Starting phenix.real_space_refine on Thu May 15 02:33:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8k_15916/05_2025/8b8k_15916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8k_15916/05_2025/8b8k_15916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b8k_15916/05_2025/8b8k_15916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8k_15916/05_2025/8b8k_15916.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8k_15916/05_2025/8b8k_15916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8k_15916/05_2025/8b8k_15916.cif" } resolution = 3.01 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= 0.020 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 2 5.49 5 S 80 5.16 5 C 8098 2.51 5 N 1976 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12324 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6121 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "B" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6121 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.27, per 1000 atoms: 0.59 Number of scatterers: 12324 At special positions: 0 Unit cell: (118.482, 108.066, 113.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 80 16.00 P 2 15.00 O 2162 8.00 N 1976 7.00 C 8098 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 596 " - pdb=" SG CYS A 601 " 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 596 " - pdb=" SG CYS B 601 " 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: 3.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 65.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 89 through 109 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.560A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 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 removed outlier: 3.526A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 342 through 345 Processing helix chain 'A' and resid 364 through 375 removed outlier: 4.032A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.934A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.694A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 488 removed outlier: 4.484A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.706A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.015A pdb=" N SER A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.835A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 3.982A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 3.815A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.407A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 875 Processing helix chain 'B' and resid 89 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 232 through 239 removed outlier: 3.557A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 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 removed outlier: 3.531A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 342 through 345 Processing helix chain 'B' and resid 364 through 375 removed outlier: 4.038A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.934A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 removed outlier: 3.720A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 488 removed outlier: 4.462A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.715A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.019A pdb=" N SER B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.837A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 3.992A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.811A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 796 through 802 removed outlier: 4.411A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 875 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 146 through 148 removed outlier: 3.543A pdb=" N SER A 190 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 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 146 through 148 removed outlier: 3.554A pdb=" N SER B 190 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 785 763 hydrogen bonds defined for protein. 2229 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: 3.74 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2011 1.32 - 1.45: 3570 1.45 - 1.57: 6941 1.57 - 1.69: 4 1.69 - 1.81: 120 Bond restraints: 12646 Sorted by residual: bond pdb=" CA ASP B 583 " pdb=" CB ASP B 583 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.27e+00 bond pdb=" CA ASP A 375 " pdb=" CB ASP A 375 " ideal model delta sigma weight residual 1.531 1.565 -0.034 3.28e-02 9.30e+02 1.09e+00 bond pdb=" CA ASP B 375 " pdb=" CB ASP B 375 " ideal model delta sigma weight residual 1.531 1.564 -0.033 3.28e-02 9.30e+02 1.03e+00 bond pdb=" CB VAL A 702 " pdb=" CG1 VAL A 702 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.17e-01 bond pdb=" CB VAL B 702 " pdb=" CG1 VAL B 702 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.15e-01 ... (remaining 12641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 16606 1.22 - 2.44: 398 2.44 - 3.67: 100 3.67 - 4.89: 10 4.89 - 6.11: 4 Bond angle restraints: 17118 Sorted by residual: angle pdb=" N VAL B 578 " pdb=" CA VAL B 578 " pdb=" C VAL B 578 " ideal model delta sigma weight residual 113.71 110.39 3.32 9.50e-01 1.11e+00 1.22e+01 angle pdb=" CA GLY B 600 " pdb=" C GLY B 600 " pdb=" O GLY B 600 " ideal model delta sigma weight residual 122.45 120.32 2.13 7.20e-01 1.93e+00 8.71e+00 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 114.12 -3.42 1.22e+00 6.72e-01 7.86e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 114.06 -3.36 1.22e+00 6.72e-01 7.59e+00 angle pdb=" CA GLY A 600 " pdb=" C GLY A 600 " pdb=" O GLY A 600 " ideal model delta sigma weight residual 122.37 120.37 2.00 7.30e-01 1.88e+00 7.47e+00 ... (remaining 17113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.03: 7354 32.03 - 64.06: 125 64.06 - 96.09: 5 96.09 - 128.12: 0 128.12 - 160.14: 2 Dihedral angle restraints: 7486 sinusoidal: 3104 harmonic: 4382 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.81 -40.81 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.43 -40.43 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" O5 P1O A1003 " pdb=" C7 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " ideal model delta sinusoidal sigma weight residual 56.91 -142.95 -160.14 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 7483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 997 0.025 - 0.050: 483 0.050 - 0.075: 255 0.075 - 0.099: 88 0.099 - 0.124: 31 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CA VAL A 715 " pdb=" N VAL A 715 " pdb=" C VAL A 715 " pdb=" CB VAL A 715 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL B 715 " pdb=" N VAL B 715 " pdb=" C VAL B 715 " pdb=" CB VAL B 715 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1851 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 597 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 598 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 597 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 598 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 580 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO B 581 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 581 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 581 " -0.023 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 195 2.67 - 3.23: 12052 3.23 - 3.78: 19675 3.78 - 4.34: 26171 4.34 - 4.90: 43669 Nonbonded interactions: 101762 Sorted by model distance: nonbonded pdb=" OG SER B 190 " pdb=" OD2 ASP B 194 " model vdw 2.111 3.040 nonbonded pdb=" OG SER A 190 " pdb=" OD2 ASP A 194 " model vdw 2.121 3.040 nonbonded pdb=" OD2 ASP B 749 " pdb=" OH TYR B 776 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASP A 749 " pdb=" OH TYR A 776 " model vdw 2.245 3.040 nonbonded pdb=" OE2 GLU A 699 " pdb="CA CA A1002 " model vdw 2.256 2.510 ... (remaining 101757 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: 0.930 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.850 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 0.034 12654 Z= 0.138 Angle : 0.499 6.111 17134 Z= 0.283 Chirality : 0.039 0.124 1854 Planarity : 0.004 0.047 2118 Dihedral : 11.832 160.144 4638 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.92 % Allowed : 4.95 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.22), residues: 1442 helix: 2.16 (0.16), residues: 920 sheet: 0.40 (0.66), residues: 62 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.003 0.001 HIS A 275 PHE 0.012 0.001 PHE A 560 TYR 0.016 0.001 TYR A 580 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.07660 ( 763) hydrogen bonds : angle 4.72890 ( 2229) SS BOND : bond 0.00127 ( 8) SS BOND : angle 0.37817 ( 16) covalent geometry : bond 0.00290 (12646) covalent geometry : angle 0.49955 (17118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: A 196 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.4759 (m-80) REVERT: A 236 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 255 TYR cc_start: 0.8186 (m-80) cc_final: 0.7805 (m-10) REVERT: A 298 ILE cc_start: 0.9013 (tp) cc_final: 0.8701 (tt) REVERT: A 370 LYS cc_start: 0.8293 (ptpp) cc_final: 0.8045 (mmtm) REVERT: A 403 GLU cc_start: 0.8060 (tt0) cc_final: 0.7610 (tm-30) REVERT: A 407 GLU cc_start: 0.8457 (tt0) cc_final: 0.8170 (tt0) REVERT: A 413 LEU cc_start: 0.8981 (tt) cc_final: 0.8723 (tt) REVERT: A 546 ASP cc_start: 0.8391 (m-30) cc_final: 0.8048 (m-30) REVERT: A 695 ASN cc_start: 0.8767 (t0) cc_final: 0.8397 (t0) REVERT: A 749 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7203 (t0) REVERT: A 770 TYR cc_start: 0.7937 (p90) cc_final: 0.7404 (t80) REVERT: A 773 MET cc_start: 0.9525 (mmm) cc_final: 0.9201 (tpp) REVERT: A 826 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8952 (tt) REVERT: B 73 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: B 196 TYR cc_start: 0.5988 (OUTLIER) cc_final: 0.4639 (m-80) REVERT: B 289 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8111 (ttt-90) REVERT: B 298 ILE cc_start: 0.9047 (tp) cc_final: 0.8705 (tt) REVERT: B 370 LYS cc_start: 0.8262 (ptpp) cc_final: 0.8018 (mmtm) REVERT: B 403 GLU cc_start: 0.8111 (tt0) cc_final: 0.7637 (tm-30) REVERT: B 407 GLU cc_start: 0.8457 (tt0) cc_final: 0.8157 (tt0) REVERT: B 413 LEU cc_start: 0.9136 (tt) cc_final: 0.8915 (tt) REVERT: B 546 ASP cc_start: 0.8310 (m-30) cc_final: 0.7991 (m-30) REVERT: B 695 ASN cc_start: 0.8770 (t0) cc_final: 0.8395 (t0) REVERT: B 749 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7171 (t0) REVERT: B 770 TYR cc_start: 0.7884 (p90) cc_final: 0.7486 (t80) REVERT: B 773 MET cc_start: 0.9502 (mmm) cc_final: 0.9161 (tpp) outliers start: 39 outliers final: 13 residues processed: 248 average time/residue: 0.2467 time to fit residues: 87.5412 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 99 GLN A 104 ASN A 234 ASN A 525 ASN A 559 GLN A 632 ASN A 710 GLN A 730 GLN B 44 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 234 ASN B 525 ASN B 559 GLN B 632 ASN B 674 GLN B 695 ASN B 710 GLN B 730 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.082724 restraints weight = 21995.979| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.63 r_work: 0.2985 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12654 Z= 0.134 Angle : 0.524 7.917 17134 Z= 0.284 Chirality : 0.039 0.136 1854 Planarity : 0.005 0.046 2118 Dihedral : 10.057 159.497 1732 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.47 % Allowed : 9.00 % Favored : 88.53 % 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: 1.55 (0.22), residues: 1442 helix: 2.16 (0.16), residues: 922 sheet: 0.33 (0.65), residues: 62 loop : -1.31 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 PHE 0.013 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.006 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 763) hydrogen bonds : angle 4.43935 ( 2229) SS BOND : bond 0.00101 ( 8) SS BOND : angle 0.37620 ( 16) covalent geometry : bond 0.00296 (12646) covalent geometry : angle 0.52386 (17118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: A 196 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.4582 (m-80) REVERT: A 255 TYR cc_start: 0.8259 (m-80) cc_final: 0.7935 (m-10) REVERT: A 298 ILE cc_start: 0.8929 (tp) cc_final: 0.8617 (tt) REVERT: A 403 GLU cc_start: 0.8115 (tt0) cc_final: 0.7690 (tm-30) REVERT: A 407 GLU cc_start: 0.8478 (tt0) cc_final: 0.8244 (tt0) REVERT: A 546 ASP cc_start: 0.8294 (m-30) cc_final: 0.7945 (m-30) REVERT: A 631 MET cc_start: 0.8320 (mmm) cc_final: 0.8000 (mmm) REVERT: A 695 ASN cc_start: 0.8809 (t0) cc_final: 0.8354 (t0) REVERT: A 770 TYR cc_start: 0.7966 (p90) cc_final: 0.7411 (t80) REVERT: A 773 MET cc_start: 0.9473 (mmm) cc_final: 0.8713 (mmt) REVERT: A 826 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8830 (tt) REVERT: B 73 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: B 142 MET cc_start: 0.8473 (ptt) cc_final: 0.8044 (ptt) REVERT: B 196 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.4468 (m-80) REVERT: B 298 ILE cc_start: 0.8924 (tp) cc_final: 0.8609 (tt) REVERT: B 334 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8291 (p) REVERT: B 403 GLU cc_start: 0.8135 (tt0) cc_final: 0.7649 (tm-30) REVERT: B 407 GLU cc_start: 0.8494 (tt0) cc_final: 0.8281 (tt0) REVERT: B 461 PHE cc_start: 0.6231 (m-80) cc_final: 0.5563 (t80) REVERT: B 546 ASP cc_start: 0.8302 (m-30) cc_final: 0.7961 (m-30) REVERT: B 695 ASN cc_start: 0.8838 (t0) cc_final: 0.8393 (t0) REVERT: B 749 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7143 (t0) REVERT: B 770 TYR cc_start: 0.7922 (p90) cc_final: 0.7509 (t80) REVERT: B 773 MET cc_start: 0.9437 (mmm) cc_final: 0.8677 (mmt) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.2533 time to fit residues: 66.1476 Evaluate side-chains 151 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 549 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.080966 restraints weight = 22500.621| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.63 r_work: 0.2950 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12654 Z= 0.174 Angle : 0.543 7.163 17134 Z= 0.294 Chirality : 0.040 0.156 1854 Planarity : 0.004 0.043 2118 Dihedral : 9.754 158.678 1723 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.07 % Allowed : 9.37 % Favored : 87.56 % 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: 1.53 (0.22), residues: 1442 helix: 2.13 (0.16), residues: 922 sheet: 0.31 (0.66), residues: 62 loop : -1.30 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 273 HIS 0.004 0.001 HIS A 143 PHE 0.019 0.002 PHE A 461 TYR 0.016 0.001 TYR B 580 ARG 0.004 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 763) hydrogen bonds : angle 4.46658 ( 2229) SS BOND : bond 0.00750 ( 8) SS BOND : angle 0.76906 ( 16) covalent geometry : bond 0.00398 (12646) covalent geometry : angle 0.54324 (17118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: A 196 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.4743 (m-80) REVERT: A 255 TYR cc_start: 0.8294 (m-80) cc_final: 0.7990 (m-10) REVERT: A 298 ILE cc_start: 0.8927 (tp) cc_final: 0.8628 (tt) REVERT: A 334 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8388 (p) REVERT: A 403 GLU cc_start: 0.8148 (tt0) cc_final: 0.7672 (tm-30) REVERT: A 407 GLU cc_start: 0.8499 (tt0) cc_final: 0.8296 (tt0) REVERT: A 481 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8757 (p) REVERT: A 546 ASP cc_start: 0.8283 (m-30) cc_final: 0.7932 (m-30) REVERT: A 695 ASN cc_start: 0.8914 (t0) cc_final: 0.8489 (t0) REVERT: A 770 TYR cc_start: 0.8035 (p90) cc_final: 0.7453 (t80) REVERT: A 773 MET cc_start: 0.9421 (mmm) cc_final: 0.8684 (mmt) REVERT: A 826 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8905 (tt) REVERT: B 73 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: B 196 TYR cc_start: 0.6064 (OUTLIER) cc_final: 0.4558 (m-80) REVERT: B 298 ILE cc_start: 0.8916 (tp) cc_final: 0.8617 (tt) REVERT: B 334 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 403 GLU cc_start: 0.8166 (tt0) cc_final: 0.7665 (tm-30) REVERT: B 461 PHE cc_start: 0.6447 (m-80) cc_final: 0.6185 (t80) REVERT: B 481 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8791 (p) REVERT: B 546 ASP cc_start: 0.8314 (m-30) cc_final: 0.7945 (m-30) REVERT: B 695 ASN cc_start: 0.8931 (t0) cc_final: 0.8488 (t0) REVERT: B 749 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7291 (t0) REVERT: B 770 TYR cc_start: 0.8074 (p90) cc_final: 0.7572 (t80) REVERT: B 773 MET cc_start: 0.9399 (mmm) cc_final: 0.8678 (mmt) outliers start: 41 outliers final: 25 residues processed: 163 average time/residue: 0.2333 time to fit residues: 55.2915 Evaluate side-chains 149 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 1 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 525 ASN A 674 GLN A 695 ASN B 111 GLN B 143 HIS B 234 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082230 restraints weight = 22209.033| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.63 r_work: 0.2973 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12654 Z= 0.131 Angle : 0.510 6.738 17134 Z= 0.274 Chirality : 0.039 0.141 1854 Planarity : 0.004 0.044 2118 Dihedral : 9.518 161.667 1723 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.22 % Allowed : 9.52 % Favored : 87.26 % 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: 1442 helix: 2.19 (0.16), residues: 922 sheet: 0.44 (0.67), residues: 62 loop : -1.27 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 273 HIS 0.003 0.001 HIS B 143 PHE 0.023 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.004 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 763) hydrogen bonds : angle 4.36754 ( 2229) SS BOND : bond 0.00365 ( 8) SS BOND : angle 0.87692 ( 16) covalent geometry : bond 0.00291 (12646) covalent geometry : angle 0.51002 (17118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: A 196 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.4538 (m-80) REVERT: A 255 TYR cc_start: 0.8292 (m-80) cc_final: 0.8056 (m-10) REVERT: A 298 ILE cc_start: 0.8913 (tp) cc_final: 0.8628 (tt) REVERT: A 334 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8395 (p) REVERT: A 403 GLU cc_start: 0.8140 (tt0) cc_final: 0.7703 (tm-30) REVERT: A 407 GLU cc_start: 0.8472 (tt0) cc_final: 0.8272 (tt0) REVERT: A 481 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8739 (p) REVERT: A 546 ASP cc_start: 0.8277 (m-30) cc_final: 0.7920 (m-30) REVERT: A 631 MET cc_start: 0.8409 (mmm) cc_final: 0.8131 (mmm) REVERT: A 695 ASN cc_start: 0.8859 (t0) cc_final: 0.8459 (t0) REVERT: A 770 TYR cc_start: 0.7858 (p90) cc_final: 0.7255 (t80) REVERT: A 773 MET cc_start: 0.9461 (mmm) cc_final: 0.8733 (mmt) REVERT: B 73 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: B 191 ARG cc_start: 0.6893 (ptt90) cc_final: 0.6602 (ptt90) REVERT: B 196 TYR cc_start: 0.6014 (OUTLIER) cc_final: 0.4446 (m-80) REVERT: B 298 ILE cc_start: 0.8901 (tp) cc_final: 0.8617 (tt) REVERT: B 403 GLU cc_start: 0.8148 (tt0) cc_final: 0.7655 (tm-30) REVERT: B 461 PHE cc_start: 0.6447 (m-80) cc_final: 0.6178 (t80) REVERT: B 481 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8781 (p) REVERT: B 543 THR cc_start: 0.8325 (p) cc_final: 0.7925 (p) REVERT: B 546 ASP cc_start: 0.8328 (m-30) cc_final: 0.8007 (m-30) REVERT: B 695 ASN cc_start: 0.8873 (t0) cc_final: 0.8455 (t0) REVERT: B 770 TYR cc_start: 0.8059 (p90) cc_final: 0.7546 (t80) REVERT: B 773 MET cc_start: 0.9425 (mmm) cc_final: 0.8689 (mmt) outliers start: 43 outliers final: 24 residues processed: 166 average time/residue: 0.2339 time to fit residues: 57.1992 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 93 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 401 GLN A 525 ASN A 674 GLN A 695 ASN B 401 GLN B 525 ASN B 549 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081838 restraints weight = 22303.446| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.63 r_work: 0.2963 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12654 Z= 0.145 Angle : 0.525 7.362 17134 Z= 0.282 Chirality : 0.040 0.134 1854 Planarity : 0.004 0.042 2118 Dihedral : 9.313 162.180 1719 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.22 % Allowed : 9.60 % Favored : 87.18 % 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: 1.59 (0.22), residues: 1442 helix: 2.17 (0.16), residues: 922 sheet: 0.44 (0.66), residues: 62 loop : -1.26 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 PHE 0.019 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.003 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 763) hydrogen bonds : angle 4.35347 ( 2229) SS BOND : bond 0.00287 ( 8) SS BOND : angle 1.07455 ( 16) covalent geometry : bond 0.00330 (12646) covalent geometry : angle 0.52469 (17118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: A 196 TYR cc_start: 0.6030 (OUTLIER) cc_final: 0.4562 (m-80) REVERT: A 255 TYR cc_start: 0.8306 (m-80) cc_final: 0.8093 (m-10) REVERT: A 298 ILE cc_start: 0.8925 (tp) cc_final: 0.8643 (tt) REVERT: A 334 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8347 (p) REVERT: A 403 GLU cc_start: 0.8155 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 481 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 546 ASP cc_start: 0.8307 (m-30) cc_final: 0.7941 (m-30) REVERT: A 695 ASN cc_start: 0.8901 (t0) cc_final: 0.8460 (t0) REVERT: A 770 TYR cc_start: 0.7913 (p90) cc_final: 0.7278 (t80) REVERT: A 773 MET cc_start: 0.9444 (mmm) cc_final: 0.8725 (mmt) REVERT: B 73 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: B 196 TYR cc_start: 0.5994 (OUTLIER) cc_final: 0.4500 (m-80) REVERT: B 298 ILE cc_start: 0.8940 (tp) cc_final: 0.8648 (tt) REVERT: B 334 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8347 (p) REVERT: B 403 GLU cc_start: 0.8160 (tt0) cc_final: 0.7669 (tm-30) REVERT: B 461 PHE cc_start: 0.6480 (m-80) cc_final: 0.6222 (t80) REVERT: B 481 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8802 (p) REVERT: B 546 ASP cc_start: 0.8355 (m-30) cc_final: 0.7959 (m-30) REVERT: B 661 LYS cc_start: 0.9218 (mmtp) cc_final: 0.8848 (mppt) REVERT: B 695 ASN cc_start: 0.8916 (t0) cc_final: 0.8490 (t0) REVERT: B 770 TYR cc_start: 0.8069 (p90) cc_final: 0.7547 (t80) REVERT: B 773 MET cc_start: 0.9357 (mmm) cc_final: 0.8706 (mmt) outliers start: 43 outliers final: 25 residues processed: 154 average time/residue: 0.2470 time to fit residues: 54.6502 Evaluate side-chains 150 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 chunk 57 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 525 ASN A 674 GLN A 695 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.082852 restraints weight = 22293.885| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.74 r_work: 0.2969 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12654 Z= 0.116 Angle : 0.502 6.784 17134 Z= 0.269 Chirality : 0.039 0.134 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.215 164.752 1718 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.00 % Allowed : 9.67 % Favored : 87.33 % 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: 1.69 (0.22), residues: 1442 helix: 2.25 (0.16), residues: 922 sheet: 0.38 (0.65), residues: 62 loop : -1.22 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 PHE 0.017 0.001 PHE A 461 TYR 0.014 0.001 TYR B 580 ARG 0.002 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 763) hydrogen bonds : angle 4.25821 ( 2229) SS BOND : bond 0.00180 ( 8) SS BOND : angle 0.84874 ( 16) covalent geometry : bond 0.00255 (12646) covalent geometry : angle 0.50157 (17118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: A 196 TYR cc_start: 0.5839 (OUTLIER) cc_final: 0.4391 (m-80) REVERT: A 298 ILE cc_start: 0.8844 (tp) cc_final: 0.8578 (tt) REVERT: A 334 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.8074 (p) REVERT: A 403 GLU cc_start: 0.8066 (tt0) cc_final: 0.7609 (tm-30) REVERT: A 481 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8631 (p) REVERT: A 546 ASP cc_start: 0.8221 (m-30) cc_final: 0.7851 (m-30) REVERT: A 631 MET cc_start: 0.8338 (mmm) cc_final: 0.8094 (mmm) REVERT: A 661 LYS cc_start: 0.9199 (mmtp) cc_final: 0.8807 (mppt) REVERT: A 695 ASN cc_start: 0.8796 (t0) cc_final: 0.8357 (t0) REVERT: A 770 TYR cc_start: 0.7809 (p90) cc_final: 0.7182 (t80) REVERT: A 773 MET cc_start: 0.9367 (mmm) cc_final: 0.8625 (mmt) REVERT: B 73 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 196 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.4334 (m-80) REVERT: B 298 ILE cc_start: 0.8853 (tp) cc_final: 0.8571 (tt) REVERT: B 334 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8061 (p) REVERT: B 403 GLU cc_start: 0.8061 (tt0) cc_final: 0.7593 (tm-30) REVERT: B 461 PHE cc_start: 0.6332 (m-80) cc_final: 0.6090 (t80) REVERT: B 543 THR cc_start: 0.8122 (p) cc_final: 0.7717 (p) REVERT: B 546 ASP cc_start: 0.8273 (m-30) cc_final: 0.7930 (m-30) REVERT: B 661 LYS cc_start: 0.9201 (mmtp) cc_final: 0.8808 (mppt) REVERT: B 695 ASN cc_start: 0.8808 (t0) cc_final: 0.8365 (t0) REVERT: B 770 TYR cc_start: 0.7953 (p90) cc_final: 0.7350 (t80) REVERT: B 773 MET cc_start: 0.9328 (mmm) cc_final: 0.8670 (mmt) outliers start: 40 outliers final: 27 residues processed: 163 average time/residue: 0.2287 time to fit residues: 55.5035 Evaluate side-chains 153 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 ASN A 674 GLN A 695 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.078856 restraints weight = 22542.446| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.58 r_work: 0.2898 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 12654 Z= 0.249 Angle : 0.610 9.079 17134 Z= 0.325 Chirality : 0.042 0.160 1854 Planarity : 0.005 0.039 2118 Dihedral : 9.439 161.997 1718 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.52 % Allowed : 9.30 % Favored : 87.18 % 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: 1.39 (0.22), residues: 1442 helix: 2.04 (0.16), residues: 912 sheet: 0.31 (0.64), residues: 62 loop : -1.30 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 829 HIS 0.003 0.001 HIS A 275 PHE 0.016 0.002 PHE A 461 TYR 0.022 0.002 TYR A 580 ARG 0.004 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04957 ( 763) hydrogen bonds : angle 4.50237 ( 2229) SS BOND : bond 0.00274 ( 8) SS BOND : angle 1.27545 ( 16) covalent geometry : bond 0.00579 (12646) covalent geometry : angle 0.60895 (17118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: A 196 TYR cc_start: 0.5921 (OUTLIER) cc_final: 0.4657 (m-80) REVERT: A 298 ILE cc_start: 0.8833 (tp) cc_final: 0.8480 (tt) REVERT: A 334 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.8074 (p) REVERT: A 403 GLU cc_start: 0.8136 (tt0) cc_final: 0.7653 (tm-30) REVERT: A 481 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8737 (p) REVERT: A 546 ASP cc_start: 0.8270 (m-30) cc_final: 0.7973 (m-30) REVERT: A 770 TYR cc_start: 0.7905 (p90) cc_final: 0.7331 (t80) REVERT: A 773 MET cc_start: 0.9309 (mmm) cc_final: 0.8831 (tpp) REVERT: B 73 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: B 196 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.4772 (m-80) REVERT: B 298 ILE cc_start: 0.8822 (tp) cc_final: 0.8472 (tt) REVERT: B 334 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 403 GLU cc_start: 0.8069 (tt0) cc_final: 0.7517 (tm-30) REVERT: B 461 PHE cc_start: 0.6597 (m-80) cc_final: 0.6376 (t80) REVERT: B 481 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8762 (p) REVERT: B 546 ASP cc_start: 0.8255 (m-30) cc_final: 0.7913 (m-30) REVERT: B 661 LYS cc_start: 0.9146 (mmtp) cc_final: 0.8789 (mppt) REVERT: B 770 TYR cc_start: 0.7933 (p90) cc_final: 0.7349 (t80) REVERT: B 773 MET cc_start: 0.9298 (mmm) cc_final: 0.8670 (mmt) outliers start: 47 outliers final: 29 residues processed: 151 average time/residue: 0.2419 time to fit residues: 53.7875 Evaluate side-chains 146 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 108 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 720 GLN B 234 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081148 restraints weight = 22428.252| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.57 r_work: 0.2940 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12654 Z= 0.147 Angle : 0.540 7.219 17134 Z= 0.287 Chirality : 0.040 0.134 1854 Planarity : 0.004 0.039 2118 Dihedral : 9.386 164.833 1718 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.00 % Allowed : 9.52 % Favored : 87.48 % 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: 1.51 (0.22), residues: 1442 helix: 2.13 (0.16), residues: 920 sheet: 0.37 (0.65), residues: 62 loop : -1.33 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 273 HIS 0.002 0.001 HIS B 844 PHE 0.016 0.001 PHE A 461 TYR 0.014 0.001 TYR B 580 ARG 0.003 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 763) hydrogen bonds : angle 4.37836 ( 2229) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.94768 ( 16) covalent geometry : bond 0.00335 (12646) covalent geometry : angle 0.53951 (17118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: A 196 TYR cc_start: 0.5890 (OUTLIER) cc_final: 0.4686 (m-80) REVERT: A 298 ILE cc_start: 0.8855 (tp) cc_final: 0.8545 (tt) REVERT: A 334 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8074 (p) REVERT: A 403 GLU cc_start: 0.8065 (tt0) cc_final: 0.7582 (tm-30) REVERT: A 481 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8727 (p) REVERT: A 546 ASP cc_start: 0.8247 (m-30) cc_final: 0.7957 (m-30) REVERT: A 661 LYS cc_start: 0.9148 (mmtp) cc_final: 0.8794 (mppt) REVERT: A 695 ASN cc_start: 0.8865 (t0) cc_final: 0.8458 (t0) REVERT: A 770 TYR cc_start: 0.7864 (p90) cc_final: 0.7191 (t80) REVERT: A 773 MET cc_start: 0.9348 (mmm) cc_final: 0.8983 (tpp) REVERT: B 73 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: B 196 TYR cc_start: 0.5755 (OUTLIER) cc_final: 0.4705 (m-80) REVERT: B 298 ILE cc_start: 0.8868 (tp) cc_final: 0.8556 (tt) REVERT: B 334 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8065 (p) REVERT: B 403 GLU cc_start: 0.8056 (tt0) cc_final: 0.7518 (tm-30) REVERT: B 481 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8708 (p) REVERT: B 546 ASP cc_start: 0.8249 (m-30) cc_final: 0.7908 (m-30) REVERT: B 661 LYS cc_start: 0.9140 (mmtp) cc_final: 0.8785 (mppt) REVERT: B 770 TYR cc_start: 0.7899 (p90) cc_final: 0.7338 (t80) REVERT: B 773 MET cc_start: 0.9334 (mmm) cc_final: 0.8666 (mmt) outliers start: 40 outliers final: 28 residues processed: 145 average time/residue: 0.2291 time to fit residues: 48.7398 Evaluate side-chains 149 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 96 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 720 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.080074 restraints weight = 22459.666| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.59 r_work: 0.2921 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12654 Z= 0.177 Angle : 0.562 8.147 17134 Z= 0.298 Chirality : 0.040 0.134 1854 Planarity : 0.004 0.039 2118 Dihedral : 9.383 164.583 1718 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.07 % Allowed : 9.45 % Favored : 87.48 % 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: 1.48 (0.22), residues: 1442 helix: 2.14 (0.16), residues: 910 sheet: 0.36 (0.65), residues: 62 loop : -1.32 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.002 0.001 HIS A 844 PHE 0.016 0.002 PHE A 461 TYR 0.016 0.001 TYR A 580 ARG 0.005 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 763) hydrogen bonds : angle 4.40628 ( 2229) SS BOND : bond 0.00185 ( 8) SS BOND : angle 1.05869 ( 16) covalent geometry : bond 0.00412 (12646) covalent geometry : angle 0.56114 (17118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: A 196 TYR cc_start: 0.5801 (OUTLIER) cc_final: 0.4604 (m-80) REVERT: A 298 ILE cc_start: 0.8861 (tp) cc_final: 0.8549 (tt) REVERT: A 334 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.8078 (p) REVERT: A 403 GLU cc_start: 0.8122 (tt0) cc_final: 0.7646 (tm-30) REVERT: A 481 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8725 (p) REVERT: A 546 ASP cc_start: 0.8258 (m-30) cc_final: 0.7975 (m-30) REVERT: A 661 LYS cc_start: 0.9150 (mmtp) cc_final: 0.8799 (mppt) REVERT: A 695 ASN cc_start: 0.8881 (t0) cc_final: 0.8485 (t0) REVERT: A 770 TYR cc_start: 0.7878 (p90) cc_final: 0.7297 (t80) REVERT: A 773 MET cc_start: 0.9284 (mmm) cc_final: 0.8959 (tpp) REVERT: B 73 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: B 192 MET cc_start: 0.5150 (ppp) cc_final: 0.4842 (ppp) REVERT: B 196 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.4806 (m-80) REVERT: B 298 ILE cc_start: 0.8876 (tp) cc_final: 0.8558 (tt) REVERT: B 334 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.8069 (p) REVERT: B 403 GLU cc_start: 0.8064 (tt0) cc_final: 0.7522 (tm-30) REVERT: B 481 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8702 (p) REVERT: B 546 ASP cc_start: 0.8268 (m-30) cc_final: 0.7965 (m-30) REVERT: B 661 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8788 (mppt) REVERT: B 695 ASN cc_start: 0.8884 (t0) cc_final: 0.8498 (t0) REVERT: B 770 TYR cc_start: 0.8026 (p90) cc_final: 0.7462 (t80) REVERT: B 773 MET cc_start: 0.9272 (mmm) cc_final: 0.8699 (mmt) outliers start: 41 outliers final: 29 residues processed: 147 average time/residue: 0.2273 time to fit residues: 49.1732 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 8 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 146 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN A 720 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081349 restraints weight = 22329.697| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.59 r_work: 0.2943 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12654 Z= 0.142 Angle : 0.543 8.886 17134 Z= 0.286 Chirality : 0.039 0.134 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.338 165.989 1718 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.85 % Allowed : 9.75 % Favored : 87.41 % 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: 1.56 (0.22), residues: 1442 helix: 2.18 (0.16), residues: 920 sheet: 0.41 (0.65), residues: 62 loop : -1.33 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 397 HIS 0.002 0.001 HIS B 844 PHE 0.020 0.001 PHE A 461 TYR 0.014 0.001 TYR A 580 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 763) hydrogen bonds : angle 4.33607 ( 2229) SS BOND : bond 0.00158 ( 8) SS BOND : angle 0.91507 ( 16) covalent geometry : bond 0.00324 (12646) covalent geometry : angle 0.54289 (17118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7250 (m-80) REVERT: A 196 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.4765 (m-80) REVERT: A 298 ILE cc_start: 0.8847 (tp) cc_final: 0.8549 (tt) REVERT: A 334 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.8082 (p) REVERT: A 403 GLU cc_start: 0.8067 (tt0) cc_final: 0.7594 (tm-30) REVERT: A 481 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8709 (p) REVERT: A 546 ASP cc_start: 0.8245 (m-30) cc_final: 0.7951 (m-30) REVERT: A 631 MET cc_start: 0.8307 (mmm) cc_final: 0.8062 (mmm) REVERT: A 661 LYS cc_start: 0.9146 (mmtp) cc_final: 0.8797 (mppt) REVERT: A 695 ASN cc_start: 0.8837 (t0) cc_final: 0.8449 (t0) REVERT: A 742 MET cc_start: 0.8629 (mmm) cc_final: 0.8425 (mmt) REVERT: A 770 TYR cc_start: 0.7856 (p90) cc_final: 0.7183 (t80) REVERT: A 773 MET cc_start: 0.9337 (mmm) cc_final: 0.8967 (tpp) REVERT: B 73 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: B 196 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.5205 (m-80) REVERT: B 298 ILE cc_start: 0.8860 (tp) cc_final: 0.8556 (tt) REVERT: B 334 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8057 (p) REVERT: B 403 GLU cc_start: 0.8068 (tt0) cc_final: 0.7563 (tm-30) REVERT: B 481 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 546 ASP cc_start: 0.8260 (m-30) cc_final: 0.7937 (m-30) REVERT: B 661 LYS cc_start: 0.9134 (mmtp) cc_final: 0.8783 (mppt) REVERT: B 695 ASN cc_start: 0.8844 (t0) cc_final: 0.8448 (t0) REVERT: B 770 TYR cc_start: 0.7895 (p90) cc_final: 0.7301 (t80) REVERT: B 773 MET cc_start: 0.9310 (mmm) cc_final: 0.8634 (mmt) outliers start: 38 outliers final: 26 residues processed: 145 average time/residue: 0.2321 time to fit residues: 49.8319 Evaluate side-chains 144 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 42 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN A 720 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081604 restraints weight = 22476.880| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.60 r_work: 0.2948 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12654 Z= 0.139 Angle : 0.545 9.543 17134 Z= 0.286 Chirality : 0.039 0.134 1854 Planarity : 0.004 0.039 2118 Dihedral : 9.272 166.226 1718 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.00 % Allowed : 9.82 % Favored : 87.18 % 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: 1.58 (0.22), residues: 1442 helix: 2.20 (0.16), residues: 920 sheet: 0.43 (0.65), residues: 62 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 397 HIS 0.002 0.001 HIS B 844 PHE 0.029 0.001 PHE B 461 TYR 0.016 0.001 TYR A 580 ARG 0.005 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 763) hydrogen bonds : angle 4.31418 ( 2229) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.92733 ( 16) covalent geometry : bond 0.00315 (12646) covalent geometry : angle 0.54416 (17118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5162.37 seconds wall clock time: 90 minutes 55.14 seconds (5455.14 seconds total)