Starting phenix.real_space_refine on Sat Aug 23 14:12:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8k_15916/08_2025/8b8k_15916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8k_15916/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8b8k_15916/08_2025/8b8k_15916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8k_15916/08_2025/8b8k_15916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b8k_15916/08_2025/8b8k_15916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8k_15916/08_2025/8b8k_15916.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.07, per 1000 atoms: 0.25 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: 1.08 Conformation dependent library (CDL) restraints added in 564.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 2.31 Time building geometry restraints manager: 1.45 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: 0.02 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: 0.010 Normalize map: mean=0, sd=1: 1.440 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.003 0.000 ARG A 399 TYR 0.016 0.001 TYR A 580 PHE 0.012 0.001 PHE A 560 TRP 0.015 0.001 TRP B 273 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00290 (12646) covalent geometry : angle 0.49955 (17118) SS BOND : bond 0.00127 ( 8) SS BOND : angle 0.37817 ( 16) hydrogen bonds : bond 0.07660 ( 763) hydrogen bonds : angle 4.72890 ( 2229) *********************** 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 : 0.493 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: 0.8722 (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: 0.7992 (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) REVERT: B 868 ILE cc_start: 0.7987 (mt) cc_final: 0.7718 (mm) outliers start: 39 outliers final: 13 residues processed: 248 average time/residue: 0.1234 time to fit residues: 43.5660 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 710 GLN B 730 GLN B 814 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.081637 restraints weight = 22325.522| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.64 r_work: 0.2960 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12654 Z= 0.156 Angle : 0.537 7.668 17134 Z= 0.291 Chirality : 0.040 0.136 1854 Planarity : 0.005 0.046 2118 Dihedral : 10.060 158.060 1732 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.62 % Allowed : 9.00 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.22), residues: 1442 helix: 2.11 (0.16), residues: 922 sheet: 0.31 (0.65), residues: 62 loop : -1.34 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 636 TYR 0.016 0.001 TYR B 580 PHE 0.013 0.001 PHE A 461 TRP 0.012 0.001 TRP A 397 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00352 (12646) covalent geometry : angle 0.53729 (17118) SS BOND : bond 0.00169 ( 8) SS BOND : angle 0.42216 ( 16) hydrogen bonds : bond 0.04654 ( 763) hydrogen bonds : angle 4.48221 ( 2229) *********************** 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 177 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: A 196 TYR cc_start: 0.6093 (OUTLIER) cc_final: 0.4574 (m-80) REVERT: A 255 TYR cc_start: 0.8283 (m-80) cc_final: 0.7949 (m-10) REVERT: A 298 ILE cc_start: 0.8952 (tp) cc_final: 0.8627 (tt) REVERT: A 403 GLU cc_start: 0.8128 (tt0) cc_final: 0.7660 (tm-30) REVERT: A 407 GLU cc_start: 0.8489 (tt0) cc_final: 0.8246 (tt0) REVERT: A 546 ASP cc_start: 0.8310 (m-30) cc_final: 0.7952 (m-30) REVERT: A 695 ASN cc_start: 0.8894 (t0) cc_final: 0.8445 (t0) REVERT: A 770 TYR cc_start: 0.7997 (p90) cc_final: 0.7434 (t80) REVERT: A 773 MET cc_start: 0.9468 (mmm) cc_final: 0.8732 (mmt) REVERT: A 826 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8852 (tt) REVERT: B 73 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: B 142 MET cc_start: 0.8496 (ptt) cc_final: 0.8148 (ptt) REVERT: B 196 TYR cc_start: 0.5955 (OUTLIER) cc_final: 0.4519 (m-80) REVERT: B 298 ILE cc_start: 0.8947 (tp) cc_final: 0.8625 (tt) REVERT: B 334 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8304 (p) REVERT: B 403 GLU cc_start: 0.8159 (tt0) cc_final: 0.7663 (tm-30) REVERT: B 407 GLU cc_start: 0.8511 (tt0) cc_final: 0.8287 (tt0) REVERT: B 461 PHE cc_start: 0.6395 (m-80) cc_final: 0.5928 (t80) REVERT: B 546 ASP cc_start: 0.8320 (m-30) cc_final: 0.7967 (m-30) REVERT: B 695 ASN cc_start: 0.8902 (t0) cc_final: 0.8452 (t0) REVERT: B 749 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7242 (t0) REVERT: B 770 TYR cc_start: 0.7961 (p90) cc_final: 0.7521 (t80) REVERT: B 773 MET cc_start: 0.9441 (mmm) cc_final: 0.8729 (mmt) outliers start: 35 outliers final: 23 residues processed: 173 average time/residue: 0.0992 time to fit residues: 25.5059 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 453 VAL Chi-restraints excluded: chain A residue 458 SER 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN 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 401 GLN B 525 ASN B 549 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.078954 restraints weight = 22594.130| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.66 r_work: 0.2902 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12654 Z= 0.234 Angle : 0.587 7.198 17134 Z= 0.318 Chirality : 0.042 0.169 1854 Planarity : 0.005 0.046 2118 Dihedral : 9.792 156.174 1723 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.30 % Allowed : 9.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.22), residues: 1442 helix: 2.03 (0.16), residues: 910 sheet: 0.32 (0.66), residues: 62 loop : -1.35 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 636 TYR 0.018 0.002 TYR A 580 PHE 0.014 0.002 PHE B 560 TRP 0.013 0.002 TRP B 273 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00549 (12646) covalent geometry : angle 0.58604 (17118) SS BOND : bond 0.00487 ( 8) SS BOND : angle 1.00295 ( 16) hydrogen bonds : bond 0.05028 ( 763) hydrogen bonds : angle 4.58853 ( 2229) *********************** 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 166 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: A 196 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.4861 (m-80) REVERT: A 255 TYR cc_start: 0.8270 (m-80) cc_final: 0.8005 (m-10) REVERT: A 298 ILE cc_start: 0.8879 (tp) cc_final: 0.8547 (tt) REVERT: A 334 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8328 (p) REVERT: A 403 GLU cc_start: 0.8171 (tt0) cc_final: 0.7682 (tm-30) REVERT: A 407 GLU cc_start: 0.8553 (tt0) cc_final: 0.8325 (tt0) REVERT: A 481 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8709 (p) REVERT: A 546 ASP cc_start: 0.8244 (m-30) cc_final: 0.7931 (m-30) REVERT: A 695 ASN cc_start: 0.8897 (t0) cc_final: 0.8507 (t0) REVERT: A 770 TYR cc_start: 0.8017 (p90) cc_final: 0.7490 (t80) REVERT: A 773 MET cc_start: 0.9370 (mmm) cc_final: 0.8677 (mmt) REVERT: B 73 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7242 (m-80) REVERT: B 196 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.4739 (m-80) REVERT: B 298 ILE cc_start: 0.8870 (tp) cc_final: 0.8543 (tt) REVERT: B 334 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8240 (p) REVERT: B 403 GLU cc_start: 0.8111 (tt0) cc_final: 0.7573 (tm-30) REVERT: B 407 GLU cc_start: 0.8582 (tt0) cc_final: 0.8357 (tt0) REVERT: B 481 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8736 (p) REVERT: B 546 ASP cc_start: 0.8274 (m-30) cc_final: 0.7897 (m-30) REVERT: B 695 ASN cc_start: 0.8901 (t0) cc_final: 0.8508 (t0) REVERT: B 749 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7240 (t0) REVERT: B 770 TYR cc_start: 0.8044 (p90) cc_final: 0.7529 (t80) REVERT: B 773 MET cc_start: 0.9347 (mmm) cc_final: 0.8663 (mmt) REVERT: B 872 LYS cc_start: 0.8299 (pttm) cc_final: 0.8071 (pttm) outliers start: 44 outliers final: 29 residues processed: 163 average time/residue: 0.1079 time to fit residues: 25.9043 Evaluate side-chains 150 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 687 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 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 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 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 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 687 LEU 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 Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 110 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 674 GLN A 695 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS 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 = 0.108217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080795 restraints weight = 22369.366| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.68 r_work: 0.2936 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12654 Z= 0.137 Angle : 0.520 6.852 17134 Z= 0.281 Chirality : 0.039 0.139 1854 Planarity : 0.004 0.044 2118 Dihedral : 9.521 160.904 1721 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.37 % Allowed : 9.97 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.22), residues: 1442 helix: 2.09 (0.16), residues: 922 sheet: 0.44 (0.67), residues: 62 loop : -1.34 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.015 0.001 TYR B 580 PHE 0.025 0.001 PHE A 461 TRP 0.013 0.001 TRP B 397 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00305 (12646) covalent geometry : angle 0.51950 (17118) SS BOND : bond 0.00210 ( 8) SS BOND : angle 0.88385 ( 16) hydrogen bonds : bond 0.04502 ( 763) hydrogen bonds : angle 4.42345 ( 2229) *********************** 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 168 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: A 196 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.4559 (m-80) REVERT: A 255 TYR cc_start: 0.8282 (m-80) cc_final: 0.8043 (m-10) REVERT: A 298 ILE cc_start: 0.8877 (tp) cc_final: 0.8563 (tt) REVERT: A 334 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 403 GLU cc_start: 0.8149 (tt0) cc_final: 0.7668 (tm-30) REVERT: A 407 GLU cc_start: 0.8505 (tt0) cc_final: 0.8302 (tt0) REVERT: A 481 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8714 (p) REVERT: A 546 ASP cc_start: 0.8236 (m-30) cc_final: 0.7891 (m-30) REVERT: A 695 ASN cc_start: 0.8837 (t0) cc_final: 0.8433 (t0) REVERT: A 770 TYR cc_start: 0.7839 (p90) cc_final: 0.7210 (t80) REVERT: A 773 MET cc_start: 0.9440 (mmm) cc_final: 0.8728 (mmt) REVERT: B 73 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: B 191 ARG cc_start: 0.6977 (ptt90) cc_final: 0.6663 (ptt90) REVERT: B 196 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.4702 (m-80) REVERT: B 298 ILE cc_start: 0.8871 (tp) cc_final: 0.8554 (tt) REVERT: B 334 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8261 (p) REVERT: B 403 GLU cc_start: 0.8122 (tt0) cc_final: 0.7599 (tm-30) REVERT: B 481 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8734 (p) REVERT: B 546 ASP cc_start: 0.8281 (m-30) cc_final: 0.7889 (m-30) REVERT: B 695 ASN cc_start: 0.8841 (t0) cc_final: 0.8415 (t0) REVERT: B 770 TYR cc_start: 0.8008 (p90) cc_final: 0.7425 (t80) REVERT: B 773 MET cc_start: 0.9410 (mmm) cc_final: 0.8673 (mmt) outliers start: 45 outliers final: 26 residues processed: 165 average time/residue: 0.1023 time to fit residues: 24.3805 Evaluate side-chains 152 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 780 THR 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 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 783 VAL 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 16 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 559 GLN A 674 GLN A 695 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN 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 = 0.3538 r_free = 0.3538 target = 0.108028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080945 restraints weight = 22489.839| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.59 r_work: 0.2936 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12654 Z= 0.154 Angle : 0.529 6.665 17134 Z= 0.286 Chirality : 0.040 0.134 1854 Planarity : 0.004 0.041 2118 Dihedral : 9.372 161.179 1720 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.37 % Allowed : 9.97 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.22), residues: 1442 helix: 2.07 (0.16), residues: 924 sheet: 0.36 (0.66), residues: 62 loop : -1.35 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 636 TYR 0.015 0.001 TYR B 580 PHE 0.020 0.001 PHE A 461 TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00354 (12646) covalent geometry : angle 0.52772 (17118) SS BOND : bond 0.00144 ( 8) SS BOND : angle 1.09960 ( 16) hydrogen bonds : bond 0.04510 ( 763) hydrogen bonds : angle 4.40349 ( 2229) *********************** 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 169 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: A 196 TYR cc_start: 0.5997 (OUTLIER) cc_final: 0.4741 (m-80) REVERT: A 255 TYR cc_start: 0.8292 (m-80) cc_final: 0.8091 (m-10) REVERT: A 298 ILE cc_start: 0.8871 (tp) cc_final: 0.8564 (tt) REVERT: A 334 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8269 (p) REVERT: A 403 GLU cc_start: 0.8113 (tt0) cc_final: 0.7621 (tm-30) REVERT: A 407 GLU cc_start: 0.8475 (tt0) cc_final: 0.8265 (tt0) REVERT: A 418 GLN cc_start: 0.8368 (tt0) cc_final: 0.8054 (tt0) REVERT: A 481 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8668 (p) REVERT: A 546 ASP cc_start: 0.8231 (m-30) cc_final: 0.7886 (m-30) REVERT: A 695 ASN cc_start: 0.8861 (t0) cc_final: 0.8428 (t0) REVERT: A 770 TYR cc_start: 0.7851 (p90) cc_final: 0.7191 (t80) REVERT: A 773 MET cc_start: 0.9412 (mmm) cc_final: 0.8622 (mmt) REVERT: B 73 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7271 (m-80) REVERT: B 196 TYR cc_start: 0.5773 (OUTLIER) cc_final: 0.4717 (m-80) REVERT: B 298 ILE cc_start: 0.8876 (tp) cc_final: 0.8563 (tt) REVERT: B 403 GLU cc_start: 0.8056 (tt0) cc_final: 0.7529 (tm-30) REVERT: B 481 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8715 (p) REVERT: B 546 ASP cc_start: 0.8269 (m-30) cc_final: 0.7882 (m-30) REVERT: B 695 ASN cc_start: 0.8861 (t0) cc_final: 0.8433 (t0) REVERT: B 770 TYR cc_start: 0.7986 (p90) cc_final: 0.7450 (t80) REVERT: B 773 MET cc_start: 0.9325 (mmm) cc_final: 0.8672 (mmt) outliers start: 45 outliers final: 29 residues processed: 162 average time/residue: 0.1131 time to fit residues: 27.0210 Evaluate side-chains 151 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 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 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 783 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 205 ASN A 525 ASN A 674 GLN A 695 ASN B 111 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.109324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.082094 restraints weight = 22508.986| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.60 r_work: 0.2955 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12654 Z= 0.131 Angle : 0.512 6.816 17134 Z= 0.276 Chirality : 0.039 0.133 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.300 164.818 1720 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.45 % Allowed : 9.60 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.22), residues: 1442 helix: 2.19 (0.16), residues: 920 sheet: 0.36 (0.65), residues: 62 loop : -1.32 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 191 TYR 0.014 0.001 TYR A 138 PHE 0.023 0.001 PHE B 461 TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00294 (12646) covalent geometry : angle 0.51152 (17118) SS BOND : bond 0.00281 ( 8) SS BOND : angle 0.89579 ( 16) hydrogen bonds : bond 0.04248 ( 763) hydrogen bonds : angle 4.31649 ( 2229) *********************** 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 174 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: A 196 TYR cc_start: 0.5912 (OUTLIER) cc_final: 0.4687 (m-80) REVERT: A 255 TYR cc_start: 0.8281 (m-80) cc_final: 0.8063 (m-10) REVERT: A 298 ILE cc_start: 0.8845 (tp) cc_final: 0.8557 (tt) REVERT: A 334 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.8078 (p) REVERT: A 403 GLU cc_start: 0.8113 (tt0) cc_final: 0.7661 (tm-30) REVERT: A 418 GLN cc_start: 0.8305 (tt0) cc_final: 0.8009 (tt0) REVERT: A 481 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8635 (p) REVERT: A 546 ASP cc_start: 0.8230 (m-30) cc_final: 0.7899 (m-30) REVERT: A 631 MET cc_start: 0.8345 (mmm) cc_final: 0.8092 (mmm) REVERT: A 695 ASN cc_start: 0.8827 (t0) cc_final: 0.8409 (t0) REVERT: A 770 TYR cc_start: 0.7816 (p90) cc_final: 0.7187 (t80) REVERT: A 773 MET cc_start: 0.9370 (mmm) cc_final: 0.9006 (tpp) REVERT: B 73 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7243 (m-80) REVERT: B 196 TYR cc_start: 0.5783 (OUTLIER) cc_final: 0.4711 (m-80) REVERT: B 298 ILE cc_start: 0.8863 (tp) cc_final: 0.8570 (tt) REVERT: B 334 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8060 (p) REVERT: B 403 GLU cc_start: 0.8054 (tt0) cc_final: 0.7535 (tm-30) REVERT: B 481 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8707 (p) REVERT: B 546 ASP cc_start: 0.8277 (m-30) cc_final: 0.7885 (m-30) REVERT: B 661 LYS cc_start: 0.9210 (mmtp) cc_final: 0.8838 (mppt) REVERT: B 695 ASN cc_start: 0.8829 (t0) cc_final: 0.8418 (t0) REVERT: B 770 TYR cc_start: 0.7970 (p90) cc_final: 0.7352 (t80) REVERT: B 773 MET cc_start: 0.9358 (mmm) cc_final: 0.8610 (mmt) outliers start: 46 outliers final: 27 residues processed: 165 average time/residue: 0.1128 time to fit residues: 27.4167 Evaluate side-chains 152 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3489 r_free = 0.3489 target = 0.104210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.077620 restraints weight = 22384.174| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.56 r_work: 0.2885 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 12654 Z= 0.300 Angle : 0.627 7.571 17134 Z= 0.339 Chirality : 0.044 0.157 1854 Planarity : 0.005 0.040 2118 Dihedral : 9.402 161.467 1718 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.37 % Allowed : 10.04 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.22), residues: 1442 helix: 1.96 (0.16), residues: 910 sheet: 0.28 (0.64), residues: 62 loop : -1.43 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 191 TYR 0.022 0.002 TYR A 580 PHE 0.017 0.002 PHE A 461 TRP 0.013 0.002 TRP A 273 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00703 (12646) covalent geometry : angle 0.62597 (17118) SS BOND : bond 0.00310 ( 8) SS BOND : angle 1.37282 ( 16) hydrogen bonds : bond 0.05140 ( 763) hydrogen bonds : angle 4.56921 ( 2229) *********************** 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 158 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: A 196 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.4723 (m-80) REVERT: A 298 ILE cc_start: 0.8897 (tp) cc_final: 0.8542 (tt) REVERT: A 334 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 403 GLU cc_start: 0.8171 (tt0) cc_final: 0.7634 (tm-30) REVERT: A 418 GLN cc_start: 0.8366 (tt0) cc_final: 0.8098 (tt0) REVERT: A 481 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8804 (p) REVERT: A 546 ASP cc_start: 0.8343 (m-30) cc_final: 0.8099 (m-30) REVERT: A 770 TYR cc_start: 0.8089 (p90) cc_final: 0.7543 (t80) REVERT: A 773 MET cc_start: 0.9359 (mmm) cc_final: 0.8915 (tpp) REVERT: B 73 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: B 196 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.4995 (m-80) REVERT: B 298 ILE cc_start: 0.8901 (tp) cc_final: 0.8545 (tt) REVERT: B 334 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8143 (p) REVERT: B 403 GLU cc_start: 0.8187 (tt0) cc_final: 0.7635 (tm-30) REVERT: B 481 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8853 (p) REVERT: B 546 ASP cc_start: 0.8353 (m-30) cc_final: 0.8057 (m-30) REVERT: B 770 TYR cc_start: 0.8101 (p90) cc_final: 0.7557 (t80) REVERT: B 773 MET cc_start: 0.9352 (mmm) cc_final: 0.8829 (tpp) outliers start: 45 outliers final: 30 residues processed: 152 average time/residue: 0.1091 time to fit residues: 24.6930 Evaluate side-chains 146 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 208 THR 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 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 761 SER 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 208 THR 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 334 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 465 LEU 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 761 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.080485 restraints weight = 22335.500| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.62 r_work: 0.2938 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2336 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= 0.140 Angle : 0.534 7.233 17134 Z= 0.288 Chirality : 0.040 0.133 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.326 165.080 1718 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.07 % Allowed : 10.34 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.22), residues: 1442 helix: 2.10 (0.16), residues: 920 sheet: 0.32 (0.65), residues: 62 loop : -1.39 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 191 TYR 0.015 0.001 TYR A 138 PHE 0.029 0.001 PHE B 461 TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00317 (12646) covalent geometry : angle 0.53345 (17118) SS BOND : bond 0.00179 ( 8) SS BOND : angle 0.90523 ( 16) hydrogen bonds : bond 0.04486 ( 763) hydrogen bonds : angle 4.39374 ( 2229) *********************** 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 158 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7301 (m-80) REVERT: A 196 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.4789 (m-80) REVERT: A 298 ILE cc_start: 0.8907 (tp) cc_final: 0.8592 (tt) REVERT: A 334 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8150 (p) REVERT: A 403 GLU cc_start: 0.8150 (tt0) cc_final: 0.7677 (tm-30) REVERT: A 418 GLN cc_start: 0.8320 (tt0) cc_final: 0.8059 (tt0) REVERT: A 481 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8792 (p) REVERT: A 546 ASP cc_start: 0.8331 (m-30) cc_final: 0.8062 (m-30) REVERT: A 695 ASN cc_start: 0.8894 (t0) cc_final: 0.8462 (t0) REVERT: A 770 TYR cc_start: 0.7917 (p90) cc_final: 0.7247 (t80) REVERT: A 773 MET cc_start: 0.9399 (mmm) cc_final: 0.9038 (tpp) REVERT: B 73 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: B 196 TYR cc_start: 0.5877 (OUTLIER) cc_final: 0.4811 (m-80) REVERT: B 298 ILE cc_start: 0.8908 (tp) cc_final: 0.8589 (tt) REVERT: B 403 GLU cc_start: 0.8160 (tt0) cc_final: 0.7659 (tm-30) REVERT: B 481 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8780 (p) REVERT: B 546 ASP cc_start: 0.8343 (m-30) cc_final: 0.8026 (m-30) REVERT: B 661 LYS cc_start: 0.9238 (mmtp) cc_final: 0.8903 (mppt) REVERT: B 695 ASN cc_start: 0.8895 (t0) cc_final: 0.8471 (t0) REVERT: B 770 TYR cc_start: 0.7935 (p90) cc_final: 0.7287 (t80) REVERT: B 773 MET cc_start: 0.9377 (mmm) cc_final: 0.8727 (mmt) outliers start: 41 outliers final: 30 residues processed: 150 average time/residue: 0.1137 time to fit residues: 25.1513 Evaluate side-chains 150 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 761 SER 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 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 349 CYS 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 761 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 0.2980 chunk 140 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN B 205 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082879 restraints weight = 22453.913| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.58 r_work: 0.2972 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12654 Z= 0.118 Angle : 0.512 7.899 17134 Z= 0.274 Chirality : 0.039 0.134 1854 Planarity : 0.004 0.041 2118 Dihedral : 9.166 166.253 1718 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.07 % Allowed : 10.49 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.22), residues: 1442 helix: 2.27 (0.16), residues: 920 sheet: 0.46 (0.65), residues: 62 loop : -1.32 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.015 0.001 TYR A 580 PHE 0.026 0.001 PHE B 461 TRP 0.015 0.001 TRP A 397 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00259 (12646) covalent geometry : angle 0.51162 (17118) SS BOND : bond 0.00191 ( 8) SS BOND : angle 0.83019 ( 16) hydrogen bonds : bond 0.04102 ( 763) hydrogen bonds : angle 4.27069 ( 2229) *********************** 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 162 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: A 196 TYR cc_start: 0.5738 (OUTLIER) cc_final: 0.4720 (m-80) REVERT: A 298 ILE cc_start: 0.8847 (tp) cc_final: 0.8568 (tt) REVERT: A 334 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.8089 (p) REVERT: A 403 GLU cc_start: 0.8108 (tt0) cc_final: 0.7660 (tm-30) REVERT: A 418 GLN cc_start: 0.8277 (tt0) cc_final: 0.8020 (tt0) REVERT: A 481 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8666 (p) REVERT: A 546 ASP cc_start: 0.8248 (m-30) cc_final: 0.7939 (m-30) REVERT: A 631 MET cc_start: 0.8343 (mmm) cc_final: 0.8115 (mmm) REVERT: A 695 ASN cc_start: 0.8833 (t0) cc_final: 0.8385 (t0) REVERT: A 770 TYR cc_start: 0.7828 (p90) cc_final: 0.7197 (t80) REVERT: A 773 MET cc_start: 0.9347 (mmm) cc_final: 0.8972 (tpp) REVERT: B 73 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: B 192 MET cc_start: 0.5180 (ppp) cc_final: 0.4896 (ppp) REVERT: B 196 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.5087 (m-80) REVERT: B 298 ILE cc_start: 0.8853 (tp) cc_final: 0.8566 (tt) REVERT: B 334 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 403 GLU cc_start: 0.8063 (tt0) cc_final: 0.7567 (tm-30) REVERT: B 407 GLU cc_start: 0.8485 (tt0) cc_final: 0.8252 (tt0) REVERT: B 481 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8691 (p) REVERT: B 546 ASP cc_start: 0.8253 (m-30) cc_final: 0.7917 (m-30) REVERT: B 631 MET cc_start: 0.8394 (mmm) cc_final: 0.8146 (mmm) REVERT: B 661 LYS cc_start: 0.9202 (mmtp) cc_final: 0.8863 (mppt) REVERT: B 695 ASN cc_start: 0.8840 (t0) cc_final: 0.8397 (t0) REVERT: B 770 TYR cc_start: 0.7992 (p90) cc_final: 0.7337 (t80) REVERT: B 773 MET cc_start: 0.9336 (mmm) cc_final: 0.8674 (mmt) outliers start: 41 outliers final: 26 residues processed: 155 average time/residue: 0.1170 time to fit residues: 26.6581 Evaluate side-chains 145 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 761 SER 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 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 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 761 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 137 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** 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 = 0.3547 r_free = 0.3547 target = 0.108617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.081363 restraints weight = 22717.436| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.61 r_work: 0.2945 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12654 Z= 0.149 Angle : 0.539 9.532 17134 Z= 0.287 Chirality : 0.040 0.135 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.196 166.117 1718 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.92 % Allowed : 10.49 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.22), residues: 1442 helix: 2.21 (0.16), residues: 920 sheet: 0.29 (0.65), residues: 62 loop : -1.33 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.018 0.001 TYR A 138 PHE 0.027 0.001 PHE B 461 TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00340 (12646) covalent geometry : angle 0.53707 (17118) SS BOND : bond 0.00272 ( 8) SS BOND : angle 1.42952 ( 16) hydrogen bonds : bond 0.04286 ( 763) hydrogen bonds : angle 4.30499 ( 2229) ********************** 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: 39 poor density : 114 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: A 191 ARG cc_start: 0.6626 (ptt90) cc_final: 0.6284 (ptt90) REVERT: A 196 TYR cc_start: 0.5743 (OUTLIER) cc_final: 0.4720 (m-80) REVERT: A 298 ILE cc_start: 0.8860 (tp) cc_final: 0.8570 (tt) REVERT: A 334 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8078 (p) REVERT: A 403 GLU cc_start: 0.8116 (tt0) cc_final: 0.7654 (tm-30) REVERT: A 418 GLN cc_start: 0.8283 (tt0) cc_final: 0.8022 (tt0) REVERT: A 481 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8671 (p) REVERT: A 546 ASP cc_start: 0.8261 (m-30) cc_final: 0.7961 (m-30) REVERT: A 631 MET cc_start: 0.8316 (mmm) cc_final: 0.8077 (mmm) REVERT: A 695 ASN cc_start: 0.8838 (t0) cc_final: 0.8438 (t0) REVERT: A 770 TYR cc_start: 0.7850 (p90) cc_final: 0.7196 (t80) REVERT: A 773 MET cc_start: 0.9325 (mmm) cc_final: 0.8949 (tpp) REVERT: B 73 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: B 196 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5335 (m-80) REVERT: B 298 ILE cc_start: 0.8849 (tp) cc_final: 0.8555 (tt) REVERT: B 334 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8065 (p) REVERT: B 403 GLU cc_start: 0.8074 (tt0) cc_final: 0.7569 (tm-30) REVERT: B 407 GLU cc_start: 0.8503 (tt0) cc_final: 0.8265 (tt0) REVERT: B 481 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8700 (p) REVERT: B 546 ASP cc_start: 0.8264 (m-30) cc_final: 0.7945 (m-30) REVERT: B 661 LYS cc_start: 0.9197 (mmtp) cc_final: 0.8863 (mppt) REVERT: B 695 ASN cc_start: 0.8848 (t0) cc_final: 0.8454 (t0) REVERT: B 770 TYR cc_start: 0.8015 (p90) cc_final: 0.7441 (t80) REVERT: B 773 MET cc_start: 0.9318 (mmm) cc_final: 0.8642 (mmt) outliers start: 39 outliers final: 29 residues processed: 145 average time/residue: 0.1139 time to fit residues: 24.4618 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 761 SER 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 208 THR 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 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 465 LEU 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 761 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 141 optimal weight: 0.0270 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 chunk 79 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- 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 ** 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 = 0.3561 r_free = 0.3561 target = 0.109589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082562 restraints weight = 22401.507| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.61 r_work: 0.2967 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12654 Z= 0.120 Angle : 0.522 9.982 17134 Z= 0.278 Chirality : 0.039 0.135 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.161 167.153 1718 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.00 % Allowed : 10.57 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.22), residues: 1442 helix: 2.25 (0.16), residues: 920 sheet: 0.32 (0.65), residues: 62 loop : -1.33 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 191 TYR 0.019 0.001 TYR A 138 PHE 0.026 0.001 PHE B 461 TRP 0.014 0.001 TRP A 397 HIS 0.001 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00265 (12646) covalent geometry : angle 0.52076 (17118) SS BOND : bond 0.00156 ( 8) SS BOND : angle 1.23013 ( 16) hydrogen bonds : bond 0.04126 ( 763) hydrogen bonds : angle 4.25132 ( 2229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.14 seconds wall clock time: 45 minutes 26.43 seconds (2726.43 seconds total)