Starting phenix.real_space_refine on Sun Dec 29 16:44:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc0_15958/12_2024/8bc0_15958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc0_15958/12_2024/8bc0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bc0_15958/12_2024/8bc0_15958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc0_15958/12_2024/8bc0_15958.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc0_15958/12_2024/8bc0_15958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc0_15958/12_2024/8bc0_15958.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.86, per 1000 atoms: 0.63 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.03 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: 3.60 Time building geometry restraints manager: 3.21 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 87 \ 0 or resid 1001 through 1003)) selection = (chain 'B' and (resid 50 through 587 or resid 591 through 870 or resid 1001 thro \ ugh 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: 0.790 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.200 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- 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 11153 Z= 0.262 Angle : 0.586 9.111 15116 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 : 17.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (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 TRP 0.030 0.002 TRP A 397 HIS 0.004 0.001 HIS A 768 PHE 0.015 0.002 PHE A 73 TYR 0.017 0.002 TYR B 580 ARG 0.004 0.000 ARG B 712 *********************** 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 : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2962 (OUTLIER) cc_final: 0.1539 (t-90) REVERT: A 211 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.3202 (mmp80) REVERT: A 386 MET cc_start: 0.6159 (mmp) cc_final: 0.5912 (mmp) REVERT: A 403 GLU cc_start: 0.7143 (tt0) cc_final: 0.6640 (tp30) REVERT: A 478 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7939 (mtt180) REVERT: A 667 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6512 (mp0) REVERT: A 699 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6565 (mm-30) REVERT: A 701 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6458 (mmt90) REVERT: A 730 GLN cc_start: 0.8495 (mt0) cc_final: 0.8260 (mm-40) REVERT: A 809 TYR cc_start: 0.5893 (p90) cc_final: 0.4419 (t80) REVERT: A 810 ARG cc_start: 0.4234 (OUTLIER) cc_final: 0.3647 (ttp80) REVERT: A 843 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6648 (mt-10) REVERT: B 93 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7336 (tmtt) REVERT: B 205 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.6936 (m-40) REVERT: B 326 LEU cc_start: 0.7149 (mt) cc_final: 0.6800 (mt) REVERT: B 528 TYR cc_start: 0.7572 (m-10) cc_final: 0.7336 (m-10) REVERT: B 573 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: B 611 ILE cc_start: 0.8299 (mt) cc_final: 0.7939 (mt) REVERT: B 619 TRP cc_start: 0.6703 (m100) cc_final: 0.5700 (m100) REVERT: B 701 ARG cc_start: 0.5133 (OUTLIER) cc_final: 0.4873 (mmm160) REVERT: B 774 ASP cc_start: 0.6791 (t0) cc_final: 0.6434 (m-30) outliers start: 83 outliers final: 37 residues processed: 363 average time/residue: 0.2395 time to fit residues: 122.0132 Evaluate side-chains 270 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 110 optimal weight: 0.0170 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 205 ASN A 275 HIS A 674 GLN A 696 ASN A 730 GLN B 99 GLN B 111 GLN B 328 GLN B 351 GLN B 401 GLN B 730 GLN B 779 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11153 Z= 0.210 Angle : 0.624 11.225 15116 Z= 0.330 Chirality : 0.041 0.162 1655 Planarity : 0.005 0.082 1862 Dihedral : 8.672 59.292 1538 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.36 % Allowed : 14.46 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1276 helix: 1.13 (0.17), residues: 822 sheet: -1.09 (0.68), residues: 50 loop : -1.61 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 397 HIS 0.008 0.001 HIS A 768 PHE 0.025 0.002 PHE A 851 TYR 0.022 0.001 TYR B 666 ARG 0.011 0.001 ARG A 219 *********************** 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 323 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 260 time to evaluate : 1.174 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: 0.3268 (OUTLIER) cc_final: 0.2106 (t-90) REVERT: A 211 ARG cc_start: 0.3435 (OUTLIER) cc_final: 0.3032 (mmp-170) REVERT: A 403 GLU cc_start: 0.6966 (tt0) cc_final: 0.6534 (tp30) REVERT: A 540 LEU cc_start: 0.6954 (mt) cc_final: 0.6727 (mt) REVERT: A 604 GLU cc_start: 0.6837 (mp0) cc_final: 0.6596 (mp0) REVERT: A 667 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6401 (mp0) REVERT: A 670 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 773 MET cc_start: 0.7768 (mmm) cc_final: 0.7260 (mmm) REVERT: A 809 TYR cc_start: 0.5638 (p90) cc_final: 0.4184 (t80) REVERT: A 838 PHE cc_start: 0.7848 (t80) cc_final: 0.7597 (t80) REVERT: A 843 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6003 (mt-10) REVERT: B 93 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7315 (tmtt) REVERT: B 204 PHE cc_start: 0.6173 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: B 524 LEU cc_start: 0.9313 (mp) cc_final: 0.9011 (mp) REVERT: B 528 TYR cc_start: 0.7217 (m-10) cc_final: 0.6764 (m-10) REVERT: B 572 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: B 573 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: B 611 ILE cc_start: 0.8127 (mt) cc_final: 0.7803 (mt) REVERT: B 619 TRP cc_start: 0.6704 (m100) cc_final: 0.5676 (m100) REVERT: B 734 ILE cc_start: 0.9115 (mt) cc_final: 0.8736 (pt) REVERT: B 774 ASP cc_start: 0.6693 (t0) cc_final: 0.6286 (m-30) REVERT: B 777 ILE cc_start: 0.6842 (mp) cc_final: 0.6523 (mp) outliers start: 63 outliers final: 37 residues processed: 307 average time/residue: 0.2417 time to fit residues: 104.0752 Evaluate side-chains 254 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 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 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 685 PHE Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 715 VAL 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 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 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 66 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 562 ASN A 632 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 99 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11153 Z= 0.298 Angle : 0.662 11.001 15116 Z= 0.353 Chirality : 0.044 0.345 1655 Planarity : 0.005 0.064 1862 Dihedral : 7.865 59.453 1504 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.61 % Allowed : 15.99 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1276 helix: 0.84 (0.17), residues: 818 sheet: -1.07 (0.69), residues: 51 loop : -1.73 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 397 HIS 0.004 0.001 HIS A 768 PHE 0.027 0.002 PHE A 385 TYR 0.019 0.002 TYR A 77 ARG 0.008 0.001 ARG A 69 *********************** 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 288 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 1.132 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: 0.3179 (OUTLIER) cc_final: 0.1845 (t-90) REVERT: A 211 ARG cc_start: 0.3458 (OUTLIER) cc_final: 0.2761 (mmp80) REVERT: A 403 GLU cc_start: 0.6883 (tt0) cc_final: 0.6378 (tp30) REVERT: A 604 GLU cc_start: 0.6950 (mp0) cc_final: 0.6661 (mp0) REVERT: A 667 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6416 (mp0) REVERT: A 699 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.5120 (tp30) REVERT: A 773 MET cc_start: 0.7802 (mmm) cc_final: 0.7044 (tpp) REVERT: A 809 TYR cc_start: 0.5748 (p90) cc_final: 0.4348 (t80) REVERT: A 836 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7031 (mp) REVERT: A 851 PHE cc_start: 0.7731 (m-80) cc_final: 0.7303 (m-80) REVERT: B 93 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7309 (tmtt) REVERT: B 204 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5959 (m-10) REVERT: B 572 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: B 573 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: B 619 TRP cc_start: 0.6690 (m100) cc_final: 0.5790 (m100) REVERT: B 662 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6829 (pp) REVERT: B 734 ILE cc_start: 0.9089 (mt) cc_final: 0.8825 (pt) REVERT: B 777 ILE cc_start: 0.6791 (mp) cc_final: 0.6378 (mp) REVERT: B 814 ASN cc_start: 0.4900 (OUTLIER) cc_final: 0.1956 (p0) outliers start: 66 outliers final: 39 residues processed: 272 average time/residue: 0.2209 time to fit residues: 86.1725 Evaluate side-chains 248 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 142 MET 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 562 ASN 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 0.0070 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 562 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11153 Z= 0.200 Angle : 0.614 11.143 15116 Z= 0.325 Chirality : 0.041 0.214 1655 Planarity : 0.005 0.056 1862 Dihedral : 7.507 58.355 1495 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.85 % Allowed : 17.94 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1276 helix: 0.99 (0.17), residues: 818 sheet: -0.93 (0.69), residues: 51 loop : -1.70 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 397 HIS 0.004 0.001 HIS A 768 PHE 0.026 0.002 PHE B 382 TYR 0.017 0.001 TYR A 423 ARG 0.010 0.000 ARG A 98 *********************** 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 275 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 1.139 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: 0.2935 (OUTLIER) cc_final: 0.1512 (t-90) REVERT: A 211 ARG cc_start: 0.3212 (OUTLIER) cc_final: 0.2825 (mmp80) REVERT: A 348 MET cc_start: 0.7003 (mmm) cc_final: 0.6645 (mmm) REVERT: A 375 ASP cc_start: 0.3877 (p0) cc_final: 0.3525 (p0) REVERT: A 403 GLU cc_start: 0.6835 (tt0) cc_final: 0.6302 (tp30) REVERT: A 604 GLU cc_start: 0.6884 (mp0) cc_final: 0.6510 (mp0) REVERT: A 667 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6378 (mp0) REVERT: A 670 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 714 MET cc_start: 0.6955 (mmm) cc_final: 0.6513 (mmp) REVERT: A 773 MET cc_start: 0.7723 (mmm) cc_final: 0.7281 (mmm) REVERT: A 809 TYR cc_start: 0.5738 (p90) cc_final: 0.4309 (t80) REVERT: A 836 LEU cc_start: 0.7139 (mp) cc_final: 0.6922 (mp) REVERT: A 851 PHE cc_start: 0.7757 (m-80) cc_final: 0.7499 (m-80) REVERT: B 93 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7304 (tmtt) REVERT: B 204 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5999 (m-10) REVERT: B 381 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6551 (mm) REVERT: B 524 LEU cc_start: 0.9319 (mp) cc_final: 0.9088 (mp) REVERT: B 528 TYR cc_start: 0.7129 (m-10) cc_final: 0.6757 (m-10) REVERT: B 572 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: B 611 ILE cc_start: 0.8288 (mt) cc_final: 0.8004 (mt) REVERT: B 619 TRP cc_start: 0.6568 (m100) cc_final: 0.5641 (m100) REVERT: B 662 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6687 (pp) REVERT: B 734 ILE cc_start: 0.9113 (mt) cc_final: 0.8839 (pt) REVERT: B 777 ILE cc_start: 0.6738 (mp) cc_final: 0.6281 (mp) outliers start: 57 outliers final: 36 residues processed: 261 average time/residue: 0.2169 time to fit residues: 81.8509 Evaluate side-chains 247 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR 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 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 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 0.0040 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11153 Z= 0.225 Angle : 0.615 11.191 15116 Z= 0.327 Chirality : 0.041 0.182 1655 Planarity : 0.005 0.059 1862 Dihedral : 7.411 58.244 1493 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.68 % Allowed : 19.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1276 helix: 0.97 (0.17), residues: 817 sheet: -0.92 (0.70), residues: 51 loop : -1.66 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 397 HIS 0.004 0.001 HIS A 768 PHE 0.020 0.002 PHE A 675 TYR 0.017 0.001 TYR A 477 ARG 0.007 0.000 ARG A 98 *********************** 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 268 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 1.260 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: 0.2948 (OUTLIER) cc_final: 0.1692 (t-90) REVERT: A 348 MET cc_start: 0.6918 (mmm) cc_final: 0.6231 (mmt) REVERT: A 375 ASP cc_start: 0.3827 (p0) cc_final: 0.3387 (p0) REVERT: A 403 GLU cc_start: 0.6916 (tt0) cc_final: 0.6379 (tp30) REVERT: A 604 GLU cc_start: 0.6819 (mp0) cc_final: 0.6436 (mp0) REVERT: A 667 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6278 (mp0) REVERT: A 714 MET cc_start: 0.6904 (mmm) cc_final: 0.6558 (mmp) REVERT: A 773 MET cc_start: 0.7737 (mmm) cc_final: 0.7021 (tpp) REVERT: A 809 TYR cc_start: 0.5775 (p90) cc_final: 0.4373 (t80) REVERT: A 851 PHE cc_start: 0.7803 (m-10) cc_final: 0.7425 (m-80) REVERT: B 93 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7309 (tmtt) REVERT: B 204 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5974 (m-10) REVERT: B 381 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6426 (mm) REVERT: B 386 MET cc_start: 0.6086 (tpp) cc_final: 0.5778 (mmm) REVERT: B 528 TYR cc_start: 0.7492 (m-10) cc_final: 0.7164 (m-10) REVERT: B 611 ILE cc_start: 0.8291 (mt) cc_final: 0.8012 (mt) REVERT: B 619 TRP cc_start: 0.6574 (m100) cc_final: 0.5640 (m100) REVERT: B 662 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6604 (pp) REVERT: B 734 ILE cc_start: 0.9118 (mt) cc_final: 0.8803 (pt) REVERT: B 777 ILE cc_start: 0.6691 (mp) cc_final: 0.6209 (mp) REVERT: B 814 ASN cc_start: 0.4687 (OUTLIER) cc_final: 0.1728 (p0) outliers start: 55 outliers final: 37 residues processed: 252 average time/residue: 0.2180 time to fit residues: 79.3738 Evaluate side-chains 247 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 298 ILE Chi-restraints excluded: chain A residue 376 SER 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 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 0.0970 chunk 105 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11153 Z= 0.228 Angle : 0.634 13.843 15116 Z= 0.335 Chirality : 0.041 0.205 1655 Planarity : 0.005 0.065 1862 Dihedral : 7.155 57.933 1488 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.76 % Allowed : 19.81 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1276 helix: 0.95 (0.17), residues: 818 sheet: -0.89 (0.70), residues: 51 loop : -1.65 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 PHE 0.023 0.002 PHE A 64 TYR 0.017 0.001 TYR A 477 ARG 0.006 0.000 ARG A 98 *********************** 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 263 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 1.255 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: 0.2739 (OUTLIER) cc_final: 0.1441 (t-90) REVERT: A 375 ASP cc_start: 0.3881 (p0) cc_final: 0.3579 (p0) REVERT: A 403 GLU cc_start: 0.6822 (tt0) cc_final: 0.6198 (tp30) REVERT: A 604 GLU cc_start: 0.6841 (mp0) cc_final: 0.6495 (mp0) REVERT: A 667 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6274 (mp0) REVERT: A 773 MET cc_start: 0.7408 (mmm) cc_final: 0.7101 (tpp) REVERT: A 809 TYR cc_start: 0.5752 (p90) cc_final: 0.4358 (t80) REVERT: A 810 ARG cc_start: 0.4075 (OUTLIER) cc_final: 0.3527 (ttp80) REVERT: A 851 PHE cc_start: 0.7812 (m-10) cc_final: 0.7413 (m-80) REVERT: B 93 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7318 (tmtt) REVERT: B 204 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.5949 (m-10) REVERT: B 381 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6421 (mm) REVERT: B 528 TYR cc_start: 0.7459 (m-10) cc_final: 0.7150 (m-10) REVERT: B 611 ILE cc_start: 0.8243 (mt) cc_final: 0.7942 (mt) REVERT: B 619 TRP cc_start: 0.6622 (m100) cc_final: 0.5689 (m100) REVERT: B 662 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6637 (pp) REVERT: B 777 ILE cc_start: 0.6523 (mp) cc_final: 0.6023 (mp) REVERT: B 814 ASN cc_start: 0.4408 (OUTLIER) cc_final: 0.3624 (p0) outliers start: 56 outliers final: 39 residues processed: 248 average time/residue: 0.2097 time to fit residues: 75.9030 Evaluate side-chains 242 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 298 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 464 ILE 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 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN 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 122 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11153 Z= 0.205 Angle : 0.640 13.048 15116 Z= 0.332 Chirality : 0.042 0.236 1655 Planarity : 0.005 0.060 1862 Dihedral : 6.889 58.973 1483 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.34 % Allowed : 21.09 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1276 helix: 0.99 (0.17), residues: 819 sheet: -0.87 (0.70), residues: 51 loop : -1.63 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 PHE 0.025 0.002 PHE B 558 TYR 0.013 0.001 TYR A 828 ARG 0.005 0.000 ARG A 98 *********************** 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 265 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 1.376 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 129 HIS cc_start: 0.2843 (OUTLIER) cc_final: 0.1538 (t-90) REVERT: A 375 ASP cc_start: 0.3777 (p0) cc_final: 0.3493 (p0) REVERT: A 403 GLU cc_start: 0.6829 (tt0) cc_final: 0.6189 (tp30) REVERT: A 604 GLU cc_start: 0.6825 (mp0) cc_final: 0.6463 (mp0) REVERT: A 667 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6334 (mp0) REVERT: A 670 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7386 (mt-10) REVERT: A 809 TYR cc_start: 0.5734 (p90) cc_final: 0.4361 (t80) REVERT: A 832 ILE cc_start: 0.5435 (OUTLIER) cc_final: 0.5210 (tp) REVERT: B 93 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7433 (tmtt) REVERT: B 204 PHE cc_start: 0.6156 (OUTLIER) cc_final: 0.5895 (m-10) REVERT: B 528 TYR cc_start: 0.7524 (m-10) cc_final: 0.7202 (m-10) REVERT: B 544 GLN cc_start: 0.5040 (tp40) cc_final: 0.3832 (mp10) REVERT: B 608 GLN cc_start: 0.7492 (tp-100) cc_final: 0.6755 (tp40) REVERT: B 611 ILE cc_start: 0.8209 (mt) cc_final: 0.7919 (mt) REVERT: B 619 TRP cc_start: 0.6599 (m100) cc_final: 0.5696 (m100) REVERT: B 662 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6655 (pp) REVERT: B 705 TRP cc_start: 0.6326 (t60) cc_final: 0.6110 (t60) REVERT: B 777 ILE cc_start: 0.6481 (mp) cc_final: 0.5950 (mp) outliers start: 51 outliers final: 38 residues processed: 253 average time/residue: 0.2216 time to fit residues: 80.8902 Evaluate side-chains 240 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11153 Z= 0.218 Angle : 0.671 12.237 15116 Z= 0.347 Chirality : 0.042 0.203 1655 Planarity : 0.005 0.066 1862 Dihedral : 6.898 59.158 1483 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.76 % Allowed : 21.34 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1276 helix: 0.95 (0.17), residues: 819 sheet: -0.74 (0.71), residues: 51 loop : -1.69 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 389 HIS 0.003 0.001 HIS A 768 PHE 0.026 0.002 PHE B 382 TYR 0.014 0.001 TYR A 299 ARG 0.004 0.000 ARG A 211 *********************** 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 262 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 1.236 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 129 HIS cc_start: 0.2417 (OUTLIER) cc_final: 0.1149 (t-90) REVERT: A 361 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6130 (mp) REVERT: A 366 GLU cc_start: 0.7707 (tp30) cc_final: 0.7276 (tp30) REVERT: A 382 PHE cc_start: 0.4228 (t80) cc_final: 0.3775 (t80) REVERT: A 385 PHE cc_start: 0.6455 (t80) cc_final: 0.6222 (t80) REVERT: A 403 GLU cc_start: 0.6794 (tt0) cc_final: 0.6276 (tp30) REVERT: A 478 ARG cc_start: 0.8121 (mtt180) cc_final: 0.7099 (mtt-85) REVERT: A 604 GLU cc_start: 0.6833 (mp0) cc_final: 0.6486 (mp0) REVERT: A 667 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6354 (mp0) REVERT: A 670 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 714 MET cc_start: 0.7440 (mmm) cc_final: 0.6963 (mmp) REVERT: A 717 GLU cc_start: 0.4633 (mp0) cc_final: 0.4167 (mp0) REVERT: A 809 TYR cc_start: 0.5721 (p90) cc_final: 0.4362 (t80) REVERT: B 93 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7422 (tmtt) REVERT: B 204 PHE cc_start: 0.6122 (OUTLIER) cc_final: 0.5871 (m-10) REVERT: B 528 TYR cc_start: 0.7746 (m-10) cc_final: 0.7372 (m-10) REVERT: B 544 GLN cc_start: 0.5005 (tp40) cc_final: 0.3825 (mp10) REVERT: B 611 ILE cc_start: 0.8187 (mt) cc_final: 0.7888 (mt) REVERT: B 619 TRP cc_start: 0.6644 (m100) cc_final: 0.5745 (m100) REVERT: B 662 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6630 (pp) REVERT: B 705 TRP cc_start: 0.6346 (t60) cc_final: 0.6116 (t60) REVERT: B 777 ILE cc_start: 0.6477 (mp) cc_final: 0.5969 (mp) REVERT: B 813 ARG cc_start: 0.5143 (mmt90) cc_final: 0.3578 (ptm-80) outliers start: 56 outliers final: 44 residues processed: 251 average time/residue: 0.2258 time to fit residues: 81.6249 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 : 1.179 ------------------------------------------------------------------------------- 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 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU 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 A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 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 413 LEU 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 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.7980 chunk 110 optimal weight: 0.0020 chunk 117 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11153 Z= 0.221 Angle : 0.681 14.741 15116 Z= 0.352 Chirality : 0.043 0.208 1655 Planarity : 0.005 0.065 1862 Dihedral : 6.734 57.663 1481 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.34 % Allowed : 22.11 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1276 helix: 0.97 (0.17), residues: 816 sheet: -0.62 (0.71), residues: 51 loop : -1.71 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 PHE 0.032 0.002 PHE A 385 TYR 0.012 0.001 TYR A 214 ARG 0.004 0.000 ARG A 211 *********************** 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 253 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 1.341 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: 0.2457 (OUTLIER) cc_final: 0.1337 (t-90) REVERT: A 361 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6109 (mp) REVERT: A 382 PHE cc_start: 0.4336 (t80) cc_final: 0.3743 (t80) REVERT: A 403 GLU cc_start: 0.6691 (tt0) cc_final: 0.6136 (tp30) REVERT: A 405 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5787 (mt-10) REVERT: A 478 ARG cc_start: 0.8108 (mtt180) cc_final: 0.7100 (mtt180) REVERT: A 604 GLU cc_start: 0.6824 (mp0) cc_final: 0.6473 (mp0) REVERT: A 667 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6425 (mp0) REVERT: A 670 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7222 (mt-10) REVERT: A 699 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.5166 (tp30) REVERT: A 714 MET cc_start: 0.7404 (mmm) cc_final: 0.6812 (mmp) REVERT: A 809 TYR cc_start: 0.5722 (p90) cc_final: 0.4370 (t80) REVERT: B 93 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7469 (tmtt) REVERT: B 204 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5873 (m-10) REVERT: B 528 TYR cc_start: 0.7764 (m-10) cc_final: 0.7412 (m-10) REVERT: B 544 GLN cc_start: 0.5000 (tp40) cc_final: 0.3825 (mp10) REVERT: B 577 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.5254 (t80) REVERT: B 608 GLN cc_start: 0.7488 (tp-100) cc_final: 0.6670 (tp40) REVERT: B 611 ILE cc_start: 0.8187 (mt) cc_final: 0.7897 (mt) REVERT: B 619 TRP cc_start: 0.6637 (m100) cc_final: 0.5756 (m100) REVERT: B 662 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6597 (pp) REVERT: B 705 TRP cc_start: 0.6317 (t60) cc_final: 0.6102 (t60) REVERT: B 777 ILE cc_start: 0.6468 (mp) cc_final: 0.5942 (mp) REVERT: B 813 ARG cc_start: 0.5142 (mmt90) cc_final: 0.3608 (ptt90) outliers start: 51 outliers final: 41 residues processed: 243 average time/residue: 0.2251 time to fit residues: 78.1466 Evaluate side-chains 242 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU 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 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 392 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 811 ASP 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 75 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11153 Z= 0.213 Angle : 0.685 13.927 15116 Z= 0.353 Chirality : 0.043 0.211 1655 Planarity : 0.005 0.067 1862 Dihedral : 6.635 57.459 1481 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.34 % Allowed : 22.19 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1276 helix: 0.98 (0.17), residues: 816 sheet: -0.54 (0.71), residues: 51 loop : -1.70 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 PHE 0.031 0.002 PHE B 382 TYR 0.019 0.001 TYR A 305 ARG 0.004 0.000 ARG A 400 ********************** 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 257 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 1.064 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 361 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6078 (mp) REVERT: A 403 GLU cc_start: 0.6802 (tt0) cc_final: 0.6254 (tp30) REVERT: A 405 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5792 (mt-10) REVERT: A 478 ARG cc_start: 0.8032 (mtt180) cc_final: 0.6996 (mtt-85) REVERT: A 604 GLU cc_start: 0.6811 (mp0) cc_final: 0.6449 (mp0) REVERT: A 608 GLN cc_start: 0.8250 (tp40) cc_final: 0.8012 (tt0) REVERT: A 667 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6403 (mp0) REVERT: A 699 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.5014 (tp30) REVERT: A 714 MET cc_start: 0.7082 (mmm) cc_final: 0.6594 (mmp) REVERT: A 809 TYR cc_start: 0.5655 (p90) cc_final: 0.4318 (t80) REVERT: B 93 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7477 (tmtt) REVERT: B 204 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5842 (m-10) REVERT: B 528 TYR cc_start: 0.7733 (m-10) cc_final: 0.7377 (m-10) REVERT: B 544 GLN cc_start: 0.4883 (tp40) cc_final: 0.3855 (mp10) REVERT: B 577 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5272 (t80) REVERT: B 608 GLN cc_start: 0.7504 (tp-100) cc_final: 0.6738 (tp40) REVERT: B 611 ILE cc_start: 0.8156 (mt) cc_final: 0.7873 (mt) REVERT: B 619 TRP cc_start: 0.6704 (m100) cc_final: 0.5820 (m100) REVERT: B 662 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6570 (pp) REVERT: B 705 TRP cc_start: 0.6306 (t60) cc_final: 0.5950 (t60) REVERT: B 777 ILE cc_start: 0.6443 (mp) cc_final: 0.5929 (mp) outliers start: 51 outliers final: 44 residues processed: 246 average time/residue: 0.2215 time to fit residues: 78.4379 Evaluate side-chains 250 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 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 296 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 392 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 811 ASP 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 31 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN A 844 HIS ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.224781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.203447 restraints weight = 21290.633| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 2.98 r_work: 0.4501 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11153 Z= 0.281 Angle : 0.718 13.880 15116 Z= 0.375 Chirality : 0.045 0.230 1655 Planarity : 0.006 0.067 1862 Dihedral : 6.651 57.841 1481 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.34 % Allowed : 22.79 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1276 helix: 0.79 (0.17), residues: 820 sheet: 0.70 (0.89), residues: 34 loop : -1.78 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 397 HIS 0.004 0.001 HIS A 768 PHE 0.032 0.002 PHE B 382 TYR 0.017 0.002 TYR B 580 ARG 0.005 0.000 ARG A 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2560.73 seconds wall clock time: 47 minutes 31.31 seconds (2851.31 seconds total)