Starting phenix.real_space_refine on Sat Aug 23 08:46:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc0_15958/08_2025/8bc0_15958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc0_15958/08_2025/8bc0_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bc0_15958/08_2025/8bc0_15958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc0_15958/08_2025/8bc0_15958.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bc0_15958/08_2025/8bc0_15958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc0_15958/08_2025/8bc0_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-2.0-5787/lib/python3.9/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: 2.21, 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: 0.91 Conformation dependent library (CDL) restraints added in 286.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.36 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: 1.61 Time building geometry restraints manager: 1.17 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.570 Find NCS groups from input model: 0.150 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 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 aren 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 covalent geometry : bond 0.00404 (11153) covalent geometry : angle 0.58614 (15116) SS BOND : bond 0.00369 ( 5) SS BOND : angle 0.81365 ( 10) hydrogen bonds : bond 0.13727 ( 673) hydrogen bonds : angle 6.38181 ( 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 : 0.308 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: 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: 0.4872 (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: 0.0937 time to fit residues: 48.0054 Evaluate side-chains 271 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.225166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.203286 restraints weight = 21634.847| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 3.06 r_work: 0.4487 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11158 Z= 0.180 Angle : 0.642 11.200 15126 Z= 0.341 Chirality : 0.042 0.167 1655 Planarity : 0.006 0.078 1862 Dihedral : 8.789 59.701 1538 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 6.04 % Allowed : 14.12 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.23), residues: 1276 helix: 1.01 (0.17), residues: 822 sheet: -1.22 (0.67), residues: 50 loop : -1.65 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 219 TYR 0.017 0.002 TYR B 666 PHE 0.026 0.002 PHE A 851 TRP 0.026 0.002 TRP A 397 HIS 0.010 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00393 (11153) covalent geometry : angle 0.63819 (15116) SS BOND : bond 0.00432 ( 5) SS BOND : angle 2.61987 ( 10) hydrogen bonds : bond 0.05491 ( 673) hydrogen bonds : angle 5.49740 ( 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 317 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 246 time to evaluate : 0.371 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: 0.3293 (OUTLIER) cc_final: 0.2161 (t-90) REVERT: A 211 ARG cc_start: 0.3484 (OUTLIER) cc_final: 0.2798 (mmp80) REVERT: A 234 ASN cc_start: 0.6569 (OUTLIER) cc_final: 0.6247 (p0) REVERT: A 403 GLU cc_start: 0.6973 (tt0) cc_final: 0.6571 (tp30) REVERT: A 604 GLU cc_start: 0.7067 (mp0) cc_final: 0.6863 (mp0) REVERT: A 608 GLN cc_start: 0.8524 (tp40) cc_final: 0.8234 (tp40) REVERT: A 667 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6523 (mp0) REVERT: A 730 GLN cc_start: 0.8575 (mt0) cc_final: 0.8364 (mm-40) REVERT: A 773 MET cc_start: 0.7867 (mmm) cc_final: 0.7264 (mmm) REVERT: A 809 TYR cc_start: 0.5707 (p90) cc_final: 0.4288 (t80) REVERT: A 843 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6749 (mt-10) REVERT: B 93 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7418 (tmtt) REVERT: B 204 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.6078 (m-10) REVERT: B 528 TYR cc_start: 0.6981 (m-10) cc_final: 0.6757 (m-10) REVERT: B 572 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6842 (m-80) REVERT: B 573 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: B 611 ILE cc_start: 0.8137 (mt) cc_final: 0.7816 (mt) REVERT: B 619 TRP cc_start: 0.6812 (m100) cc_final: 0.5847 (m100) REVERT: B 701 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.5060 (mmm160) REVERT: B 734 ILE cc_start: 0.9061 (mt) cc_final: 0.8693 (pt) REVERT: B 774 ASP cc_start: 0.6828 (t0) cc_final: 0.6341 (m-30) REVERT: B 777 ILE cc_start: 0.6635 (mp) cc_final: 0.6311 (mp) outliers start: 71 outliers final: 41 residues processed: 297 average time/residue: 0.0916 time to fit residues: 38.6998 Evaluate side-chains 263 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 127 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 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: 4.9990 chunk 46 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 562 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 = 0.4848 r_free = 0.4848 target = 0.223608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.201466 restraints weight = 22159.091| |-----------------------------------------------------------------------------| r_work (start): 0.4587 rms_B_bonded: 3.05 r_work: 0.4473 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11158 Z= 0.193 Angle : 0.653 11.154 15126 Z= 0.347 Chirality : 0.043 0.213 1655 Planarity : 0.005 0.062 1862 Dihedral : 8.150 59.170 1512 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.87 % Allowed : 16.16 % Favored : 77.98 % 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 aren not related in a simple way. whole: -0.08 (0.23), residues: 1276 helix: 0.88 (0.17), residues: 814 sheet: -1.14 (0.68), residues: 51 loop : -1.77 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.023 0.002 TYR A 423 PHE 0.032 0.002 PHE A 385 TRP 0.025 0.002 TRP A 397 HIS 0.005 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00431 (11153) covalent geometry : angle 0.65002 (15116) SS BOND : bond 0.00246 ( 5) SS BOND : angle 2.67215 ( 10) hydrogen bonds : bond 0.05434 ( 673) hydrogen bonds : angle 5.49177 ( 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 300 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 0.417 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: A 129 HIS cc_start: 0.2966 (OUTLIER) cc_final: 0.1809 (t-90) REVERT: A 211 ARG cc_start: 0.3294 (OUTLIER) cc_final: 0.2611 (mmp80) REVERT: A 403 GLU cc_start: 0.6813 (tt0) cc_final: 0.6276 (tp30) REVERT: A 595 GLU cc_start: 0.5382 (mp0) cc_final: 0.3209 (tt0) REVERT: A 604 GLU cc_start: 0.6952 (mp0) cc_final: 0.6703 (mp0) REVERT: A 608 GLN cc_start: 0.8518 (tp40) cc_final: 0.8298 (tp40) REVERT: A 667 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6527 (mp0) REVERT: A 714 MET cc_start: 0.7389 (tpt) cc_final: 0.6950 (mmp) REVERT: A 730 GLN cc_start: 0.8426 (mt0) cc_final: 0.8211 (mm-40) REVERT: A 773 MET cc_start: 0.7851 (mmm) cc_final: 0.6785 (tpp) REVERT: A 836 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6823 (mp) REVERT: A 843 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6802 (mt-10) REVERT: A 851 PHE cc_start: 0.7833 (m-80) cc_final: 0.7478 (m-80) REVERT: B 93 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7411 (tmtt) REVERT: B 204 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.6282 (m-10) REVERT: B 405 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6212 (mt-10) REVERT: B 524 LEU cc_start: 0.9321 (mp) cc_final: 0.9069 (mp) REVERT: B 528 TYR cc_start: 0.7112 (m-10) cc_final: 0.6804 (m-10) REVERT: B 572 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6799 (m-80) REVERT: B 573 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: B 619 TRP cc_start: 0.6771 (m100) cc_final: 0.5832 (m100) REVERT: B 662 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6841 (pp) REVERT: B 701 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.5118 (mmm160) REVERT: B 734 ILE cc_start: 0.9014 (mt) cc_final: 0.8772 (pt) REVERT: B 777 ILE cc_start: 0.6654 (mp) cc_final: 0.6280 (mp) outliers start: 69 outliers final: 42 residues processed: 281 average time/residue: 0.0877 time to fit residues: 35.4821 Evaluate side-chains 261 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL 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 765 TYR 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 836 LEU 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 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 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: 3.9990 chunk 105 optimal weight: 0.0370 chunk 125 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 632 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.225812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.204061 restraints weight = 22129.894| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 3.06 r_work: 0.4505 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.2890 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= 0.149 Angle : 0.619 10.974 15126 Z= 0.327 Chirality : 0.041 0.190 1655 Planarity : 0.005 0.060 1862 Dihedral : 7.772 58.202 1504 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.93 % Allowed : 18.11 % Favored : 76.96 % 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 aren not related in a simple way. whole: 0.07 (0.23), residues: 1276 helix: 1.00 (0.17), residues: 816 sheet: -0.96 (0.71), residues: 51 loop : -1.75 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 542 TYR 0.016 0.001 TYR A 477 PHE 0.030 0.002 PHE A 385 TRP 0.022 0.001 TRP A 397 HIS 0.004 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00320 (11153) covalent geometry : angle 0.61865 (15116) SS BOND : bond 0.00301 ( 5) SS BOND : angle 1.06091 ( 10) hydrogen bonds : bond 0.05051 ( 673) hydrogen bonds : angle 5.34175 ( 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 283 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 225 time to evaluate : 0.348 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: 0.2869 (OUTLIER) cc_final: 0.1485 (t-90) REVERT: A 211 ARG cc_start: 0.3456 (OUTLIER) cc_final: 0.2977 (mmp-170) REVERT: A 403 GLU cc_start: 0.6310 (tt0) cc_final: 0.5872 (tp30) REVERT: A 595 GLU cc_start: 0.5376 (mp0) cc_final: 0.3249 (tt0) REVERT: A 604 GLU cc_start: 0.6964 (mp0) cc_final: 0.6660 (mp0) REVERT: A 608 GLN cc_start: 0.8505 (tp40) cc_final: 0.8276 (tp40) REVERT: A 613 MET cc_start: 0.7668 (mtp) cc_final: 0.7292 (mtp) REVERT: A 667 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6503 (mp0) REVERT: A 670 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7203 (mt-10) REVERT: A 730 GLN cc_start: 0.8483 (mt0) cc_final: 0.8250 (mm-40) REVERT: A 773 MET cc_start: 0.7832 (mmm) cc_final: 0.7169 (mmm) REVERT: A 836 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6881 (mp) REVERT: A 851 PHE cc_start: 0.7895 (m-80) cc_final: 0.7581 (m-80) REVERT: B 93 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7389 (tmtt) REVERT: B 204 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6433 (m-10) REVERT: B 405 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6218 (mt-10) REVERT: B 524 LEU cc_start: 0.9370 (mp) cc_final: 0.8996 (mp) REVERT: B 528 TYR cc_start: 0.7098 (m-10) cc_final: 0.6626 (m-10) REVERT: B 572 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: B 573 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: B 608 GLN cc_start: 0.7535 (tp-100) cc_final: 0.6833 (tp40) REVERT: B 611 ILE cc_start: 0.8269 (mt) cc_final: 0.8023 (mt) REVERT: B 619 TRP cc_start: 0.6632 (m100) cc_final: 0.5670 (m100) REVERT: B 662 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6765 (pp) REVERT: B 734 ILE cc_start: 0.9050 (mt) cc_final: 0.8819 (pt) REVERT: B 777 ILE cc_start: 0.6603 (mp) cc_final: 0.6218 (mp) REVERT: B 814 ASN cc_start: 0.4576 (OUTLIER) cc_final: 0.1743 (p0) REVERT: B 842 MET cc_start: 0.7356 (tpp) cc_final: 0.7073 (tpp) outliers start: 58 outliers final: 37 residues processed: 269 average time/residue: 0.0806 time to fit residues: 31.7263 Evaluate side-chains 254 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 366 GLU 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 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU 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 836 LEU 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 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 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 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: 5.9990 chunk 46 optimal weight: 0.0060 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** 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 = 0.4859 r_free = 0.4859 target = 0.224396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.202513 restraints weight = 21696.174| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 3.04 r_work: 0.4490 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11158 Z= 0.184 Angle : 0.649 11.135 15126 Z= 0.344 Chirality : 0.042 0.195 1655 Planarity : 0.005 0.064 1862 Dihedral : 7.641 58.311 1497 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.61 % Allowed : 18.11 % Favored : 76.28 % 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 aren not related in a simple way. whole: -0.04 (0.23), residues: 1276 helix: 0.91 (0.17), residues: 816 sheet: -1.07 (0.71), residues: 51 loop : -1.76 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 649 TYR 0.019 0.002 TYR A 569 PHE 0.032 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 covalent geometry : bond 0.00410 (11153) covalent geometry : angle 0.64526 (15116) SS BOND : bond 0.00284 ( 5) SS BOND : angle 2.61041 ( 10) hydrogen bonds : bond 0.05250 ( 673) hydrogen bonds : angle 5.40600 ( 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 278 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 212 time to evaluate : 0.343 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: 0.2680 (OUTLIER) cc_final: 0.1426 (t-90) REVERT: A 294 GLU cc_start: 0.3841 (mp0) cc_final: 0.3560 (mp0) REVERT: A 403 GLU cc_start: 0.6884 (tt0) cc_final: 0.6284 (tp30) REVERT: A 604 GLU cc_start: 0.7021 (mp0) cc_final: 0.6677 (mp0) REVERT: A 667 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6444 (mp0) REVERT: A 730 GLN cc_start: 0.8460 (mt0) cc_final: 0.8217 (mm-40) REVERT: A 773 MET cc_start: 0.7868 (mmm) cc_final: 0.7058 (tpp) REVERT: A 836 LEU cc_start: 0.7124 (mp) cc_final: 0.6859 (mp) REVERT: A 851 PHE cc_start: 0.7959 (m-10) cc_final: 0.7532 (m-80) REVERT: B 93 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7409 (tmtt) REVERT: B 204 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6388 (m-10) REVERT: B 463 TRP cc_start: 0.6769 (m100) cc_final: 0.6527 (m100) REVERT: B 572 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: B 573 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: B 611 ILE cc_start: 0.8283 (mt) cc_final: 0.8003 (mt) REVERT: B 619 TRP cc_start: 0.6697 (m100) cc_final: 0.5734 (m100) REVERT: B 662 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6866 (pp) REVERT: B 777 ILE cc_start: 0.6446 (mp) cc_final: 0.6017 (mp) REVERT: B 814 ASN cc_start: 0.4288 (OUTLIER) cc_final: 0.1454 (p0) outliers start: 66 outliers final: 45 residues processed: 261 average time/residue: 0.0873 time to fit residues: 33.5167 Evaluate side-chains 254 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 401 GLN Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 562 ASN 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 699 GLU Chi-restraints excluded: chain A residue 765 TYR 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 379 THR 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 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 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: 3.9990 chunk 109 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 814 ASN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.225425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.203849 restraints weight = 21865.449| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 3.04 r_work: 0.4505 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11158 Z= 0.161 Angle : 0.621 10.713 15126 Z= 0.330 Chirality : 0.042 0.201 1655 Planarity : 0.005 0.065 1862 Dihedral : 7.387 58.969 1492 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.36 % Allowed : 19.13 % Favored : 75.51 % 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 aren not related in a simple way. whole: -0.03 (0.23), residues: 1276 helix: 0.91 (0.17), residues: 817 sheet: -1.10 (0.70), residues: 51 loop : -1.75 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 649 TYR 0.020 0.002 TYR A 299 PHE 0.035 0.002 PHE A 385 TRP 0.026 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00351 (11153) covalent geometry : angle 0.62031 (15116) SS BOND : bond 0.00246 ( 5) SS BOND : angle 1.41613 ( 10) hydrogen bonds : bond 0.05111 ( 673) hydrogen bonds : angle 5.33942 ( 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 275 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 212 time to evaluate : 0.270 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: 0.2422 (OUTLIER) cc_final: 0.1189 (t-90) REVERT: A 296 ILE cc_start: 0.6634 (OUTLIER) cc_final: 0.6427 (mm) REVERT: A 320 CYS cc_start: 0.6112 (m) cc_final: 0.5788 (m) REVERT: A 403 GLU cc_start: 0.6720 (tt0) cc_final: 0.6056 (tp30) REVERT: A 478 ARG cc_start: 0.8208 (mtt180) cc_final: 0.6932 (mtt180) REVERT: A 604 GLU cc_start: 0.7004 (mp0) cc_final: 0.6651 (mp0) REVERT: A 667 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6415 (mp0) REVERT: A 670 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 699 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.5434 (tp30) REVERT: A 714 MET cc_start: 0.7019 (mmm) cc_final: 0.6666 (mmp) REVERT: A 730 GLN cc_start: 0.8467 (mt0) cc_final: 0.8221 (mm-40) REVERT: A 773 MET cc_start: 0.7528 (mmm) cc_final: 0.7114 (tpp) REVERT: A 836 LEU cc_start: 0.7078 (mp) cc_final: 0.6821 (mp) REVERT: A 851 PHE cc_start: 0.7974 (m-10) cc_final: 0.7519 (m-80) REVERT: B 93 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7393 (tmtt) REVERT: B 204 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.6302 (m-10) REVERT: B 381 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6406 (mm) REVERT: B 396 PHE cc_start: 0.4355 (OUTLIER) cc_final: 0.3291 (m-80) REVERT: B 524 LEU cc_start: 0.9356 (mp) cc_final: 0.9148 (mp) REVERT: B 528 TYR cc_start: 0.7188 (m-10) cc_final: 0.6888 (m-10) REVERT: B 572 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: B 573 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: B 608 GLN cc_start: 0.7431 (tp-100) cc_final: 0.6724 (tp40) REVERT: B 611 ILE cc_start: 0.8270 (mt) cc_final: 0.8008 (mt) REVERT: B 619 TRP cc_start: 0.6713 (m100) cc_final: 0.5752 (m100) REVERT: B 662 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6791 (pp) REVERT: B 777 ILE cc_start: 0.6279 (mp) cc_final: 0.5799 (mp) outliers start: 63 outliers final: 44 residues processed: 264 average time/residue: 0.0803 time to fit residues: 31.5372 Evaluate side-chains 250 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 196 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 379 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 562 ASN 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 765 TYR 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 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 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 PHE 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 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 755 VAL Chi-restraints excluded: chain B residue 771 TYR 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: 10.0000 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 559 GLN ** 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 = 0.4865 r_free = 0.4865 target = 0.225332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.203947 restraints weight = 21820.039| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 3.01 r_work: 0.4509 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11158 Z= 0.159 Angle : 0.641 14.621 15126 Z= 0.335 Chirality : 0.042 0.209 1655 Planarity : 0.005 0.067 1862 Dihedral : 7.347 59.125 1491 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.27 % Allowed : 19.64 % Favored : 75.09 % 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 aren not related in a simple way. whole: -0.02 (0.23), residues: 1276 helix: 0.92 (0.17), residues: 818 sheet: -1.07 (0.71), residues: 51 loop : -1.77 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 400 TYR 0.014 0.001 TYR A 828 PHE 0.033 0.002 PHE A 385 TRP 0.024 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00350 (11153) covalent geometry : angle 0.63713 (15116) SS BOND : bond 0.00226 ( 5) SS BOND : angle 2.85830 ( 10) hydrogen bonds : bond 0.05066 ( 673) hydrogen bonds : angle 5.30475 ( 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 277 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 0.267 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: 0.2372 (OUTLIER) cc_final: 0.1260 (t-90) REVERT: A 296 ILE cc_start: 0.6572 (OUTLIER) cc_final: 0.6329 (mm) REVERT: A 320 CYS cc_start: 0.5997 (m) cc_final: 0.5731 (m) REVERT: A 375 ASP cc_start: 0.4098 (p0) cc_final: 0.3750 (p0) REVERT: A 403 GLU cc_start: 0.6744 (tt0) cc_final: 0.6071 (tp30) REVERT: A 478 ARG cc_start: 0.8115 (mtt180) cc_final: 0.6899 (mtt180) REVERT: A 604 GLU cc_start: 0.7022 (mp0) cc_final: 0.6658 (mp0) REVERT: A 667 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6340 (mp0) REVERT: A 670 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7134 (mt-10) REVERT: A 699 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.5344 (tp30) REVERT: A 714 MET cc_start: 0.6973 (mmm) cc_final: 0.6641 (mmp) REVERT: A 717 GLU cc_start: 0.4887 (mp0) cc_final: 0.4312 (mp0) REVERT: A 730 GLN cc_start: 0.8487 (mt0) cc_final: 0.8265 (mm-40) REVERT: A 773 MET cc_start: 0.7499 (mmm) cc_final: 0.7164 (tpp) REVERT: A 836 LEU cc_start: 0.7117 (mp) cc_final: 0.6819 (mp) REVERT: B 93 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7501 (tmtt) REVERT: B 204 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.6340 (m-10) REVERT: B 381 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6386 (mm) REVERT: B 528 TYR cc_start: 0.7400 (m-10) cc_final: 0.7146 (m-10) REVERT: B 572 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: B 573 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: B 611 ILE cc_start: 0.8248 (mt) cc_final: 0.7970 (mt) REVERT: B 619 TRP cc_start: 0.6756 (m100) cc_final: 0.5789 (m100) REVERT: B 662 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6738 (pp) REVERT: B 777 ILE cc_start: 0.6259 (mp) cc_final: 0.5772 (mp) REVERT: B 786 ILE cc_start: 0.3857 (OUTLIER) cc_final: 0.3291 (mm) outliers start: 62 outliers final: 45 residues processed: 266 average time/residue: 0.0850 time to fit residues: 33.4453 Evaluate side-chains 258 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 379 THR 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 562 ASN 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 668 TYR 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 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 381 ILE 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 712 ARG Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 786 ILE 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: 0.0030 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 83 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.227221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.206124 restraints weight = 21764.942| |-----------------------------------------------------------------------------| r_work (start): 0.4638 rms_B_bonded: 3.02 r_work: 0.4525 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11158 Z= 0.140 Angle : 0.632 12.784 15126 Z= 0.331 Chirality : 0.042 0.205 1655 Planarity : 0.005 0.068 1862 Dihedral : 7.265 57.897 1491 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.76 % Allowed : 21.17 % 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 aren not related in a simple way. whole: 0.04 (0.23), residues: 1276 helix: 0.95 (0.17), residues: 818 sheet: -0.95 (0.72), residues: 51 loop : -1.72 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.014 0.001 TYR A 828 PHE 0.033 0.002 PHE A 385 TRP 0.023 0.001 TRP A 397 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00298 (11153) covalent geometry : angle 0.63030 (15116) SS BOND : bond 0.00232 ( 5) SS BOND : angle 1.87461 ( 10) hydrogen bonds : bond 0.04888 ( 673) hydrogen bonds : angle 5.25408 ( 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 275 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.290 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: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2303 (OUTLIER) cc_final: 0.1306 (t-90) REVERT: A 296 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6254 (mm) REVERT: A 320 CYS cc_start: 0.5518 (m) cc_final: 0.5289 (m) REVERT: A 348 MET cc_start: 0.6723 (mmm) cc_final: 0.6493 (mmp) REVERT: A 375 ASP cc_start: 0.3771 (p0) cc_final: 0.3533 (p0) REVERT: A 403 GLU cc_start: 0.6873 (tt0) cc_final: 0.6306 (tp30) REVERT: A 478 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7048 (mtt-85) REVERT: A 553 MET cc_start: 0.7758 (ttp) cc_final: 0.7433 (tpt) REVERT: A 604 GLU cc_start: 0.6953 (mp0) cc_final: 0.6627 (mp0) REVERT: A 667 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6457 (mp0) REVERT: A 714 MET cc_start: 0.6905 (mmm) cc_final: 0.6597 (mmp) REVERT: A 836 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6827 (mp) REVERT: B 93 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7511 (tmtt) REVERT: B 204 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.6305 (m-10) REVERT: B 528 TYR cc_start: 0.7344 (m-10) cc_final: 0.7018 (m-10) REVERT: B 544 GLN cc_start: 0.5312 (tp40) cc_final: 0.3993 (mp10) REVERT: B 608 GLN cc_start: 0.7578 (tp-100) cc_final: 0.6828 (tp40) REVERT: B 611 ILE cc_start: 0.8194 (mt) cc_final: 0.7938 (mt) REVERT: B 619 TRP cc_start: 0.6730 (m100) cc_final: 0.5799 (m100) REVERT: B 662 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6632 (pp) REVERT: B 777 ILE cc_start: 0.6340 (mp) cc_final: 0.5867 (mp) outliers start: 56 outliers final: 43 residues processed: 266 average time/residue: 0.0850 time to fit residues: 32.8730 Evaluate side-chains 246 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 597 ASP 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 682 VAL 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 A residue 836 LEU 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 464 ILE Chi-restraints excluded: chain B residue 529 GLU 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 712 ARG Chi-restraints excluded: chain B residue 755 VAL 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: 0.6980 chunk 50 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 118 optimal weight: 0.0060 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.226735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.206098 restraints weight = 21505.547| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 3.00 r_work: 0.4531 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.3730 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= 0.146 Angle : 0.656 12.862 15126 Z= 0.340 Chirality : 0.042 0.209 1655 Planarity : 0.005 0.069 1862 Dihedral : 7.063 57.456 1487 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.34 % Allowed : 21.51 % Favored : 74.15 % 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 aren not related in a simple way. whole: 0.08 (0.23), residues: 1276 helix: 0.98 (0.17), residues: 819 sheet: -0.73 (0.72), residues: 51 loop : -1.72 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 400 TYR 0.012 0.001 TYR B 299 PHE 0.033 0.002 PHE B 382 TRP 0.022 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00316 (11153) covalent geometry : angle 0.65539 (15116) SS BOND : bond 0.00206 ( 5) SS BOND : angle 1.51109 ( 10) hydrogen bonds : bond 0.04880 ( 673) hydrogen bonds : angle 5.28173 ( 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 259 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.318 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 320 CYS cc_start: 0.5508 (m) cc_final: 0.4904 (m) REVERT: A 403 GLU cc_start: 0.6736 (tt0) cc_final: 0.6121 (tp30) REVERT: A 478 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7015 (mtt-85) REVERT: A 553 MET cc_start: 0.7806 (ttp) cc_final: 0.7420 (tpt) REVERT: A 597 ASP cc_start: 0.6126 (OUTLIER) cc_final: 0.4051 (p0) REVERT: A 604 GLU cc_start: 0.7025 (mp0) cc_final: 0.6365 (mp0) REVERT: A 667 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6511 (mp0) REVERT: A 699 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.4961 (tp30) REVERT: A 714 MET cc_start: 0.6905 (mmm) cc_final: 0.6667 (mmp) REVERT: B 93 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7537 (tmtt) REVERT: B 204 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.6179 (m-10) REVERT: B 528 TYR cc_start: 0.7391 (m-10) cc_final: 0.7078 (m-10) REVERT: B 608 GLN cc_start: 0.7560 (tp-100) cc_final: 0.6846 (tp40) REVERT: B 611 ILE cc_start: 0.8174 (mt) cc_final: 0.7919 (mt) REVERT: B 619 TRP cc_start: 0.6707 (m100) cc_final: 0.5787 (m100) REVERT: B 662 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6677 (pp) REVERT: B 813 ARG cc_start: 0.5108 (mmt90) cc_final: 0.3497 (ptt90) outliers start: 51 outliers final: 44 residues processed: 251 average time/residue: 0.0828 time to fit residues: 30.6789 Evaluate side-chains 253 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 379 THR 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 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 618 ILE 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 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 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 529 GLU 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 712 ARG Chi-restraints excluded: chain B residue 755 VAL 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: 5.9990 chunk 64 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4877 r_free = 0.4877 target = 0.226285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.205097 restraints weight = 21860.092| |-----------------------------------------------------------------------------| r_work (start): 0.4627 rms_B_bonded: 3.03 r_work: 0.4518 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.3788 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= 0.157 Angle : 0.680 14.670 15126 Z= 0.350 Chirality : 0.043 0.217 1655 Planarity : 0.005 0.069 1862 Dihedral : 6.942 57.497 1485 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.25 % Allowed : 22.02 % Favored : 73.72 % 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 aren not related in a simple way. whole: 0.06 (0.23), residues: 1276 helix: 0.95 (0.17), residues: 820 sheet: -0.64 (0.71), residues: 51 loop : -1.72 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 400 TYR 0.012 0.001 TYR B 580 PHE 0.034 0.002 PHE B 382 TRP 0.021 0.001 TRP A 397 HIS 0.004 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00346 (11153) covalent geometry : angle 0.67882 (15116) SS BOND : bond 0.00226 ( 5) SS BOND : angle 1.40037 ( 10) hydrogen bonds : bond 0.04970 ( 673) hydrogen bonds : angle 5.34500 ( 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 258 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.279 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: symmetry clash REVERT: A 320 CYS cc_start: 0.5776 (m) cc_final: 0.5454 (m) REVERT: A 403 GLU cc_start: 0.6724 (tt0) cc_final: 0.6152 (tp30) REVERT: A 478 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7039 (mtt-85) REVERT: A 553 MET cc_start: 0.7820 (ttp) cc_final: 0.7444 (tpt) REVERT: A 597 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.4067 (p0) REVERT: A 604 GLU cc_start: 0.7026 (mp0) cc_final: 0.6362 (mp0) REVERT: A 667 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6546 (mp0) REVERT: A 699 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.5269 (tp30) REVERT: A 714 MET cc_start: 0.6914 (mmm) cc_final: 0.6686 (mmp) REVERT: B 93 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7545 (tmtt) REVERT: B 204 PHE cc_start: 0.6418 (OUTLIER) cc_final: 0.6161 (m-10) REVERT: B 528 TYR cc_start: 0.7713 (m-10) cc_final: 0.7340 (m-10) REVERT: B 608 GLN cc_start: 0.7406 (tp-100) cc_final: 0.6712 (tp40) REVERT: B 611 ILE cc_start: 0.8133 (mt) cc_final: 0.7864 (mt) REVERT: B 619 TRP cc_start: 0.6713 (m100) cc_final: 0.5803 (m100) REVERT: B 662 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6696 (pp) REVERT: B 777 ILE cc_start: 0.6348 (mp) cc_final: 0.5867 (mp) outliers start: 50 outliers final: 44 residues processed: 251 average time/residue: 0.0839 time to fit residues: 30.8438 Evaluate side-chains 250 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 379 THR 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 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 618 ILE 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 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 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 529 GLU 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 712 ARG Chi-restraints excluded: chain B residue 755 VAL 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: 0.5980 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 77 optimal weight: 0.0980 chunk 116 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.226761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.205731 restraints weight = 21898.870| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 3.03 r_work: 0.4526 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11158 Z= 0.152 Angle : 0.689 14.062 15126 Z= 0.352 Chirality : 0.043 0.215 1655 Planarity : 0.005 0.068 1862 Dihedral : 6.825 57.229 1485 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.08 % Allowed : 22.79 % Favored : 73.13 % 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 aren not related in a simple way. whole: 0.06 (0.23), residues: 1276 helix: 0.94 (0.17), residues: 821 sheet: -0.56 (0.71), residues: 51 loop : -1.74 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 400 TYR 0.019 0.001 TYR A 305 PHE 0.031 0.002 PHE B 382 TRP 0.019 0.001 TRP A 397 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00333 (11153) covalent geometry : angle 0.68864 (15116) SS BOND : bond 0.00210 ( 5) SS BOND : angle 1.28069 ( 10) hydrogen bonds : bond 0.04879 ( 673) hydrogen bonds : angle 5.34588 ( 1992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2440.34 seconds wall clock time: 42 minutes 38.71 seconds (2558.71 seconds total)