) REVERT: B 572 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: B 573 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: B 611 ILE cc_start: 0.8053 (mt) cc_final: 0.7763 (mt) REVERT: B 619 TRP cc_start: 0.6689 (m100) cc_final: 0.5715 (m100) REVERT: B 662 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6481 (pp) REVERT: B 734 ILE cc_start: 0.9057 (mt) cc_final: 0.8725 (pt) REVERT: B 777 ILE cc_start: 0.6523 (mp) cc_final: 0.6144 (mp) REVERT: B 814 ASN cc_start: 0.4321 (OUTLIER) cc_final: 0.3746 (p0) outliers start: 57 outliers final: 38 residues processed: 268 average time/residue: 0.0759 time to fit residues: 29.9444 Evaluate side-chains 246 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** 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 = 0.4863 r_free = 0.4863 target = 0.225002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.203111 restraints weight = 21612.764| |-----------------------------------------------------------------------------| r_work (start): 0.4605 rms_B_bonded: 3.06 r_work: 0.4498 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11158 Z= 0.188 Angle : 0.657 13.879 15126 Z= 0.345 Chirality : 0.043 0.197 1655 Planarity : 0.005 0.062 1862 Dihedral : 7.496 58.817 1495 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.02 % Allowed : 19.05 % Favored : 75.94 % 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: 0.02 (0.23), residues: 1276 helix: 0.94 (0.17), residues: 816 sheet: -0.95 (0.70), residues: 51 loop : -1.72 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 98 TYR 0.018 0.002 TYR A 477 PHE 0.028 0.002 PHE A 385 TRP 0.026 0.002 TRP A 397 HIS 0.004 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (11153) covalent geometry : angle 0.65465 / 0.34 (15116) SS BOND : bond 0.00343 / 0.22 ( 5) SS BOND : angle 2.26740 / 1.23 ( 10) hydrogen bonds : bond 0.05284 / 3.44 ( 673) hydrogen bonds : angle 5.38102 / 3.85 ( 1992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2552 (OUTLIER) cc_final: 0.1284 (t-90) REVERT: A 294 GLU cc_start: 0.3857 (mp0) cc_final: 0.3649 (mp0) REVERT: A 320 CYS cc_start: 0.6244 (m) cc_final: 0.5458 (m) REVERT: A 375 ASP cc_start: 0.4205 (p0) cc_final: 0.3791 (p0) REVERT: A 400 ARG cc_start: 0.6881 (tpt-90) cc_final: 0.6628 (mmm160) REVERT: A 403 GLU cc_start: 0.6632 (tt0) cc_final: 0.6121 (tp30) REVERT: A 595 GLU cc_start: 0.5254 (mp0) cc_final: 0.3109 (tt0) REVERT: A 667 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6398 (mp0) REVERT: A 670 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 699 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.5200 (tp30) REVERT: A 730 GLN cc_start: 0.8485 (mt0) cc_final: 0.8252 (mm-40) REVERT: A 851 PHE cc_start: 0.7967 (m-10) cc_final: 0.7550 (m-80) REVERT: B 93 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7379 (tmtt) REVERT: B 204 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6398 (m-10) REVERT: B 463 TRP cc_start: 0.7125 (m100) cc_final: 0.6857 (m100) REVERT: B 528 TYR cc_start: 0.7258 (m-10) cc_final: 0.6950 (m-10) REVERT: B 572 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: B 573 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: B 611 ILE cc_start: 0.8139 (mt) cc_final: 0.7876 (mt) REVERT: B 619 TRP cc_start: 0.6708 (m100) cc_final: 0.5761 (m100) REVERT: B 662 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6795 (pp) REVERT: B 777 ILE cc_start: 0.6420 (mp) cc_final: 0.6012 (mp) REVERT: B 814 ASN cc_start: 0.4751 (OUTLIER) cc_final: 0.1893 (p0) outliers start: 59 outliers final: 42 residues processed: 259 average time/residue: 0.0893 time to fit residues: 34.2345 Evaluate side-chains 249 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 47 optimal weight: 1.9990 chunk 109 optimal weight: 0.0000 chunk 38 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.227895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.206832 restraints weight = 22046.338| |-----------------------------------------------------------------------------| r_work (start): 0.4645 rms_B_bonded: 3.04 r_work: 0.4534 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11158 Z= 0.141 Angle : 0.612 11.291 15126 Z= 0.321 Chirality : 0.041 0.193 1655 Planarity : 0.005 0.064 1862 Dihedral : 7.200 57.819 1490 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.19 % Allowed : 20.15 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1276 helix: 1.09 (0.17), residues: 817 sheet: -0.89 (0.70), residues: 51 loop : -1.66 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 98 TYR 0.018 0.001 TYR A 299 PHE 0.025 0.001 PHE B 382 TRP 0.024 0.001 TRP A 397 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (11153) covalent geometry : angle 0.61154 / 0.32 (15116) SS BOND : bond 0.00235 / 0.15 ( 5) SS BOND : angle 1.32767 / 0.70 ( 10) hydrogen bonds : bond 0.04926 / 3.24 ( 673) hydrogen bonds : angle 5.25146 / 3.75 ( 1992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2604 (OUTLIER) cc_final: 0.1377 (t-90) REVERT: A 296 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6322 (mm) REVERT: A 348 MET cc_start: 0.6524 (mmm) cc_final: 0.6188 (mmm) REVERT: A 375 ASP cc_start: 0.3828 (p0) cc_final: 0.3414 (p0) REVERT: A 403 GLU cc_start: 0.6651 (tt0) cc_final: 0.6109 (tp30) REVERT: A 478 ARG cc_start: 0.8159 (mtt180) cc_final: 0.6912 (mtt180) REVERT: A 553 MET cc_start: 0.7734 (ttp) cc_final: 0.7416 (tpt) REVERT: A 667 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6550 (mp0) REVERT: A 670 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 699 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.4966 (tp30) REVERT: A 730 GLN cc_start: 0.8499 (mt0) cc_final: 0.8271 (mm-40) REVERT: A 773 MET cc_start: 0.7610 (tpp) cc_final: 0.7221 (mmm) REVERT: B 93 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7448 (tmtt) REVERT: B 204 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6285 (m-10) REVERT: B 528 TYR cc_start: 0.7097 (m-10) cc_final: 0.6795 (m-10) REVERT: B 544 GLN cc_start: 0.5238 (tp40) cc_final: 0.3947 (mp10) REVERT: B 559 GLN cc_start: 0.7961 (mm110) cc_final: 0.7694 (mm-40) REVERT: B 572 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: B 573 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: B 608 GLN cc_start: 0.7540 (tp-100) cc_final: 0.6794 (tp40) REVERT: B 611 ILE cc_start: 0.8005 (mt) cc_final: 0.7735 (mt) REVERT: B 619 TRP cc_start: 0.6733 (m100) cc_final: 0.5782 (m100) REVERT: B 662 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6635 (pp) REVERT: B 777 ILE cc_start: 0.6324 (mp) cc_final: 0.5851 (mp) REVERT: B 842 MET cc_start: 0.7423 (tpp) cc_final: 0.7196 (tpp) outliers start: 61 outliers final: 38 residues processed: 268 average time/residue: 0.0862 time to fit residues: 34.3357 Evaluate side-chains 247 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 201 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 124 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.225423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.204047 restraints weight = 21578.389| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 2.95 r_work: 0.4504 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11158 Z= 0.183 Angle : 0.668 11.918 15126 Z= 0.352 Chirality : 0.043 0.218 1655 Planarity : 0.005 0.063 1862 Dihedral : 7.163 59.647 1488 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.27 % Allowed : 20.66 % Favored : 74.06 % 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: 0.01 (0.23), residues: 1276 helix: 0.92 (0.17), residues: 817 sheet: -0.90 (0.71), residues: 51 loop : -1.71 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 98 TYR 0.015 0.002 TYR A 580 PHE 0.036 0.002 PHE A 558 TRP 0.020 0.002 TRP A 397 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (11153) covalent geometry : angle 0.66456 / 0.35 (15116) SS BOND : bond 0.00680 / 0.48 ( 5) SS BOND : angle 2.76452 / 1.52 ( 10) hydrogen bonds : bond 0.05153 / 3.36 ( 673) hydrogen bonds : angle 5.37236 / 3.82 ( 1992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2489 (OUTLIER) cc_final: 0.1241 (t-90) REVERT: A 348 MET cc_start: 0.6312 (mmm) cc_final: 0.5974 (mmm) REVERT: A 403 GLU cc_start: 0.6676 (tt0) cc_final: 0.6105 (tp30) REVERT: A 478 ARG cc_start: 0.8117 (mtt180) cc_final: 0.6938 (mtt180) REVERT: A 553 MET cc_start: 0.7903 (ttp) cc_final: 0.7479 (tpt) REVERT: A 604 GLU cc_start: 0.7153 (pm20) cc_final: 0.6931 (pm20) REVERT: A 667 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6426 (mp0) REVERT: A 670 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7395 (mt-10) REVERT: A 699 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.5216 (tp30) REVERT: B 93 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7521 (tmtt) REVERT: B 204 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: B 396 PHE cc_start: 0.3863 (OUTLIER) cc_final: 0.3242 (m-80) REVERT: B 528 TYR cc_start: 0.7172 (m-10) cc_final: 0.6809 (m-10) REVERT: B 544 GLN cc_start: 0.5322 (tp40) cc_final: 0.3976 (mp10) REVERT: B 611 ILE cc_start: 0.8068 (mt) cc_final: 0.7780 (mt) REVERT: B 619 TRP cc_start: 0.6738 (m100) cc_final: 0.5792 (m100) REVERT: B 662 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6792 (pp) REVERT: B 777 ILE cc_start: 0.6261 (mp) cc_final: 0.5802 (mp) outliers start: 62 outliers final: 42 residues processed: 252 average time/residue: 0.0841 time to fit residues: 31.0586 Evaluate side-chains 239 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 40 optimal weight: 0.0870 chunk 83 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.227752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.206744 restraints weight = 21664.683| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 3.02 r_work: 0.4534 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11158 Z= 0.144 Angle : 0.642 10.805 15126 Z= 0.338 Chirality : 0.042 0.204 1655 Planarity : 0.005 0.065 1862 Dihedral : 6.936 58.266 1484 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.08 % Allowed : 22.36 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1276 helix: 0.97 (0.17), residues: 820 sheet: -0.72 (0.72), residues: 51 loop : -1.70 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.013 0.001 TYR B 299 PHE 0.030 0.002 PHE A 558 TRP 0.023 0.002 TRP A 397 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (11153) covalent geometry : angle 0.64079 / 0.34 (15116) SS BOND : bond 0.00363 / 0.25 ( 5) SS BOND : angle 1.92539 / 1.02 ( 10) hydrogen bonds : bond 0.04926 / 3.21 ( 673) hydrogen bonds : angle 5.29057 / 3.77 ( 1992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2360 (OUTLIER) cc_final: 0.1263 (t-90) REVERT: A 296 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6193 (mm) REVERT: A 348 MET cc_start: 0.6409 (mmm) cc_final: 0.6153 (mmm) REVERT: A 382 PHE cc_start: 0.4421 (t80) cc_final: 0.4006 (t80) REVERT: A 403 GLU cc_start: 0.6707 (tt0) cc_final: 0.6099 (tp30) REVERT: A 478 ARG cc_start: 0.8206 (mtt180) cc_final: 0.6986 (mtt180) REVERT: A 604 GLU cc_start: 0.7238 (pm20) cc_final: 0.7023 (pm20) REVERT: A 667 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6425 (mp0) REVERT: A 670 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 699 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.4955 (tp30) REVERT: A 773 MET cc_start: 0.7954 (tpp) cc_final: 0.7650 (mmm) REVERT: B 93 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7547 (tmtt) REVERT: B 204 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.6251 (m-10) REVERT: B 528 TYR cc_start: 0.7318 (m-10) cc_final: 0.6932 (m-10) REVERT: B 544 GLN cc_start: 0.5179 (tp40) cc_final: 0.3934 (mp10) REVERT: B 608 GLN cc_start: 0.7558 (tp-100) cc_final: 0.6775 (tp40) REVERT: B 611 ILE cc_start: 0.8004 (mt) cc_final: 0.7739 (mt) REVERT: B 619 TRP cc_start: 0.6727 (m100) cc_final: 0.5809 (m100) REVERT: B 662 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6497 (pp) REVERT: B 777 ILE cc_start: 0.6301 (mp) cc_final: 0.5815 (mp) REVERT: B 813 ARG cc_start: 0.5116 (mmt90) cc_final: 0.3541 (ptm-80) outliers start: 48 outliers final: 39 residues processed: 253 average time/residue: 0.0889 time to fit residues: 32.9858 Evaluate side-chains 238 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 118 optimal weight: 0.0270 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** 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 = 0.4886 r_free = 0.4886 target = 0.227422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.206741 restraints weight = 21439.944| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 2.93 r_work: 0.4534 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11158 Z= 0.149 Angle : 0.655 13.320 15126 Z= 0.342 Chirality : 0.043 0.203 1655 Planarity : 0.005 0.066 1862 Dihedral : 6.852 57.834 1484 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.25 % Allowed : 22.87 % Favored : 72.87 % 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: 0.07 (0.23), residues: 1276 helix: 0.93 (0.17), residues: 821 sheet: -0.55 (0.72), residues: 51 loop : -1.69 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 400 TYR 0.012 0.001 TYR B 299 PHE 0.040 0.002 PHE A 558 TRP 0.021 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (11153) covalent geometry : angle 0.65418 / 0.34 (15116) SS BOND : bond 0.00208 / 0.13 ( 5) SS BOND : angle 1.56107 / 0.81 ( 10) hydrogen bonds : bond 0.04901 / 3.20 ( 673) hydrogen bonds : angle 5.28354 / 3.76 ( 1992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.6408 (mmm) cc_final: 0.6057 (mmm) REVERT: A 403 GLU cc_start: 0.6744 (tt0) cc_final: 0.6152 (tp30) REVERT: A 478 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7015 (mtt-85) REVERT: A 667 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6564 (mp0) REVERT: A 670 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 93 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7530 (tmtt) REVERT: B 204 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.6132 (m-10) REVERT: B 528 TYR cc_start: 0.7298 (m-10) cc_final: 0.6944 (m-10) REVERT: B 544 GLN cc_start: 0.4926 (tp40) cc_final: 0.3861 (mp10) REVERT: B 577 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5088 (t80) REVERT: B 611 ILE cc_start: 0.8033 (mt) cc_final: 0.7781 (mt) REVERT: B 619 TRP cc_start: 0.6714 (m100) cc_final: 0.5784 (m100) REVERT: B 662 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6576 (pp) REVERT: B 777 ILE cc_start: 0.6325 (mp) cc_final: 0.5867 (mp) REVERT: B 813 ARG cc_start: 0.5107 (mmt90) cc_final: 0.3528 (ptt90) outliers start: 50 outliers final: 43 residues processed: 247 average time/residue: 0.0870 time to fit residues: 31.4871 Evaluate side-chains 243 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 86 optimal weight: 0.0670 chunk 64 optimal weight: 0.2980 chunk 67 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** 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 = 0.4884 r_free = 0.4884 target = 0.226794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.206147 restraints weight = 21950.421| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 3.02 r_work: 0.4527 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11158 Z= 0.149 Angle : 0.676 15.132 15126 Z= 0.349 Chirality : 0.043 0.207 1655 Planarity : 0.006 0.068 1862 Dihedral : 6.692 57.655 1482 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.25 % Allowed : 22.87 % Favored : 72.87 % 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: 0.09 (0.23), residues: 1276 helix: 0.95 (0.17), residues: 820 sheet: -0.47 (0.72), residues: 51 loop : -1.70 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 400 TYR 0.017 0.001 TYR A 305 PHE 0.031 0.002 PHE A 558 TRP 0.037 0.002 TRP A 397 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (11153) covalent geometry : angle 0.67531 / 0.35 (15116) SS BOND : bond 0.00199 / 0.12 ( 5) SS BOND : angle 1.37821 / 0.72 ( 10) hydrogen bonds : bond 0.04883 / 3.18 ( 673) hydrogen bonds : angle 5.31159 / 3.77 ( 1992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.6412 (mmm) cc_final: 0.6119 (mmm) REVERT: A 403 GLU cc_start: 0.6582 (tt0) cc_final: 0.6168 (tp30) REVERT: A 478 ARG cc_start: 0.8198 (mtt180) cc_final: 0.6982 (mtt-85) REVERT: A 553 MET cc_start: 0.7650 (ttp) cc_final: 0.7279 (tpt) REVERT: A 633 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7637 (mp) REVERT: A 667 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6514 (mp0) REVERT: A 670 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7129 (mt-10) REVERT: A 699 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.5076 (tp30) REVERT: A 711 PHE cc_start: 0.6947 (m-80) cc_final: 0.6595 (m-80) REVERT: A 773 MET cc_start: 0.8007 (tpp) cc_final: 0.7692 (mmm) REVERT: B 93 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7547 (tmtt) REVERT: B 204 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.6193 (m-10) REVERT: B 528 TYR cc_start: 0.7556 (m-10) cc_final: 0.7165 (m-10) REVERT: B 544 GLN cc_start: 0.5024 (tp40) cc_final: 0.3927 (mp10) REVERT: B 577 PHE cc_start: 0.6143 (OUTLIER) cc_final: 0.5123 (t80) REVERT: B 608 GLN cc_start: 0.7577 (tp-100) cc_final: 0.6765 (tp40) REVERT: B 611 ILE cc_start: 0.8049 (mt) cc_final: 0.7793 (mt) REVERT: B 619 TRP cc_start: 0.6640 (m100) cc_final: 0.5733 (m100) REVERT: B 662 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6501 (pp) REVERT: B 777 ILE cc_start: 0.6303 (mp) cc_final: 0.5875 (mp) REVERT: B 813 ARG cc_start: 0.5220 (mmt90) cc_final: 0.3579 (ptt90) outliers start: 50 outliers final: 41 residues processed: 245 average time/residue: 0.0941 time to fit residues: 33.9573 Evaluate side-chains 245 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** 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 = 0.4870 r_free = 0.4870 target = 0.225301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.204153 restraints weight = 22040.489| |-----------------------------------------------------------------------------| r_work (start): 0.4623 rms_B_bonded: 3.05 r_work: 0.4511 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11158 Z= 0.166 Angle : 0.688 14.213 15126 Z= 0.358 Chirality : 0.044 0.235 1655 Planarity : 0.005 0.067 1862 Dihedral : 6.662 57.911 1481 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.34 % Allowed : 23.47 % Favored : 72.19 % 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: -0.02 (0.23), residues: 1276 helix: 0.87 (0.17), residues: 820 sheet: -0.42 (0.73), residues: 51 loop : -1.74 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 400 TYR 0.020 0.001 TYR A 299 PHE 0.030 0.002 PHE A 558 TRP 0.036 0.002 TRP A 397 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (11153) covalent geometry : angle 0.68765 / 0.36 (15116) SS BOND : bond 0.00251 / 0.16 ( 5) SS BOND : angle 1.27731 / 0.67 ( 10) hydrogen bonds : bond 0.04997 / 3.25 ( 673) hydrogen bonds : angle 5.37136 / 3.80 ( 1992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.77 seconds wall clock time: 40 minutes 10.83 seconds (2410.83 seconds total)