Starting phenix.real_space_refine on Wed May 14 12:20:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8j_15914/05_2025/8b8j_15914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8j_15914/05_2025/8b8j_15914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b8j_15914/05_2025/8b8j_15914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8j_15914/05_2025/8b8j_15914.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8j_15914/05_2025/8b8j_15914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8j_15914/05_2025/8b8j_15914.cif" } resolution = 2.96 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 76 5.16 5 C 7686 2.51 5 N 1884 2.21 5 O 2034 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-5687/modules/chem_data/mon_lib" Total number of atoms: 11686 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5840 Classifications: {'peptide': 709} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 8 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} Restraints were copied for chains: B Time building chain proxies: 12.08, per 1000 atoms: 1.03 Number of scatterers: 11686 At special positions: 0 Unit cell: (126.294, 83.328, 113.274, 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 76 16.00 O 2034 8.00 N 1884 7.00 C 7686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, 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=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " 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: 3.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 64.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 90 through 108 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.513A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 Processing helix chain 'A' and resid 447 through 473 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.568A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.505A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 638 removed outlier: 3.880A pdb=" N LYS A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 617 " --> pdb=" O MET A 613 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Proline residue: A 628 - end of helix removed outlier: 3.525A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 662 through 681 removed outlier: 3.796A pdb=" N TYR A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.953A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.599A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 762 through 766 Processing helix chain 'A' and resid 797 through 802 removed outlier: 3.769A pdb=" N LEU A 801 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 802 " --> pdb=" O TYR A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 797 through 802' Processing helix chain 'A' and resid 825 through 856 Processing helix chain 'A' and resid 861 through 875 removed outlier: 3.601A pdb=" N SER A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 108 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 364 through 375 removed outlier: 3.512A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 Processing helix chain 'B' and resid 447 through 473 Processing helix chain 'B' and resid 474 through 488 Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.568A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.504A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 removed outlier: 3.879A pdb=" N LYS B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Proline residue: B 628 - end of helix removed outlier: 3.525A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 662 through 681 removed outlier: 3.797A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.953A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.599A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 759 Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 797 through 802 removed outlier: 3.770A pdb=" N LEU B 801 " --> pdb=" O PRO B 797 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 802 " --> pdb=" O TYR B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 797 through 802' Processing helix chain 'B' and resid 825 through 856 Processing helix chain 'B' and resid 861 through 875 removed outlier: 3.601A pdb=" N SER B 866 " --> pdb=" O LYS B 862 " (cutoff:3.500A) 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 347 through 348 removed outlier: 3.627A pdb=" N TRP A 359 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 657 through 658 removed outlier: 6.940A pdb=" N GLN A 657 " --> pdb=" O ARG A 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 348 removed outlier: 3.628A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 657 through 658 removed outlier: 6.942A pdb=" N GLN B 657 " --> pdb=" O ARG B 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 785 720 hydrogen bonds defined for protein. 2106 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: 3.64 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3544 1.34 - 1.46: 2910 1.46 - 1.58: 5430 1.58 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 11998 Sorted by residual: bond pdb=" C PRO A 763 " pdb=" N PRO A 764 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.60e-01 bond pdb=" C PRO B 763 " pdb=" N PRO B 764 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.32e-01 bond pdb=" C GLY B 387 " pdb=" O GLY B 387 " ideal model delta sigma weight residual 1.234 1.243 -0.010 1.21e-02 6.83e+03 6.18e-01 bond pdb=" C VAL B 384 " pdb=" O VAL B 384 " ideal model delta sigma weight residual 1.237 1.245 -0.009 1.13e-02 7.83e+03 5.83e-01 bond pdb=" C PHE A 382 " pdb=" O PHE A 382 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.26e-02 6.30e+03 5.78e-01 ... (remaining 11993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16137 1.99 - 3.97: 111 3.97 - 5.96: 14 5.96 - 7.94: 2 7.94 - 9.93: 2 Bond angle restraints: 16266 Sorted by residual: angle pdb=" CA LEU A 662 " pdb=" CB LEU A 662 " pdb=" CG LEU A 662 " ideal model delta sigma weight residual 116.30 126.23 -9.93 3.50e+00 8.16e-02 8.04e+00 angle pdb=" CA LEU B 662 " pdb=" CB LEU B 662 " pdb=" CG LEU B 662 " ideal model delta sigma weight residual 116.30 126.20 -9.90 3.50e+00 8.16e-02 7.99e+00 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 114.03 -3.33 1.22e+00 6.72e-01 7.47e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 114.02 -3.32 1.22e+00 6.72e-01 7.42e+00 angle pdb=" C PRO B 541 " pdb=" N ARG B 542 " pdb=" CA ARG B 542 " ideal model delta sigma weight residual 125.02 129.32 -4.30 1.76e+00 3.23e-01 5.98e+00 ... (remaining 16261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 6739 17.49 - 34.97: 290 34.97 - 52.45: 29 52.45 - 69.94: 8 69.94 - 87.42: 2 Dihedral angle restraints: 7068 sinusoidal: 2882 harmonic: 4186 Sorted by residual: dihedral pdb=" CA LYS A 590 " pdb=" C LYS A 590 " pdb=" N TYR A 591 " pdb=" CA TYR A 591 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LYS B 590 " pdb=" C LYS B 590 " pdb=" N TYR B 591 " pdb=" CA TYR B 591 " ideal model delta harmonic sigma weight residual -180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLU B 539 " pdb=" CB GLU B 539 " pdb=" CG GLU B 539 " pdb=" CD GLU B 539 " ideal model delta sinusoidal sigma weight residual 60.00 117.32 -57.32 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1077 0.028 - 0.055: 429 0.055 - 0.083: 210 0.083 - 0.110: 54 0.110 - 0.138: 16 Chirality restraints: 1786 Sorted by residual: chirality pdb=" CB ILE A 474 " pdb=" CA ILE A 474 " pdb=" CG1 ILE A 474 " pdb=" CG2 ILE A 474 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CB ILE B 474 " pdb=" CA ILE B 474 " pdb=" CG1 ILE B 474 " pdb=" CG2 ILE B 474 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ARG B 542 " pdb=" N ARG B 542 " pdb=" C ARG B 542 " pdb=" CB ARG B 542 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1783 not shown) Planarity restraints: 2010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 762 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 763 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 763 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 763 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 762 " -0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 763 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 763 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 763 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 818 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO A 819 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 819 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 819 " 0.020 5.00e-02 4.00e+02 ... (remaining 2007 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1522 2.75 - 3.29: 12048 3.29 - 3.82: 20078 3.82 - 4.36: 22392 4.36 - 4.90: 39120 Nonbonded interactions: 95160 Sorted by model distance: nonbonded pdb=" O CYS B 365 " pdb=" OG SER B 368 " model vdw 2.211 3.040 nonbonded pdb=" O CYS A 365 " pdb=" OG SER A 368 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP A 375 " pdb=" OG SER A 748 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP B 375 " pdb=" OG SER B 748 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASN A 778 " pdb=" NH1 ARG A 808 " model vdw 2.258 3.120 ... (remaining 95155 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.510 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.003 0.030 12006 Z= 0.136 Angle : 0.464 9.926 16282 Z= 0.249 Chirality : 0.038 0.138 1786 Planarity : 0.004 0.043 2010 Dihedral : 9.830 87.425 4348 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.25 % Allowed : 5.25 % Favored : 93.50 % 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: 2.21 (0.23), residues: 1382 helix: 2.62 (0.17), residues: 848 sheet: 1.10 (0.58), residues: 64 loop : -0.73 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 397 HIS 0.002 0.000 HIS A 249 PHE 0.014 0.001 PHE B 560 TYR 0.013 0.001 TYR A 580 ARG 0.002 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.11598 ( 720) hydrogen bonds : angle 5.28926 ( 2106) SS BOND : bond 0.00177 ( 8) SS BOND : angle 0.63597 ( 16) covalent geometry : bond 0.00292 (11998) covalent geometry : angle 0.46378 (16266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.8677 (m-40) cc_final: 0.8347 (p0) REVERT: A 326 LEU cc_start: 0.8975 (mt) cc_final: 0.8741 (mt) REVERT: A 385 PHE cc_start: 0.8610 (t80) cc_final: 0.8405 (t80) REVERT: A 406 TYR cc_start: 0.8568 (t80) cc_final: 0.8228 (t80) REVERT: A 409 ASP cc_start: 0.8854 (m-30) cc_final: 0.8369 (t0) REVERT: A 461 PHE cc_start: 0.8306 (t80) cc_final: 0.7785 (m-10) REVERT: A 524 LEU cc_start: 0.9711 (mm) cc_final: 0.9280 (tp) REVERT: A 527 ILE cc_start: 0.9626 (mm) cc_final: 0.9386 (mt) REVERT: A 544 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7156 (tp40) REVERT: A 548 GLU cc_start: 0.8978 (tp30) cc_final: 0.8711 (mm-30) REVERT: A 553 MET cc_start: 0.8156 (tpp) cc_final: 0.7720 (tpp) REVERT: A 597 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (t70) REVERT: B 296 ILE cc_start: 0.7948 (mp) cc_final: 0.7609 (mm) REVERT: B 327 ASP cc_start: 0.7904 (t0) cc_final: 0.7663 (t0) REVERT: B 409 ASP cc_start: 0.8527 (m-30) cc_final: 0.8112 (t0) REVERT: B 548 GLU cc_start: 0.9093 (tp30) cc_final: 0.8529 (tp30) REVERT: B 749 ASP cc_start: 0.7937 (t70) cc_final: 0.7211 (t0) REVERT: B 855 TYR cc_start: 0.7994 (t80) cc_final: 0.7739 (t80) outliers start: 16 outliers final: 3 residues processed: 204 average time/residue: 1.0285 time to fit residues: 231.1397 Evaluate side-chains 121 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 685 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 308 GLN A 351 GLN A 401 GLN A 559 GLN A 726 GLN A 730 GLN A 820 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 401 GLN B 674 GLN B 695 ASN B 726 GLN B 730 GLN B 824 HIS B 830 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.120815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086882 restraints weight = 21821.689| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.99 r_work: 0.3054 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 12006 Z= 0.245 Angle : 0.679 13.147 16282 Z= 0.356 Chirality : 0.045 0.239 1786 Planarity : 0.005 0.051 2010 Dihedral : 5.036 54.249 1570 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.06 % Allowed : 11.29 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.22), residues: 1382 helix: 1.91 (0.16), residues: 876 sheet: 1.42 (0.62), residues: 44 loop : -0.81 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 829 HIS 0.005 0.001 HIS B 818 PHE 0.027 0.002 PHE B 462 TYR 0.016 0.002 TYR B 580 ARG 0.014 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 720) hydrogen bonds : angle 4.49021 ( 2106) SS BOND : bond 0.01303 ( 8) SS BOND : angle 1.94490 ( 16) covalent geometry : bond 0.00560 (11998) covalent geometry : angle 0.67679 (16266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.8445 (OUTLIER) cc_final: 0.7879 (t-90) REVERT: A 234 ASN cc_start: 0.8719 (m-40) cc_final: 0.8461 (p0) REVERT: A 282 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6561 (tptt) REVERT: A 348 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8556 (mmm) REVERT: A 409 ASP cc_start: 0.8741 (m-30) cc_final: 0.8250 (t0) REVERT: A 524 LEU cc_start: 0.9728 (mm) cc_final: 0.9460 (mt) REVERT: A 527 ILE cc_start: 0.9722 (mm) cc_final: 0.9507 (mt) REVERT: A 548 GLU cc_start: 0.9033 (tp30) cc_final: 0.8305 (tp30) REVERT: A 553 MET cc_start: 0.8435 (tpp) cc_final: 0.7982 (tpp) REVERT: A 595 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8086 (mt-10) REVERT: A 659 MET cc_start: 0.8987 (ttm) cc_final: 0.8768 (ttm) REVERT: B 242 TYR cc_start: 0.8725 (m-80) cc_final: 0.8389 (m-80) REVERT: B 409 ASP cc_start: 0.8601 (m-30) cc_final: 0.8174 (t0) REVERT: B 538 PHE cc_start: 0.8524 (t80) cc_final: 0.8011 (t80) REVERT: B 548 GLU cc_start: 0.9157 (tp30) cc_final: 0.8575 (mp0) REVERT: B 855 TYR cc_start: 0.8064 (t80) cc_final: 0.7859 (t80) outliers start: 39 outliers final: 18 residues processed: 155 average time/residue: 1.1180 time to fit residues: 189.5023 Evaluate side-chains 121 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 30.0000 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 695 ASN B 111 GLN B 559 GLN B 730 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087357 restraints weight = 21853.496| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.98 r_work: 0.3092 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12006 Z= 0.139 Angle : 0.579 11.131 16282 Z= 0.299 Chirality : 0.040 0.191 1786 Planarity : 0.004 0.045 2010 Dihedral : 4.514 55.851 1565 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.59 % Allowed : 13.71 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1382 helix: 2.08 (0.17), residues: 870 sheet: 1.39 (0.60), residues: 44 loop : -0.86 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.003 0.001 HIS A 249 PHE 0.023 0.002 PHE B 462 TYR 0.015 0.001 TYR B 580 ARG 0.012 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 720) hydrogen bonds : angle 4.34694 ( 2106) SS BOND : bond 0.00529 ( 8) SS BOND : angle 1.78296 ( 16) covalent geometry : bond 0.00305 (11998) covalent geometry : angle 0.57689 (16266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.449 Fit side-chains REVERT: A 108 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.8221 (t-90) REVERT: A 234 ASN cc_start: 0.8732 (m-40) cc_final: 0.8476 (p0) REVERT: A 348 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8672 (mmm) REVERT: A 386 MET cc_start: 0.8269 (tpp) cc_final: 0.8009 (mmm) REVERT: A 409 ASP cc_start: 0.8806 (m-30) cc_final: 0.8297 (t0) REVERT: A 471 VAL cc_start: 0.9007 (t) cc_final: 0.8798 (t) REVERT: A 527 ILE cc_start: 0.9688 (mm) cc_final: 0.9456 (mt) REVERT: A 548 GLU cc_start: 0.8970 (tp30) cc_final: 0.8665 (mp0) REVERT: A 553 MET cc_start: 0.8399 (tpp) cc_final: 0.7907 (tpp) REVERT: A 668 TYR cc_start: 0.9188 (m-80) cc_final: 0.8950 (m-80) REVERT: B 409 ASP cc_start: 0.8539 (m-30) cc_final: 0.8113 (t0) REVERT: B 538 PHE cc_start: 0.8508 (t80) cc_final: 0.8206 (t80) REVERT: B 548 GLU cc_start: 0.9122 (tp30) cc_final: 0.8556 (mp0) REVERT: B 668 TYR cc_start: 0.9176 (m-80) cc_final: 0.8890 (m-80) REVERT: B 754 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9063 (mp) REVERT: B 855 TYR cc_start: 0.8044 (t80) cc_final: 0.7818 (t80) outliers start: 33 outliers final: 8 residues processed: 141 average time/residue: 1.0523 time to fit residues: 163.3934 Evaluate side-chains 111 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086516 restraints weight = 21899.940| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.93 r_work: 0.3082 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12006 Z= 0.150 Angle : 0.581 10.598 16282 Z= 0.299 Chirality : 0.041 0.186 1786 Planarity : 0.005 0.046 2010 Dihedral : 4.198 23.400 1562 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.21 % Allowed : 13.95 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1382 helix: 2.08 (0.17), residues: 868 sheet: 1.40 (0.60), residues: 44 loop : -0.88 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 829 HIS 0.003 0.001 HIS A 249 PHE 0.024 0.002 PHE B 462 TYR 0.017 0.001 TYR B 406 ARG 0.013 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 720) hydrogen bonds : angle 4.27246 ( 2106) SS BOND : bond 0.00296 ( 8) SS BOND : angle 1.71836 ( 16) covalent geometry : bond 0.00334 (11998) covalent geometry : angle 0.57843 (16266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 1.339 Fit side-chains REVERT: A 108 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.8153 (t-90) REVERT: A 234 ASN cc_start: 0.8742 (m-40) cc_final: 0.8516 (p0) REVERT: A 348 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8628 (mmm) REVERT: A 386 MET cc_start: 0.8204 (tpp) cc_final: 0.7954 (mmm) REVERT: A 409 ASP cc_start: 0.8736 (m-30) cc_final: 0.8215 (t0) REVERT: A 471 VAL cc_start: 0.8947 (t) cc_final: 0.8744 (t) REVERT: A 527 ILE cc_start: 0.9697 (mm) cc_final: 0.9442 (mt) REVERT: A 548 GLU cc_start: 0.8992 (tp30) cc_final: 0.8639 (mp0) REVERT: A 553 MET cc_start: 0.8419 (tpp) cc_final: 0.7938 (tpp) REVERT: B 409 ASP cc_start: 0.8621 (m-30) cc_final: 0.8221 (t0) REVERT: B 458 SER cc_start: 0.8938 (m) cc_final: 0.8644 (p) REVERT: B 507 MET cc_start: 0.4823 (pmt) cc_final: 0.4552 (pmm) REVERT: B 538 PHE cc_start: 0.8465 (t80) cc_final: 0.8154 (t80) REVERT: B 548 GLU cc_start: 0.9122 (tp30) cc_final: 0.8551 (mp0) REVERT: B 749 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.7790 (t0) REVERT: B 754 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9065 (mp) REVERT: B 855 TYR cc_start: 0.8065 (t80) cc_final: 0.7864 (t80) outliers start: 41 outliers final: 15 residues processed: 138 average time/residue: 1.0054 time to fit residues: 153.0606 Evaluate side-chains 120 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 131 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 74 optimal weight: 0.0030 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087274 restraints weight = 21598.074| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.90 r_work: 0.3096 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12006 Z= 0.132 Angle : 0.575 14.147 16282 Z= 0.293 Chirality : 0.040 0.151 1786 Planarity : 0.004 0.048 2010 Dihedral : 4.167 23.234 1562 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.35 % Allowed : 15.44 % Favored : 82.21 % 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: 1.64 (0.22), residues: 1382 helix: 2.11 (0.17), residues: 868 sheet: 1.53 (0.63), residues: 42 loop : -0.94 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 397 HIS 0.003 0.001 HIS A 249 PHE 0.025 0.001 PHE B 462 TYR 0.012 0.001 TYR B 580 ARG 0.015 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 720) hydrogen bonds : angle 4.24925 ( 2106) SS BOND : bond 0.00281 ( 8) SS BOND : angle 1.65098 ( 16) covalent geometry : bond 0.00293 (11998) covalent geometry : angle 0.57308 (16266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.335 Fit side-chains REVERT: A 108 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.8113 (t-90) REVERT: A 234 ASN cc_start: 0.8743 (m-40) cc_final: 0.8523 (p0) REVERT: A 282 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6354 (tptt) REVERT: A 409 ASP cc_start: 0.8783 (m-30) cc_final: 0.8264 (t0) REVERT: A 527 ILE cc_start: 0.9696 (mm) cc_final: 0.9438 (mt) REVERT: A 548 GLU cc_start: 0.9005 (tp30) cc_final: 0.8644 (mp0) REVERT: A 553 MET cc_start: 0.8402 (tpp) cc_final: 0.7940 (tpp) REVERT: A 668 TYR cc_start: 0.9163 (m-80) cc_final: 0.8864 (m-80) REVERT: B 386 MET cc_start: 0.8452 (tpp) cc_final: 0.8158 (mmm) REVERT: B 409 ASP cc_start: 0.8610 (m-30) cc_final: 0.8205 (t0) REVERT: B 458 SER cc_start: 0.8857 (m) cc_final: 0.8617 (p) REVERT: B 538 PHE cc_start: 0.8508 (t80) cc_final: 0.8177 (t80) REVERT: B 548 GLU cc_start: 0.9101 (tp30) cc_final: 0.8560 (mp0) REVERT: B 754 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9102 (mp) REVERT: B 855 TYR cc_start: 0.8056 (t80) cc_final: 0.7849 (t80) outliers start: 30 outliers final: 19 residues processed: 130 average time/residue: 1.0629 time to fit residues: 151.9957 Evaluate side-chains 125 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 863 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 54 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 62 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 0.0010 chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.122877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088043 restraints weight = 21736.558| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.93 r_work: 0.3109 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12006 Z= 0.121 Angle : 0.567 13.344 16282 Z= 0.289 Chirality : 0.039 0.144 1786 Planarity : 0.005 0.050 2010 Dihedral : 4.117 24.048 1562 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.66 % Allowed : 15.44 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.22), residues: 1382 helix: 2.16 (0.17), residues: 874 sheet: 1.40 (0.61), residues: 44 loop : -0.92 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 397 HIS 0.003 0.001 HIS A 249 PHE 0.026 0.001 PHE B 462 TYR 0.011 0.001 TYR B 580 ARG 0.016 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 720) hydrogen bonds : angle 4.20389 ( 2106) SS BOND : bond 0.00314 ( 8) SS BOND : angle 1.63781 ( 16) covalent geometry : bond 0.00261 (11998) covalent geometry : angle 0.56498 (16266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.271 Fit side-chains REVERT: A 73 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6041 (m-80) REVERT: A 108 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8163 (t-90) REVERT: A 113 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6992 (pm20) REVERT: A 142 MET cc_start: 0.8039 (mtp) cc_final: 0.7794 (mtm) REVERT: A 234 ASN cc_start: 0.8758 (m-40) cc_final: 0.8528 (p0) REVERT: A 282 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6285 (tptt) REVERT: A 409 ASP cc_start: 0.8769 (m-30) cc_final: 0.8229 (t0) REVERT: A 527 ILE cc_start: 0.9703 (mm) cc_final: 0.9457 (mt) REVERT: A 548 GLU cc_start: 0.9008 (tp30) cc_final: 0.8644 (mp0) REVERT: A 553 MET cc_start: 0.8407 (tpp) cc_final: 0.7970 (tpp) REVERT: A 595 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 668 TYR cc_start: 0.9158 (m-80) cc_final: 0.8885 (m-80) REVERT: B 142 MET cc_start: 0.7455 (mtp) cc_final: 0.7077 (mtm) REVERT: B 386 MET cc_start: 0.8420 (tpp) cc_final: 0.8188 (mmm) REVERT: B 409 ASP cc_start: 0.8716 (m-30) cc_final: 0.8299 (t0) REVERT: B 458 SER cc_start: 0.8897 (m) cc_final: 0.8661 (p) REVERT: B 507 MET cc_start: 0.4632 (pmt) cc_final: 0.4166 (pmm) REVERT: B 524 LEU cc_start: 0.9690 (mt) cc_final: 0.9357 (pp) REVERT: B 538 PHE cc_start: 0.8495 (t80) cc_final: 0.8139 (t80) REVERT: B 548 GLU cc_start: 0.9105 (tp30) cc_final: 0.8562 (mp0) REVERT: B 636 ARG cc_start: 0.7515 (mmp-170) cc_final: 0.7303 (mmp-170) REVERT: B 668 TYR cc_start: 0.9162 (m-80) cc_final: 0.8873 (m-80) REVERT: B 749 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.7923 (t0) REVERT: B 754 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9123 (mp) outliers start: 34 outliers final: 16 residues processed: 138 average time/residue: 1.0079 time to fit residues: 154.1008 Evaluate side-chains 129 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 863 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 674 GLN A 695 ASN A 730 GLN A 830 HIS ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS B 674 GLN B 695 ASN B 730 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084316 restraints weight = 22151.358| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.93 r_work: 0.3037 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12006 Z= 0.213 Angle : 0.630 12.548 16282 Z= 0.321 Chirality : 0.042 0.167 1786 Planarity : 0.005 0.059 2010 Dihedral : 4.180 23.067 1562 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.98 % Allowed : 15.20 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1382 helix: 2.00 (0.17), residues: 878 sheet: 1.24 (0.59), residues: 44 loop : -0.96 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 829 HIS 0.003 0.001 HIS A 249 PHE 0.027 0.002 PHE B 462 TYR 0.012 0.001 TYR A 138 ARG 0.017 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 720) hydrogen bonds : angle 4.32308 ( 2106) SS BOND : bond 0.00473 ( 8) SS BOND : angle 1.92459 ( 16) covalent geometry : bond 0.00489 (11998) covalent geometry : angle 0.62776 (16266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.452 Fit side-chains REVERT: A 94 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8112 (tp40) REVERT: A 96 ARG cc_start: 0.8419 (ptm160) cc_final: 0.8059 (ptp-110) REVERT: A 108 HIS cc_start: 0.8581 (OUTLIER) cc_final: 0.8206 (t-90) REVERT: A 113 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: A 282 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6441 (tptt) REVERT: A 386 MET cc_start: 0.8376 (tpp) cc_final: 0.8117 (mmm) REVERT: A 409 ASP cc_start: 0.8785 (m-30) cc_final: 0.8266 (t0) REVERT: A 527 ILE cc_start: 0.9718 (mm) cc_final: 0.9455 (mt) REVERT: A 548 GLU cc_start: 0.9065 (tp30) cc_final: 0.8374 (tp30) REVERT: A 553 MET cc_start: 0.8434 (tpp) cc_final: 0.7953 (tpp) REVERT: A 595 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 717 GLU cc_start: 0.8349 (mp0) cc_final: 0.8121 (mp0) REVERT: A 742 MET cc_start: 0.8955 (mtt) cc_final: 0.8662 (mtm) REVERT: B 142 MET cc_start: 0.7642 (mtp) cc_final: 0.7309 (mtm) REVERT: B 409 ASP cc_start: 0.8616 (m-30) cc_final: 0.8219 (t0) REVERT: B 458 SER cc_start: 0.8907 (m) cc_final: 0.8674 (p) REVERT: B 538 PHE cc_start: 0.8386 (t80) cc_final: 0.7957 (t80) REVERT: B 548 GLU cc_start: 0.9101 (tp30) cc_final: 0.8537 (mp0) REVERT: B 742 MET cc_start: 0.8765 (mpt) cc_final: 0.8444 (mtp) REVERT: B 749 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8094 (t0) outliers start: 38 outliers final: 21 residues processed: 143 average time/residue: 1.0664 time to fit residues: 167.2151 Evaluate side-chains 129 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 863 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 112 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 695 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 695 ASN B 730 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.122163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087234 restraints weight = 21728.431| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.92 r_work: 0.3084 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12006 Z= 0.126 Angle : 0.592 13.619 16282 Z= 0.298 Chirality : 0.040 0.143 1786 Planarity : 0.005 0.057 2010 Dihedral : 4.132 22.816 1562 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.59 % Allowed : 16.38 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1382 helix: 2.11 (0.17), residues: 876 sheet: 1.33 (0.60), residues: 44 loop : -0.99 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.003 0.001 HIS A 249 PHE 0.028 0.001 PHE B 462 TYR 0.012 0.001 TYR B 580 ARG 0.015 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 720) hydrogen bonds : angle 4.24663 ( 2106) SS BOND : bond 0.00207 ( 8) SS BOND : angle 1.73250 ( 16) covalent geometry : bond 0.00277 (11998) covalent geometry : angle 0.59027 (16266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.235 Fit side-chains REVERT: A 108 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.8224 (t-90) REVERT: A 282 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6489 (tptm) REVERT: A 386 MET cc_start: 0.8240 (tpp) cc_final: 0.7995 (mmm) REVERT: A 409 ASP cc_start: 0.8774 (m-30) cc_final: 0.8238 (t0) REVERT: A 527 ILE cc_start: 0.9720 (mm) cc_final: 0.9464 (mt) REVERT: A 548 GLU cc_start: 0.9036 (tp30) cc_final: 0.8624 (mp0) REVERT: A 553 MET cc_start: 0.8425 (tpp) cc_final: 0.7967 (tpp) REVERT: A 595 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7937 (mt-10) REVERT: A 668 TYR cc_start: 0.9166 (m-80) cc_final: 0.8886 (m-80) REVERT: A 742 MET cc_start: 0.8991 (mtt) cc_final: 0.8673 (mtm) REVERT: B 142 MET cc_start: 0.7503 (mtp) cc_final: 0.7155 (mtm) REVERT: B 386 MET cc_start: 0.8443 (tpp) cc_final: 0.8015 (mmm) REVERT: B 409 ASP cc_start: 0.8728 (m-30) cc_final: 0.8301 (t0) REVERT: B 458 SER cc_start: 0.8943 (m) cc_final: 0.8717 (p) REVERT: B 503 LEU cc_start: 0.1689 (OUTLIER) cc_final: 0.0858 (tt) REVERT: B 524 LEU cc_start: 0.9690 (mt) cc_final: 0.9369 (pp) REVERT: B 538 PHE cc_start: 0.8411 (t80) cc_final: 0.7981 (t80) REVERT: B 548 GLU cc_start: 0.9084 (tp30) cc_final: 0.8557 (mp0) REVERT: B 668 TYR cc_start: 0.9171 (m-80) cc_final: 0.8879 (m-80) REVERT: B 742 MET cc_start: 0.8813 (mpt) cc_final: 0.8429 (mtp) REVERT: B 749 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8054 (t0) outliers start: 33 outliers final: 21 residues processed: 138 average time/residue: 1.0172 time to fit residues: 154.8243 Evaluate side-chains 129 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.120782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085994 restraints weight = 21794.315| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.95 r_work: 0.3074 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12006 Z= 0.155 Angle : 0.606 12.660 16282 Z= 0.309 Chirality : 0.041 0.158 1786 Planarity : 0.005 0.065 2010 Dihedral : 4.149 22.900 1562 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.59 % Allowed : 16.85 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1382 helix: 2.14 (0.17), residues: 866 sheet: 0.40 (0.54), residues: 64 loop : -0.89 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 397 HIS 0.003 0.001 HIS A 249 PHE 0.028 0.002 PHE B 462 TYR 0.015 0.001 TYR B 827 ARG 0.017 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 720) hydrogen bonds : angle 4.26374 ( 2106) SS BOND : bond 0.00233 ( 8) SS BOND : angle 1.77797 ( 16) covalent geometry : bond 0.00353 (11998) covalent geometry : angle 0.60415 (16266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.312 Fit side-chains REVERT: A 51 GLU cc_start: 0.7708 (mp0) cc_final: 0.7190 (mp0) REVERT: A 96 ARG cc_start: 0.8424 (ptm160) cc_final: 0.8043 (ptp-110) REVERT: A 108 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.8179 (t-90) REVERT: A 142 MET cc_start: 0.7744 (mpp) cc_final: 0.7503 (mpp) REVERT: A 282 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6517 (tptm) REVERT: A 386 MET cc_start: 0.8260 (tpp) cc_final: 0.8034 (mmm) REVERT: A 409 ASP cc_start: 0.8767 (m-30) cc_final: 0.8241 (t0) REVERT: A 524 LEU cc_start: 0.9729 (mt) cc_final: 0.9433 (pp) REVERT: A 527 ILE cc_start: 0.9723 (mm) cc_final: 0.9474 (mt) REVERT: A 548 GLU cc_start: 0.9056 (tp30) cc_final: 0.8329 (tp30) REVERT: A 553 MET cc_start: 0.8447 (tpp) cc_final: 0.8000 (tpp) REVERT: A 595 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8003 (mt-10) REVERT: A 742 MET cc_start: 0.8980 (mtt) cc_final: 0.8696 (mtm) REVERT: A 773 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8273 (mmm) REVERT: B 142 MET cc_start: 0.7505 (mtp) cc_final: 0.7173 (mtm) REVERT: B 386 MET cc_start: 0.8446 (tpp) cc_final: 0.8037 (mmm) REVERT: B 409 ASP cc_start: 0.8739 (m-30) cc_final: 0.8311 (t0) REVERT: B 458 SER cc_start: 0.8913 (m) cc_final: 0.8686 (p) REVERT: B 503 LEU cc_start: 0.1739 (OUTLIER) cc_final: 0.0782 (tt) REVERT: B 524 LEU cc_start: 0.9680 (mt) cc_final: 0.9343 (pp) REVERT: B 529 GLU cc_start: 0.8774 (tt0) cc_final: 0.8210 (pt0) REVERT: B 538 PHE cc_start: 0.8378 (t80) cc_final: 0.7944 (t80) REVERT: B 548 GLU cc_start: 0.9091 (tp30) cc_final: 0.8532 (mp0) REVERT: B 742 MET cc_start: 0.8770 (mpt) cc_final: 0.8420 (mtp) REVERT: B 749 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8038 (t0) outliers start: 33 outliers final: 22 residues processed: 137 average time/residue: 1.0498 time to fit residues: 158.7054 Evaluate side-chains 136 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086170 restraints weight = 21626.677| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.95 r_work: 0.3077 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12006 Z= 0.148 Angle : 0.612 12.672 16282 Z= 0.309 Chirality : 0.040 0.157 1786 Planarity : 0.005 0.059 2010 Dihedral : 4.142 22.818 1562 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.51 % Allowed : 16.69 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1382 helix: 2.14 (0.17), residues: 868 sheet: 1.34 (0.60), residues: 44 loop : -1.01 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 397 HIS 0.003 0.001 HIS A 249 PHE 0.029 0.001 PHE B 462 TYR 0.013 0.001 TYR A 138 ARG 0.015 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 720) hydrogen bonds : angle 4.25973 ( 2106) SS BOND : bond 0.00282 ( 8) SS BOND : angle 1.78416 ( 16) covalent geometry : bond 0.00336 (11998) covalent geometry : angle 0.60957 (16266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8239 (t-90) REVERT: A 282 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6519 (tptm) REVERT: A 386 MET cc_start: 0.8248 (tpp) cc_final: 0.8034 (mmm) REVERT: A 409 ASP cc_start: 0.8773 (m-30) cc_final: 0.8243 (t0) REVERT: A 524 LEU cc_start: 0.9693 (mt) cc_final: 0.9435 (pp) REVERT: A 527 ILE cc_start: 0.9720 (mm) cc_final: 0.9470 (mt) REVERT: A 553 MET cc_start: 0.8436 (tpp) cc_final: 0.7989 (tpp) REVERT: A 595 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8075 (mt-10) REVERT: A 742 MET cc_start: 0.8997 (mtt) cc_final: 0.8708 (mtm) REVERT: B 142 MET cc_start: 0.7543 (mtp) cc_final: 0.7208 (mtm) REVERT: B 386 MET cc_start: 0.8511 (tpp) cc_final: 0.8105 (mmm) REVERT: B 409 ASP cc_start: 0.8742 (m-30) cc_final: 0.8287 (t0) REVERT: B 458 SER cc_start: 0.8975 (m) cc_final: 0.8758 (p) REVERT: B 503 LEU cc_start: 0.1750 (OUTLIER) cc_final: 0.0797 (tt) REVERT: B 524 LEU cc_start: 0.9684 (mt) cc_final: 0.9347 (pp) REVERT: B 529 GLU cc_start: 0.8775 (tt0) cc_final: 0.8212 (pt0) REVERT: B 538 PHE cc_start: 0.8522 (t80) cc_final: 0.7992 (t80) REVERT: B 548 GLU cc_start: 0.9082 (tp30) cc_final: 0.8536 (mp0) REVERT: B 742 MET cc_start: 0.8762 (mpt) cc_final: 0.8412 (mtp) REVERT: B 749 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8026 (t0) outliers start: 32 outliers final: 23 residues processed: 135 average time/residue: 1.0717 time to fit residues: 160.8226 Evaluate side-chains 133 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 122 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.121430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086567 restraints weight = 21713.988| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.95 r_work: 0.3083 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12006 Z= 0.143 Angle : 0.606 12.506 16282 Z= 0.307 Chirality : 0.041 0.160 1786 Planarity : 0.005 0.059 2010 Dihedral : 4.159 22.848 1562 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.51 % Allowed : 16.69 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1382 helix: 2.15 (0.17), residues: 868 sheet: 1.37 (0.59), residues: 44 loop : -1.01 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.004 0.001 HIS A 108 PHE 0.029 0.001 PHE B 462 TYR 0.014 0.001 TYR B 827 ARG 0.015 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 720) hydrogen bonds : angle 4.26105 ( 2106) SS BOND : bond 0.00278 ( 8) SS BOND : angle 1.77178 ( 16) covalent geometry : bond 0.00322 (11998) covalent geometry : angle 0.60397 (16266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6530.13 seconds wall clock time: 113 minutes 31.12 seconds (6811.12 seconds total)