Starting phenix.real_space_refine on Tue Jul 29 23:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8j_15914/07_2025/8b8j_15914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8j_15914/07_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_15914/07_2025/8b8j_15914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8j_15914/07_2025/8b8j_15914.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8j_15914/07_2025/8b8j_15914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8j_15914/07_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-5711/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: 12.16, per 1000 atoms: 1.04 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 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: 1.05 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: 3.72 Time building geometry restraints manager: 3.58 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: 0.09 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: 1.270 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.910 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:19.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.080 ------------------------------------------------------------------------------- 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 : 1.295 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: 1.1708 time to fit residues: 263.1736 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 : 1.856 ------------------------------------------------------------------------------- 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 = 0.086876 restraints weight = 21821.696| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.99 r_work: 0.3053 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- 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 1.94491 ( 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 : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.8445 (OUTLIER) cc_final: 0.7878 (t-90) REVERT: A 234 ASN cc_start: 0.8719 (m-40) cc_final: 0.8462 (p0) REVERT: A 282 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6561 (tptt) REVERT: A 348 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8558 (mmm) REVERT: A 409 ASP cc_start: 0.8742 (m-30) cc_final: 0.8251 (t0) REVERT: A 524 LEU cc_start: 0.9729 (mm) cc_final: 0.9460 (mt) REVERT: A 527 ILE cc_start: 0.9721 (mm) cc_final: 0.9506 (mt) REVERT: A 548 GLU cc_start: 0.9034 (tp30) cc_final: 0.8306 (tp30) REVERT: A 553 MET cc_start: 0.8436 (tpp) cc_final: 0.7982 (tpp) REVERT: A 595 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8088 (mt-10) REVERT: A 659 MET cc_start: 0.8988 (ttm) cc_final: 0.8770 (ttm) REVERT: B 242 TYR cc_start: 0.8724 (m-80) cc_final: 0.8389 (m-80) REVERT: B 409 ASP cc_start: 0.8600 (m-30) cc_final: 0.8173 (t0) REVERT: B 538 PHE cc_start: 0.8525 (t80) cc_final: 0.8013 (t80) REVERT: B 548 GLU cc_start: 0.9156 (tp30) cc_final: 0.8575 (mp0) REVERT: B 855 TYR cc_start: 0.8068 (t80) cc_final: 0.7862 (t80) outliers start: 39 outliers final: 18 residues processed: 155 average time/residue: 1.7891 time to fit residues: 305.7175 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 : 1.883 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3819 r_free = 0.3819 target = 0.122354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087182 restraints weight = 21850.304| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.98 r_work: 0.3086 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12006 Z= 0.141 Angle : 0.583 11.133 16282 Z= 0.301 Chirality : 0.041 0.191 1786 Planarity : 0.005 0.046 2010 Dihedral : 4.523 55.742 1565 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.82 % Allowed : 13.71 % Favored : 83.46 % 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: 2.07 (0.17), residues: 870 sheet: 1.38 (0.59), 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 0.04701 ( 720) hydrogen bonds : angle 4.35453 ( 2106) SS BOND : bond 0.00300 ( 8) SS BOND : angle 1.81704 ( 16) covalent geometry : bond 0.00309 (11998) covalent geometry : angle 0.58063 (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 153 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.8225 (t-90) REVERT: A 234 ASN cc_start: 0.8737 (m-40) cc_final: 0.8478 (p0) REVERT: A 348 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8655 (mmm) REVERT: A 386 MET cc_start: 0.8262 (tpp) cc_final: 0.8003 (mmm) REVERT: A 409 ASP cc_start: 0.8805 (m-30) cc_final: 0.8297 (t0) REVERT: A 471 VAL cc_start: 0.9002 (t) cc_final: 0.8793 (t) REVERT: A 527 ILE cc_start: 0.9685 (mm) cc_final: 0.9457 (mt) REVERT: A 548 GLU cc_start: 0.8980 (tp30) cc_final: 0.8665 (mp0) REVERT: A 553 MET cc_start: 0.8383 (tpp) cc_final: 0.7950 (tpp) REVERT: B 409 ASP cc_start: 0.8536 (m-30) cc_final: 0.8107 (t0) REVERT: B 538 PHE cc_start: 0.8502 (t80) cc_final: 0.8184 (t80) REVERT: B 548 GLU cc_start: 0.9129 (tp30) cc_final: 0.8552 (mp0) REVERT: B 668 TYR cc_start: 0.9173 (m-80) cc_final: 0.8881 (m-80) REVERT: B 754 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9060 (mp) REVERT: B 855 TYR cc_start: 0.8041 (t80) cc_final: 0.7825 (t80) outliers start: 36 outliers final: 9 residues processed: 142 average time/residue: 1.2520 time to fit residues: 194.3967 Evaluate side-chains 111 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 99 GLN 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: 3.9990 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN B 525 ASN B 559 GLN B 730 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.120991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085802 restraints weight = 21895.702| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.93 r_work: 0.3068 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12006 Z= 0.170 Angle : 0.598 14.493 16282 Z= 0.307 Chirality : 0.041 0.178 1786 Planarity : 0.005 0.046 2010 Dihedral : 4.486 56.228 1565 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.06 % Allowed : 14.03 % Favored : 82.92 % 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: 1.60 (0.22), residues: 1382 helix: 2.02 (0.17), residues: 878 sheet: 1.32 (0.60), residues: 44 loop : -0.88 (0.29), residues: 460 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 0.023 0.002 PHE B 462 TYR 0.013 0.001 TYR A 827 ARG 0.013 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04739 ( 720) hydrogen bonds : angle 4.31188 ( 2106) SS BOND : bond 0.00572 ( 8) SS BOND : angle 1.77043 ( 16) covalent geometry : bond 0.00385 (11998) covalent geometry : angle 0.59534 (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 143 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.417 Fit side-chains REVERT: A 108 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8165 (t-90) REVERT: A 234 ASN cc_start: 0.8731 (m-40) cc_final: 0.8510 (p0) REVERT: A 348 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8635 (mmm) REVERT: A 409 ASP cc_start: 0.8741 (m-30) cc_final: 0.8218 (t0) REVERT: A 471 VAL cc_start: 0.8961 (t) cc_final: 0.8760 (t) REVERT: A 527 ILE cc_start: 0.9688 (mm) cc_final: 0.9438 (mt) REVERT: A 548 GLU cc_start: 0.9003 (tp30) cc_final: 0.8644 (mp0) REVERT: A 553 MET cc_start: 0.8417 (tpp) cc_final: 0.7925 (tpp) REVERT: A 773 MET cc_start: 0.8604 (mmt) cc_final: 0.8338 (tpp) REVERT: B 409 ASP cc_start: 0.8551 (m-30) cc_final: 0.8136 (t0) REVERT: B 458 SER cc_start: 0.8728 (m) cc_final: 0.8413 (p) REVERT: B 507 MET cc_start: 0.4722 (pmt) cc_final: 0.4436 (pmm) REVERT: B 538 PHE cc_start: 0.8456 (t80) cc_final: 0.8152 (t80) REVERT: B 548 GLU cc_start: 0.9132 (tp30) cc_final: 0.8580 (mp0) REVERT: B 754 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9064 (mp) REVERT: B 855 TYR cc_start: 0.8048 (t80) cc_final: 0.7835 (t80) outliers start: 39 outliers final: 15 residues processed: 137 average time/residue: 1.7003 time to fit residues: 257.8542 Evaluate side-chains 118 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 3.108 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 100 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 74 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 830 HIS B 730 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.120863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085810 restraints weight = 21645.825| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.90 r_work: 0.3060 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3642 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= 0.159 Angle : 0.589 13.046 16282 Z= 0.302 Chirality : 0.041 0.157 1786 Planarity : 0.005 0.048 2010 Dihedral : 4.213 22.718 1562 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.06 % Allowed : 14.73 % 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: 1.60 (0.22), residues: 1382 helix: 2.06 (0.17), residues: 866 sheet: 1.42 (0.60), residues: 44 loop : -0.92 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 249 PHE 0.025 0.002 PHE B 462 TYR 0.013 0.001 TYR B 406 ARG 0.014 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 720) hydrogen bonds : angle 4.31335 ( 2106) SS BOND : bond 0.00303 ( 8) SS BOND : angle 1.76264 ( 16) covalent geometry : bond 0.00362 (11998) covalent geometry : angle 0.58668 (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 145 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 1.419 Fit side-chains REVERT: A 108 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8114 (t-90) REVERT: A 282 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6479 (tptt) REVERT: A 386 MET cc_start: 0.8412 (tpp) cc_final: 0.8088 (mmm) REVERT: A 409 ASP cc_start: 0.8782 (m-30) cc_final: 0.8274 (t0) REVERT: A 527 ILE cc_start: 0.9696 (mm) cc_final: 0.9441 (mt) REVERT: A 548 GLU cc_start: 0.9030 (tp30) cc_final: 0.8683 (mp0) REVERT: A 553 MET cc_start: 0.8459 (tpp) cc_final: 0.7967 (tpp) REVERT: A 595 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8016 (mt-10) REVERT: A 742 MET cc_start: 0.8936 (mtt) cc_final: 0.8604 (mtm) REVERT: A 773 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8463 (tpp) REVERT: B 409 ASP cc_start: 0.8618 (m-30) cc_final: 0.8219 (t0) REVERT: B 458 SER cc_start: 0.8977 (m) cc_final: 0.8691 (p) REVERT: B 538 PHE cc_start: 0.8501 (t80) cc_final: 0.8176 (t80) REVERT: B 548 GLU cc_start: 0.9101 (tp30) cc_final: 0.8552 (mp0) REVERT: B 749 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8088 (t0) REVERT: B 754 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9130 (mp) outliers start: 39 outliers final: 23 residues processed: 136 average time/residue: 1.6971 time to fit residues: 250.8025 Evaluate side-chains 130 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain A residue 371 LEU 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 754 LEU 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 296 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 54 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 0.0020 chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 HIS B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.120835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085957 restraints weight = 21789.251| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.94 r_work: 0.3071 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12006 Z= 0.149 Angle : 0.585 12.779 16282 Z= 0.300 Chirality : 0.040 0.152 1786 Planarity : 0.005 0.049 2010 Dihedral : 4.190 22.606 1562 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.37 % Allowed : 14.89 % Favored : 81.74 % 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: 1.62 (0.22), residues: 1382 helix: 2.09 (0.17), residues: 868 sheet: 1.40 (0.62), residues: 42 loop : -0.94 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 249 PHE 0.026 0.001 PHE B 462 TYR 0.016 0.001 TYR B 406 ARG 0.016 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 720) hydrogen bonds : angle 4.26669 ( 2106) SS BOND : bond 0.00230 ( 8) SS BOND : angle 1.78239 ( 16) covalent geometry : bond 0.00337 (11998) covalent geometry : angle 0.58277 (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 152 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 1.438 Fit side-chains REVERT: A 108 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8098 (t-90) REVERT: A 142 MET cc_start: 0.8068 (mtp) cc_final: 0.7806 (mtm) REVERT: A 282 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6514 (tptm) REVERT: A 386 MET cc_start: 0.8361 (tpp) cc_final: 0.8098 (mmm) REVERT: A 409 ASP cc_start: 0.8787 (m-30) cc_final: 0.8265 (t0) REVERT: A 527 ILE cc_start: 0.9702 (mm) cc_final: 0.9461 (mt) REVERT: A 534 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7850 (mpp) REVERT: A 548 GLU cc_start: 0.9016 (tp30) cc_final: 0.8614 (mp0) REVERT: A 553 MET cc_start: 0.8441 (tpp) cc_final: 0.7961 (tpp) REVERT: A 595 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 773 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8441 (tpp) REVERT: B 386 MET cc_start: 0.8498 (tpp) cc_final: 0.8074 (mmm) REVERT: B 409 ASP cc_start: 0.8627 (m-30) cc_final: 0.8218 (t0) REVERT: B 458 SER cc_start: 0.8900 (m) cc_final: 0.8667 (p) REVERT: B 524 LEU cc_start: 0.9695 (mt) cc_final: 0.9314 (pp) REVERT: B 538 PHE cc_start: 0.8520 (t80) cc_final: 0.8146 (t80) REVERT: B 548 GLU cc_start: 0.9102 (tp30) cc_final: 0.8552 (mp0) REVERT: B 742 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8427 (mtp) REVERT: B 749 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8066 (t0) REVERT: B 754 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9144 (mp) outliers start: 43 outliers final: 25 residues processed: 142 average time/residue: 1.0975 time to fit residues: 171.6702 Evaluate side-chains 137 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 534 MET 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 754 LEU 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 296 ILE Chi-restraints excluded: chain B residue 464 ILE 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 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 742 MET 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: 0.9990 chunk 118 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.121172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086344 restraints weight = 22056.786| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.93 r_work: 0.3074 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3928 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= 0.137 Angle : 0.580 11.987 16282 Z= 0.296 Chirality : 0.040 0.149 1786 Planarity : 0.005 0.051 2010 Dihedral : 4.149 22.418 1562 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.74 % Allowed : 15.83 % Favored : 81.43 % 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: 1.63 (0.22), residues: 1382 helix: 2.10 (0.17), residues: 870 sheet: 1.39 (0.60), residues: 44 loop : -0.96 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 249 PHE 0.027 0.001 PHE B 462 TYR 0.015 0.001 TYR B 406 ARG 0.017 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 720) hydrogen bonds : angle 4.24059 ( 2106) SS BOND : bond 0.00248 ( 8) SS BOND : angle 1.75351 ( 16) covalent geometry : bond 0.00305 (11998) covalent geometry : angle 0.57720 (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 143 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8197 (t-90) REVERT: A 142 MET cc_start: 0.8095 (mtp) cc_final: 0.7814 (mtm) REVERT: A 282 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6442 (tptt) REVERT: A 386 MET cc_start: 0.8339 (tpp) cc_final: 0.8108 (mmm) REVERT: A 409 ASP cc_start: 0.8780 (m-30) cc_final: 0.8249 (t0) REVERT: A 527 ILE cc_start: 0.9717 (mm) cc_final: 0.9444 (mt) REVERT: A 553 MET cc_start: 0.8448 (tpp) cc_final: 0.7983 (tpp) REVERT: A 595 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8030 (mt-10) REVERT: A 742 MET cc_start: 0.8982 (mtt) cc_final: 0.8619 (mtm) REVERT: B 386 MET cc_start: 0.8457 (tpp) cc_final: 0.8170 (mmm) REVERT: B 409 ASP cc_start: 0.8631 (m-30) cc_final: 0.8220 (t0) REVERT: B 458 SER cc_start: 0.8922 (m) cc_final: 0.8679 (p) REVERT: B 507 MET cc_start: 0.4684 (pmt) cc_final: 0.4332 (pmm) REVERT: B 524 LEU cc_start: 0.9710 (mt) cc_final: 0.9402 (pp) REVERT: B 538 PHE cc_start: 0.8392 (t80) cc_final: 0.7976 (t80) REVERT: B 548 GLU cc_start: 0.9065 (tp30) cc_final: 0.8551 (mp0) REVERT: B 636 ARG cc_start: 0.7487 (mmp-170) cc_final: 0.7269 (mmp-170) REVERT: B 742 MET cc_start: 0.8817 (mpt) cc_final: 0.8426 (mtp) REVERT: B 749 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8024 (t0) outliers start: 35 outliers final: 24 residues processed: 136 average time/residue: 1.0554 time to fit residues: 158.4968 Evaluate side-chains 129 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 371 LEU 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 664 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 49 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 296 ILE 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 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 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: 3.9990 chunk 1 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 chunk 104 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.121887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087273 restraints weight = 21761.180| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.95 r_work: 0.3090 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4045 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= 0.131 Angle : 0.581 11.593 16282 Z= 0.296 Chirality : 0.040 0.154 1786 Planarity : 0.005 0.059 2010 Dihedral : 4.112 22.694 1562 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.51 % Allowed : 16.61 % Favored : 80.88 % 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: 2.15 (0.17), residues: 874 sheet: 1.44 (0.61), residues: 44 loop : -0.90 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 249 PHE 0.028 0.001 PHE B 462 TYR 0.014 0.001 TYR A 827 ARG 0.016 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 720) hydrogen bonds : angle 4.24155 ( 2106) SS BOND : bond 0.00305 ( 8) SS BOND : angle 1.73597 ( 16) covalent geometry : bond 0.00292 (11998) covalent geometry : angle 0.57828 (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: 32 poor density : 114 time to evaluate : 1.285 Fit side-chains REVERT: A 96 ARG cc_start: 0.8390 (ptm160) cc_final: 0.8035 (ptp-110) REVERT: A 108 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.8099 (t-90) REVERT: A 386 MET cc_start: 0.8258 (tpp) cc_final: 0.8044 (mmm) REVERT: A 409 ASP cc_start: 0.8765 (m-30) cc_final: 0.8231 (t0) REVERT: A 527 ILE cc_start: 0.9716 (mm) cc_final: 0.9461 (mt) REVERT: A 548 GLU cc_start: 0.9043 (tp30) cc_final: 0.8625 (mp0) REVERT: A 553 MET cc_start: 0.8428 (tpp) cc_final: 0.7975 (tpp) REVERT: A 595 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 668 TYR cc_start: 0.9169 (m-80) cc_final: 0.8883 (m-80) REVERT: A 742 MET cc_start: 0.8978 (mtt) cc_final: 0.8599 (mtm) REVERT: B 386 MET cc_start: 0.8418 (tpp) cc_final: 0.8169 (mmm) REVERT: B 409 ASP cc_start: 0.8730 (m-30) cc_final: 0.8300 (t0) REVERT: B 458 SER cc_start: 0.8935 (m) cc_final: 0.8712 (p) REVERT: B 524 LEU cc_start: 0.9685 (mt) cc_final: 0.9330 (pp) REVERT: B 529 GLU cc_start: 0.8775 (tt0) cc_final: 0.8205 (pt0) REVERT: B 538 PHE cc_start: 0.8392 (t80) cc_final: 0.7959 (t80) REVERT: B 548 GLU cc_start: 0.9089 (tp30) cc_final: 0.8529 (mp0) REVERT: B 636 ARG cc_start: 0.7500 (mmp-170) cc_final: 0.7287 (mmp-170) REVERT: B 742 MET cc_start: 0.8809 (mpt) cc_final: 0.8412 (mtp) REVERT: B 749 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8028 (t0) outliers start: 32 outliers final: 21 residues processed: 139 average time/residue: 1.0663 time to fit residues: 163.0142 Evaluate side-chains 129 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 685 PHE Chi-restraints excluded: chain A residue 734 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 134 optimal weight: 0.0970 chunk 61 optimal weight: 0.0070 chunk 53 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.122007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087390 restraints weight = 21824.276| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.91 r_work: 0.3088 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12006 Z= 0.127 Angle : 0.589 11.885 16282 Z= 0.298 Chirality : 0.040 0.176 1786 Planarity : 0.005 0.067 2010 Dihedral : 4.107 22.958 1562 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.12 % Allowed : 17.08 % 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: 1.75 (0.22), residues: 1382 helix: 2.18 (0.17), residues: 874 sheet: 1.48 (0.60), residues: 44 loop : -0.90 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 249 PHE 0.028 0.001 PHE B 462 TYR 0.014 0.001 TYR B 827 ARG 0.018 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 720) hydrogen bonds : angle 4.21027 ( 2106) SS BOND : bond 0.00224 ( 8) SS BOND : angle 1.74065 ( 16) covalent geometry : bond 0.00282 (11998) covalent geometry : angle 0.58644 (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 137 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8201 (t-90) REVERT: A 386 MET cc_start: 0.8262 (tpp) cc_final: 0.8057 (mmm) REVERT: A 409 ASP cc_start: 0.8761 (m-30) cc_final: 0.8213 (t0) REVERT: A 524 LEU cc_start: 0.9727 (mt) cc_final: 0.9453 (pp) REVERT: A 527 ILE cc_start: 0.9722 (mm) cc_final: 0.9470 (mt) REVERT: A 553 MET cc_start: 0.8437 (tpp) cc_final: 0.7988 (tpp) REVERT: A 595 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8149 (mt-10) REVERT: A 668 TYR cc_start: 0.9169 (m-80) cc_final: 0.8911 (m-80) REVERT: A 742 MET cc_start: 0.8937 (mtt) cc_final: 0.8567 (mtm) REVERT: B 386 MET cc_start: 0.8412 (tpp) cc_final: 0.8171 (mmm) REVERT: B 409 ASP cc_start: 0.8730 (m-30) cc_final: 0.8263 (t0) REVERT: B 458 SER cc_start: 0.8982 (m) cc_final: 0.8761 (p) REVERT: B 503 LEU cc_start: 0.1965 (OUTLIER) cc_final: 0.0999 (tt) REVERT: B 524 LEU cc_start: 0.9691 (mt) cc_final: 0.9327 (pp) REVERT: B 529 GLU cc_start: 0.8772 (tt0) cc_final: 0.8211 (pt0) REVERT: B 538 PHE cc_start: 0.8393 (t80) cc_final: 0.7968 (t80) REVERT: B 548 GLU cc_start: 0.9085 (tp30) cc_final: 0.8534 (mp0) REVERT: B 636 ARG cc_start: 0.7497 (mmp-170) cc_final: 0.7282 (mmp-170) REVERT: B 742 MET cc_start: 0.8808 (mpt) cc_final: 0.8416 (mtp) REVERT: B 749 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8008 (t0) outliers start: 27 outliers final: 24 residues processed: 131 average time/residue: 0.9911 time to fit residues: 144.0058 Evaluate side-chains 134 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 315 VAL Chi-restraints excluded: chain A residue 365 CYS 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 115 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 375 ASP 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: 0.6980 chunk 37 optimal weight: 5.9990 chunk 119 optimal weight: 0.0070 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.121851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087213 restraints weight = 21677.257| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.91 r_work: 0.3095 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4172 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= 0.132 Angle : 0.593 12.098 16282 Z= 0.299 Chirality : 0.040 0.155 1786 Planarity : 0.005 0.066 2010 Dihedral : 4.088 22.534 1562 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.51 % Allowed : 16.77 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.73 (0.22), residues: 1382 helix: 2.18 (0.17), residues: 876 sheet: 1.44 (0.60), residues: 44 loop : -0.97 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 108 PHE 0.029 0.001 PHE B 462 TYR 0.013 0.001 TYR B 406 ARG 0.016 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 720) hydrogen bonds : angle 4.21479 ( 2106) SS BOND : bond 0.00263 ( 8) SS BOND : angle 1.73623 ( 16) covalent geometry : bond 0.00295 (11998) covalent geometry : angle 0.59040 (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 142 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.311 Fit side-chains REVERT: A 96 ARG cc_start: 0.8411 (ptm160) cc_final: 0.8035 (ptp-110) REVERT: A 108 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8209 (t-170) REVERT: A 386 MET cc_start: 0.8254 (tpp) cc_final: 0.8049 (mmm) REVERT: A 409 ASP cc_start: 0.8722 (m-30) cc_final: 0.8162 (t0) REVERT: A 524 LEU cc_start: 0.9694 (mt) cc_final: 0.9428 (pp) REVERT: A 527 ILE cc_start: 0.9724 (mm) cc_final: 0.9472 (mt) REVERT: A 548 GLU cc_start: 0.9042 (tp30) cc_final: 0.8315 (tp30) REVERT: A 553 MET cc_start: 0.8405 (tpp) cc_final: 0.7954 (tpp) REVERT: A 595 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 668 TYR cc_start: 0.9173 (m-80) cc_final: 0.8887 (m-80) REVERT: A 742 MET cc_start: 0.8935 (mtt) cc_final: 0.8560 (mtm) REVERT: A 749 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.7966 (t0) REVERT: B 386 MET cc_start: 0.8388 (tpp) cc_final: 0.8146 (mmm) REVERT: B 409 ASP cc_start: 0.8728 (m-30) cc_final: 0.8265 (t0) REVERT: B 458 SER cc_start: 0.8979 (m) cc_final: 0.8758 (p) REVERT: B 503 LEU cc_start: 0.1686 (OUTLIER) cc_final: 0.0750 (tt) REVERT: B 524 LEU cc_start: 0.9646 (mt) cc_final: 0.9273 (pp) REVERT: B 529 GLU cc_start: 0.8777 (tt0) cc_final: 0.8200 (pt0) REVERT: B 538 PHE cc_start: 0.8452 (t80) cc_final: 0.7998 (t80) REVERT: B 548 GLU cc_start: 0.9077 (tp30) cc_final: 0.8539 (mp0) REVERT: B 636 ARG cc_start: 0.7529 (mmp-170) cc_final: 0.7309 (mmp-170) REVERT: B 742 MET cc_start: 0.8792 (mpt) cc_final: 0.8406 (mtp) REVERT: B 749 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8012 (t0) outliers start: 32 outliers final: 23 residues processed: 134 average time/residue: 1.1368 time to fit residues: 167.9609 Evaluate side-chains 134 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 315 VAL Chi-restraints excluded: chain A residue 365 CYS 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 749 ASP 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 122 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 730 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.120509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085753 restraints weight = 21811.813| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.91 r_work: 0.3068 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.004 0.047 12006 Z= 0.170 Angle : 0.615 12.439 16282 Z= 0.313 Chirality : 0.041 0.156 1786 Planarity : 0.006 0.153 2010 Dihedral : 4.188 22.336 1562 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.82 % Allowed : 16.54 % Favored : 80.64 % 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: 1.67 (0.22), residues: 1382 helix: 2.14 (0.17), residues: 870 sheet: 1.33 (0.60), residues: 44 loop : -0.96 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 829 HIS 0.003 0.001 HIS A 108 PHE 0.029 0.002 PHE B 462 TYR 0.014 0.001 TYR B 827 ARG 0.019 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 720) hydrogen bonds : angle 4.23954 ( 2106) SS BOND : bond 0.00291 ( 8) SS BOND : angle 1.80456 ( 16) covalent geometry : bond 0.00388 (11998) covalent geometry : angle 0.61279 (16266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7637.79 seconds wall clock time: 138 minutes 40.88 seconds (8320.88 seconds total)