Starting phenix.real_space_refine on Fri Jul 3 06:25:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b8k_15916/07_2026/8b8k_15916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8k_15916/07_2026/8b8k_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_15916/07_2026/8b8k_15916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8k_15916/07_2026/8b8k_15916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b8k_15916/07_2026/8b8k_15916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8k_15916/07_2026/8b8k_15916.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8b8k_15916/07_2026/8b8k_15916.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b8k_15916/07_2026/8b8k_15916.cif" } 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-dev-6108/lib/python3.11/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: 2.56, per 1000 atoms: 0.21 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: 0.96 Conformation dependent library (CDL) restraints added in 573.8 milliseconds 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: 0.33 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: 1.49 Time building geometry restraints manager: 1.33 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 - 15.06: 6915 15.06 - 30.13: 406 30.13 - 45.19: 100 45.19 - 60.26: 43 60.26 - 75.32: 4 Dihedral angle restraints: 7468 sinusoidal: 3086 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=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N MET B 192 " pdb=" CA MET B 192 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 7465 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.970 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 11.180 75.322 4620 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 are 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/Z covalent geometry : bond 0.00290 / 0.14 (12646) covalent geometry : angle 0.49955 / 0.28 (17118) SS BOND : bond 0.00127 / 0.07 ( 8) SS BOND : angle 0.37817 / 0.27 ( 16) hydrogen bonds : bond 0.07660 / 4.76 ( 763) hydrogen bonds : angle 4.72890 / 3.34 ( 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 : 0.474 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: 0.7584 (m-80) REVERT: A 196 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.4759 (m-80) REVERT: A 236 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 255 TYR cc_start: 0.8186 (m-80) cc_final: 0.7805 (m-10) REVERT: A 298 ILE cc_start: 0.9013 (tp) cc_final: 0.8701 (tt) REVERT: A 370 LYS cc_start: 0.8293 (ptpp) cc_final: 0.8045 (mmtm) REVERT: A 403 GLU cc_start: 0.8060 (tt0) cc_final: 0.7610 (tm-30) REVERT: A 407 GLU cc_start: 0.8457 (tt0) cc_final: 0.8170 (tt0) REVERT: A 413 LEU cc_start: 0.8981 (tt) cc_final: 0.8723 (tt) REVERT: A 546 ASP cc_start: 0.8391 (m-30) cc_final: 0.8048 (m-30) REVERT: A 695 ASN cc_start: 0.8767 (t0) cc_final: 0.8397 (t0) REVERT: A 749 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7203 (t0) REVERT: A 770 TYR cc_start: 0.7937 (p90) cc_final: 0.7404 (t80) REVERT: A 773 MET cc_start: 0.9525 (mmm) cc_final: 0.9201 (tpp) REVERT: A 826 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8952 (tt) REVERT: B 73 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: B 196 TYR cc_start: 0.5988 (OUTLIER) cc_final: 0.4639 (m-80) REVERT: B 289 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8111 (ttt-90) REVERT: B 298 ILE cc_start: 0.9047 (tp) cc_final: 0.8705 (tt) REVERT: B 370 LYS cc_start: 0.8262 (ptpp) cc_final: 0.8018 (mmtm) REVERT: B 403 GLU cc_start: 0.8111 (tt0) cc_final: 0.7637 (tm-30) REVERT: B 407 GLU cc_start: 0.8457 (tt0) cc_final: 0.8157 (tt0) REVERT: B 413 LEU cc_start: 0.9136 (tt) cc_final: 0.8915 (tt) REVERT: B 546 ASP cc_start: 0.8310 (m-30) cc_final: 0.7992 (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) outliers start: 39 outliers final: 13 residues processed: 248 average time/residue: 0.1086 time to fit residues: 38.7585 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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... A 44 GLN A 99 GLN A 104 ASN A 193 ASN A 234 ASN A 525 ASN A 559 GLN A 632 ASN A 710 GLN A 730 GLN B 44 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 234 ASN B 525 ASN B 559 GLN B 632 ASN B 710 GLN B 730 GLN B 814 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.081586 restraints weight = 22330.851| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.63 r_work: 0.2960 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12654 Z= 0.159 Angle : 0.539 7.581 17134 Z= 0.292 Chirality : 0.039 0.136 1854 Planarity : 0.005 0.046 2118 Dihedral : 7.841 58.356 1714 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.70 % Allowed : 8.92 % 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 are not related in a simple way. whole: 1.49 (0.22), residues: 1442 helix: 2.12 (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/Z covalent geometry : bond 0.00363 / 0.16 (12646) covalent geometry : angle 0.53890 / 0.29 (17118) SS BOND : bond 0.00164 / 0.09 ( 8) SS BOND : angle 0.40338 / 0.23 ( 16) hydrogen bonds : bond 0.04648 / 3.02 ( 763) hydrogen bonds : angle 4.48179 / 3.13 ( 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 175 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: A 192 MET cc_start: 0.5822 (ptt) cc_final: 0.5602 (ptt) REVERT: A 196 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.4576 (m-80) REVERT: A 255 TYR cc_start: 0.8277 (m-80) cc_final: 0.7954 (m-10) REVERT: A 298 ILE cc_start: 0.8952 (tp) cc_final: 0.8629 (tt) REVERT: A 403 GLU cc_start: 0.8124 (tt0) cc_final: 0.7655 (tm-30) REVERT: A 407 GLU cc_start: 0.8496 (tt0) cc_final: 0.8249 (tt0) REVERT: A 546 ASP cc_start: 0.8374 (m-30) cc_final: 0.8003 (m-30) REVERT: A 695 ASN cc_start: 0.8893 (t0) cc_final: 0.8461 (t0) REVERT: A 749 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7333 (t0) REVERT: A 770 TYR cc_start: 0.7997 (p90) cc_final: 0.7441 (t80) REVERT: A 773 MET cc_start: 0.9469 (mmm) cc_final: 0.8722 (mmt) REVERT: A 826 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8862 (tt) REVERT: B 73 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: B 142 MET cc_start: 0.8505 (ptt) cc_final: 0.8100 (ptt) REVERT: B 196 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4558 (m-80) REVERT: B 298 ILE cc_start: 0.8944 (tp) cc_final: 0.8621 (tt) REVERT: B 334 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 403 GLU cc_start: 0.8152 (tt0) cc_final: 0.7659 (tm-30) REVERT: B 407 GLU cc_start: 0.8518 (tt0) cc_final: 0.8296 (tt0) REVERT: B 461 PHE cc_start: 0.6262 (m-80) cc_final: 0.5697 (t80) REVERT: B 546 ASP cc_start: 0.8315 (m-30) cc_final: 0.7967 (m-30) REVERT: B 695 ASN cc_start: 0.8891 (t0) cc_final: 0.8454 (t0) REVERT: B 749 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7200 (t0) REVERT: B 770 TYR cc_start: 0.7965 (p90) cc_final: 0.7526 (t80) REVERT: B 773 MET cc_start: 0.9445 (mmm) cc_final: 0.8721 (mmt) outliers start: 36 outliers final: 23 residues processed: 171 average time/residue: 0.0966 time to fit residues: 24.4831 Evaluate side-chains 149 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.081627 restraints weight = 22414.888| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.65 r_work: 0.2960 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12654 Z= 0.149 Angle : 0.531 7.060 17134 Z= 0.287 Chirality : 0.040 0.163 1854 Planarity : 0.004 0.045 2118 Dihedral : 7.467 59.288 1705 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.92 % Allowed : 9.37 % Favored : 87.71 % 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 are not related in a simple way. whole: 1.52 (0.22), residues: 1442 helix: 2.13 (0.16), residues: 922 sheet: 0.31 (0.66), residues: 62 loop : -1.30 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 636 TYR 0.015 0.001 TYR B 580 PHE 0.019 0.001 PHE A 461 TRP 0.012 0.001 TRP A 397 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (12646) covalent geometry : angle 0.53052 / 0.29 (17118) SS BOND : bond 0.00515 / 0.32 ( 8) SS BOND : angle 0.74530 / 0.42 ( 16) hydrogen bonds : bond 0.04560 / 2.97 ( 763) hydrogen bonds : angle 4.44747 / 3.11 ( 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 167 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: A 196 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.4713 (m-80) REVERT: A 255 TYR cc_start: 0.8280 (m-80) cc_final: 0.7974 (m-10) REVERT: A 298 ILE cc_start: 0.8921 (tp) cc_final: 0.8626 (tt) REVERT: A 334 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8370 (p) REVERT: A 403 GLU cc_start: 0.8150 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 481 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8751 (p) REVERT: A 546 ASP cc_start: 0.8277 (m-30) cc_final: 0.7927 (m-30) REVERT: A 695 ASN cc_start: 0.8909 (t0) cc_final: 0.8487 (t0) REVERT: A 770 TYR cc_start: 0.7995 (p90) cc_final: 0.7438 (t80) REVERT: A 773 MET cc_start: 0.9433 (mmm) cc_final: 0.8687 (mmt) REVERT: A 826 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8895 (tt) REVERT: B 73 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: B 191 ARG cc_start: 0.6682 (ptt90) cc_final: 0.6477 (ptm-80) REVERT: B 196 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.4548 (m-80) REVERT: B 298 ILE cc_start: 0.8911 (tp) cc_final: 0.8617 (tt) REVERT: B 334 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 403 GLU cc_start: 0.8157 (tt0) cc_final: 0.7660 (tm-30) REVERT: B 461 PHE cc_start: 0.6387 (m-80) cc_final: 0.6131 (t80) REVERT: B 481 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8787 (p) REVERT: B 543 THR cc_start: 0.8352 (p) cc_final: 0.7954 (p) REVERT: B 546 ASP cc_start: 0.8314 (m-30) cc_final: 0.8033 (m-30) REVERT: B 695 ASN cc_start: 0.8911 (t0) cc_final: 0.8486 (t0) REVERT: B 749 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7267 (t0) REVERT: B 770 TYR cc_start: 0.8063 (p90) cc_final: 0.7562 (t80) REVERT: B 773 MET cc_start: 0.9401 (mmm) cc_final: 0.8650 (mmt) outliers start: 39 outliers final: 23 residues processed: 162 average time/residue: 0.0981 time to fit residues: 23.4850 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 401 GLN A 525 ASN A 549 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS B 401 GLN B 525 ASN B 549 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.078934 restraints weight = 22583.210| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.65 r_work: 0.2901 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12654 Z= 0.236 Angle : 0.580 7.220 17134 Z= 0.314 Chirality : 0.042 0.144 1854 Planarity : 0.005 0.043 2118 Dihedral : 7.484 59.389 1705 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.60 % Allowed : 9.15 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.22), residues: 1442 helix: 2.00 (0.16), residues: 912 sheet: 0.39 (0.66), residues: 62 loop : -1.33 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 636 TYR 0.018 0.002 TYR A 580 PHE 0.023 0.002 PHE A 461 TRP 0.012 0.002 TRP B 273 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (12646) covalent geometry : angle 0.57886 / 0.31 (17118) SS BOND : bond 0.00367 / 0.21 ( 8) SS BOND : angle 1.14428 / 0.63 ( 16) hydrogen bonds : bond 0.04967 / 3.23 ( 763) hydrogen bonds : angle 4.55007 / 3.19 ( 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 170 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: A 196 TYR cc_start: 0.6187 (OUTLIER) cc_final: 0.4643 (m-80) REVERT: A 255 TYR cc_start: 0.8280 (m-80) cc_final: 0.8034 (m-10) REVERT: A 298 ILE cc_start: 0.8883 (tp) cc_final: 0.8553 (tt) REVERT: A 334 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8306 (p) REVERT: A 403 GLU cc_start: 0.8171 (tt0) cc_final: 0.7682 (tm-30) REVERT: A 481 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8710 (p) REVERT: A 546 ASP cc_start: 0.8256 (m-30) cc_final: 0.7933 (m-30) REVERT: A 695 ASN cc_start: 0.8898 (t0) cc_final: 0.8499 (t0) REVERT: A 770 TYR cc_start: 0.8007 (p90) cc_final: 0.7474 (t80) REVERT: A 773 MET cc_start: 0.9381 (mmm) cc_final: 0.8662 (mmt) REVERT: B 73 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: B 196 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.4433 (m-80) REVERT: B 298 ILE cc_start: 0.8874 (tp) cc_final: 0.8547 (tt) REVERT: B 334 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 403 GLU cc_start: 0.8110 (tt0) cc_final: 0.7572 (tm-30) REVERT: B 481 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8739 (p) REVERT: B 546 ASP cc_start: 0.8289 (m-30) cc_final: 0.7924 (m-30) REVERT: B 695 ASN cc_start: 0.8900 (t0) cc_final: 0.8500 (t0) REVERT: B 770 TYR cc_start: 0.8050 (p90) cc_final: 0.7513 (t80) REVERT: B 773 MET cc_start: 0.9356 (mmm) cc_final: 0.8659 (mmt) outliers start: 48 outliers final: 29 residues processed: 166 average time/residue: 0.0937 time to fit residues: 23.2125 Evaluate side-chains 151 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 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 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 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 874 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 119 optimal weight: 0.0670 chunk 139 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 674 GLN A 695 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN 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 = 0.3542 r_free = 0.3542 target = 0.108437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081031 restraints weight = 22369.493| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.68 r_work: 0.2940 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1994 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= 0.138 Angle : 0.521 6.809 17134 Z= 0.282 Chirality : 0.040 0.134 1854 Planarity : 0.004 0.041 2118 Dihedral : 7.208 59.854 1703 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.30 % Allowed : 9.82 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.22), residues: 1442 helix: 2.08 (0.16), residues: 922 sheet: 0.44 (0.67), residues: 62 loop : -1.33 (0.28), residues: 458 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 0.017 0.001 PHE A 461 TRP 0.013 0.001 TRP A 397 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (12646) covalent geometry : angle 0.52063 / 0.28 (17118) SS BOND : bond 0.00255 / 0.16 ( 8) SS BOND : angle 0.95357 / 0.53 ( 16) hydrogen bonds : bond 0.04462 / 2.90 ( 763) hydrogen bonds : angle 4.39980 / 3.08 ( 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 167 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: A 196 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.4562 (m-80) REVERT: A 255 TYR cc_start: 0.8282 (m-80) cc_final: 0.8030 (m-10) REVERT: A 298 ILE cc_start: 0.8886 (tp) cc_final: 0.8580 (tt) REVERT: A 334 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8300 (p) REVERT: A 403 GLU cc_start: 0.8154 (tt0) cc_final: 0.7672 (tm-30) REVERT: A 418 GLN cc_start: 0.8276 (tt0) cc_final: 0.8009 (tt0) REVERT: A 481 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8712 (p) REVERT: A 546 ASP cc_start: 0.8252 (m-30) cc_final: 0.7903 (m-30) REVERT: A 695 ASN cc_start: 0.8834 (t0) cc_final: 0.8421 (t0) REVERT: A 770 TYR cc_start: 0.7841 (p90) cc_final: 0.7212 (t80) REVERT: A 773 MET cc_start: 0.9435 (mmm) cc_final: 0.8696 (mmt) REVERT: B 73 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: B 196 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.4864 (m-80) REVERT: B 298 ILE cc_start: 0.8874 (tp) cc_final: 0.8563 (tt) REVERT: B 403 GLU cc_start: 0.8112 (tt0) cc_final: 0.7594 (tm-30) REVERT: B 481 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8734 (p) REVERT: B 546 ASP cc_start: 0.8295 (m-30) cc_final: 0.7901 (m-30) REVERT: B 695 ASN cc_start: 0.8833 (t0) cc_final: 0.8418 (t0) REVERT: B 770 TYR cc_start: 0.8032 (p90) cc_final: 0.7424 (t80) REVERT: B 773 MET cc_start: 0.9411 (mmm) cc_final: 0.8654 (mmt) outliers start: 44 outliers final: 28 residues processed: 163 average time/residue: 0.1008 time to fit residues: 24.1352 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.0270 chunk 92 optimal weight: 0.0470 chunk 74 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 111 optimal weight: 0.0270 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 205 ASN A 525 ASN A 674 GLN A 695 ASN B 111 GLN B 205 ASN B 275 HIS B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.110600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083692 restraints weight = 22404.786| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.58 r_work: 0.2986 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 12654 Z= 0.112 Angle : 0.501 7.259 17134 Z= 0.270 Chirality : 0.039 0.142 1854 Planarity : 0.004 0.040 2118 Dihedral : 6.919 59.440 1702 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 9.97 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.22), residues: 1442 helix: 2.25 (0.16), residues: 920 sheet: 0.41 (0.66), residues: 62 loop : -1.29 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 636 TYR 0.014 0.001 TYR A 528 PHE 0.021 0.001 PHE B 461 TRP 0.013 0.001 TRP A 397 HIS 0.007 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (12646) covalent geometry : angle 0.50017 / 0.27 (17118) SS BOND : bond 0.00184 / 0.11 ( 8) SS BOND : angle 0.79173 / 0.45 ( 16) hydrogen bonds : bond 0.04049 / 2.63 ( 763) hydrogen bonds : angle 4.25507 / 2.98 ( 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 175 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: A 196 TYR cc_start: 0.5898 (OUTLIER) cc_final: 0.4430 (m-80) REVERT: A 255 TYR cc_start: 0.8271 (m-80) cc_final: 0.8051 (m-10) REVERT: A 298 ILE cc_start: 0.8848 (tp) cc_final: 0.8585 (tt) REVERT: A 334 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 403 GLU cc_start: 0.8060 (tt0) cc_final: 0.7611 (tm-30) REVERT: A 418 GLN cc_start: 0.8284 (tt0) cc_final: 0.8045 (tt0) REVERT: A 481 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 546 ASP cc_start: 0.8215 (m-30) cc_final: 0.7872 (m-30) REVERT: A 631 MET cc_start: 0.8354 (mmm) cc_final: 0.8116 (mmm) REVERT: A 695 ASN cc_start: 0.8815 (t0) cc_final: 0.8365 (t0) REVERT: A 770 TYR cc_start: 0.7907 (p90) cc_final: 0.7313 (t80) REVERT: A 773 MET cc_start: 0.9369 (mmm) cc_final: 0.8603 (mmt) REVERT: B 73 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: B 196 TYR cc_start: 0.5852 (OUTLIER) cc_final: 0.5181 (m-80) REVERT: B 298 ILE cc_start: 0.8863 (tp) cc_final: 0.8574 (tt) REVERT: B 403 GLU cc_start: 0.8052 (tt0) cc_final: 0.7589 (tm-30) REVERT: B 543 THR cc_start: 0.8114 (p) cc_final: 0.7708 (p) REVERT: B 546 ASP cc_start: 0.8270 (m-30) cc_final: 0.7937 (m-30) REVERT: B 631 MET cc_start: 0.8382 (mmm) cc_final: 0.8121 (mmm) REVERT: B 661 LYS cc_start: 0.9209 (mmtp) cc_final: 0.8831 (mppt) REVERT: B 695 ASN cc_start: 0.8816 (t0) cc_final: 0.8364 (t0) REVERT: B 770 TYR cc_start: 0.7938 (p90) cc_final: 0.7348 (t80) REVERT: B 773 MET cc_start: 0.9344 (mmm) cc_final: 0.8651 (mmt) outliers start: 40 outliers final: 24 residues processed: 166 average time/residue: 0.0953 time to fit residues: 23.2228 Evaluate side-chains 152 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 349 CYS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 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 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 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: 1.9990 chunk 85 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.080758 restraints weight = 22331.240| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.58 r_work: 0.2937 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12654 Z= 0.169 Angle : 0.546 7.387 17134 Z= 0.293 Chirality : 0.040 0.147 1854 Planarity : 0.004 0.039 2118 Dihedral : 6.914 59.523 1700 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.07 % Allowed : 9.45 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.22), residues: 1442 helix: 2.14 (0.16), residues: 924 sheet: 0.36 (0.65), residues: 62 loop : -1.25 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 277 TYR 0.018 0.001 TYR A 580 PHE 0.023 0.002 PHE B 461 TRP 0.011 0.001 TRP B 397 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (12646) covalent geometry : angle 0.54558 / 0.29 (17118) SS BOND : bond 0.00168 / 0.09 ( 8) SS BOND : angle 0.95608 / 0.53 ( 16) hydrogen bonds : bond 0.04421 / 2.87 ( 763) hydrogen bonds : angle 4.32388 / 3.02 ( 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 159 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: A 196 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.4811 (m-80) REVERT: A 298 ILE cc_start: 0.8863 (tp) cc_final: 0.8553 (tt) REVERT: A 334 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8073 (p) REVERT: A 403 GLU cc_start: 0.8117 (tt0) cc_final: 0.7659 (tm-30) REVERT: A 481 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8670 (p) REVERT: A 546 ASP cc_start: 0.8244 (m-30) cc_final: 0.7931 (m-30) REVERT: A 695 ASN cc_start: 0.8871 (t0) cc_final: 0.8480 (t0) REVERT: A 770 TYR cc_start: 0.7983 (p90) cc_final: 0.7344 (t80) REVERT: A 773 MET cc_start: 0.9301 (mmm) cc_final: 0.8971 (tpp) REVERT: B 73 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: B 196 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.5156 (m-80) REVERT: B 298 ILE cc_start: 0.8883 (tp) cc_final: 0.8575 (tt) REVERT: B 334 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8060 (p) REVERT: B 403 GLU cc_start: 0.8048 (tt0) cc_final: 0.7525 (tm-30) REVERT: B 481 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8722 (p) REVERT: B 546 ASP cc_start: 0.8234 (m-30) cc_final: 0.7859 (m-30) REVERT: B 661 LYS cc_start: 0.9210 (mmtp) cc_final: 0.8838 (mppt) REVERT: B 695 ASN cc_start: 0.8863 (t0) cc_final: 0.8474 (t0) REVERT: B 770 TYR cc_start: 0.8010 (p90) cc_final: 0.7455 (t80) REVERT: B 773 MET cc_start: 0.9338 (mmm) cc_final: 0.8562 (mmt) outliers start: 41 outliers final: 28 residues processed: 150 average time/residue: 0.1092 time to fit residues: 24.2067 Evaluate side-chains 150 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 93 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080518 restraints weight = 22464.520| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.60 r_work: 0.2930 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2377 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= 0.166 Angle : 0.544 7.359 17134 Z= 0.292 Chirality : 0.040 0.133 1854 Planarity : 0.004 0.040 2118 Dihedral : 6.873 59.980 1700 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.92 % Allowed : 9.97 % Favored : 87.11 % 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 are not related in a simple way. whole: 1.55 (0.22), residues: 1442 helix: 2.18 (0.16), residues: 910 sheet: 0.30 (0.65), residues: 62 loop : -1.25 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 277 TYR 0.016 0.001 TYR B 580 PHE 0.015 0.001 PHE A 461 TRP 0.011 0.001 TRP A 273 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (12646) covalent geometry : angle 0.54307 / 0.29 (17118) SS BOND : bond 0.00197 / 0.11 ( 8) SS BOND : angle 0.92500 / 0.51 ( 16) hydrogen bonds : bond 0.04468 / 2.90 ( 763) hydrogen bonds : angle 4.34138 / 3.04 ( 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 153 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: A 196 TYR cc_start: 0.5953 (OUTLIER) cc_final: 0.4721 (m-80) REVERT: A 298 ILE cc_start: 0.8862 (tp) cc_final: 0.8550 (tt) REVERT: A 334 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8082 (p) REVERT: A 403 GLU cc_start: 0.8080 (tt0) cc_final: 0.7604 (tm-30) REVERT: A 481 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8681 (p) REVERT: A 546 ASP cc_start: 0.8254 (m-30) cc_final: 0.7958 (m-30) REVERT: A 661 LYS cc_start: 0.9207 (mmtp) cc_final: 0.8834 (mppt) REVERT: A 770 TYR cc_start: 0.7872 (p90) cc_final: 0.7208 (t80) REVERT: A 773 MET cc_start: 0.9337 (mmm) cc_final: 0.8963 (tpp) REVERT: B 73 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: B 196 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5235 (m-80) REVERT: B 298 ILE cc_start: 0.8869 (tp) cc_final: 0.8551 (tt) REVERT: B 334 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8068 (p) REVERT: B 403 GLU cc_start: 0.8053 (tt0) cc_final: 0.7509 (tm-30) REVERT: B 407 GLU cc_start: 0.8540 (tt0) cc_final: 0.8296 (tt0) REVERT: B 481 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 546 ASP cc_start: 0.8254 (m-30) cc_final: 0.7917 (m-30) REVERT: B 661 LYS cc_start: 0.9209 (mmtp) cc_final: 0.8846 (mppt) REVERT: B 695 ASN cc_start: 0.8851 (t0) cc_final: 0.8470 (t0) REVERT: B 770 TYR cc_start: 0.7897 (p90) cc_final: 0.7310 (t80) REVERT: B 773 MET cc_start: 0.9320 (mmm) cc_final: 0.8643 (mmt) REVERT: B 872 LYS cc_start: 0.8393 (pttm) cc_final: 0.8148 (ptpp) outliers start: 39 outliers final: 28 residues processed: 148 average time/residue: 0.1090 time to fit residues: 23.8306 Evaluate side-chains 149 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 140 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 0.0000 chunk 42 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081774 restraints weight = 22459.256| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.62 r_work: 0.2951 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2427 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= 0.132 Angle : 0.524 8.287 17134 Z= 0.281 Chirality : 0.039 0.132 1854 Planarity : 0.004 0.040 2118 Dihedral : 6.746 58.941 1700 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.00 % Allowed : 10.04 % 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 are not related in a simple way. whole: 1.65 (0.22), residues: 1442 helix: 2.23 (0.16), residues: 920 sheet: 0.37 (0.65), residues: 62 loop : -1.24 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.017 0.001 TYR A 138 PHE 0.014 0.001 PHE A 461 TRP 0.012 0.001 TRP B 397 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12646) covalent geometry : angle 0.52411 / 0.28 (17118) SS BOND : bond 0.00142 / 0.08 ( 8) SS BOND : angle 0.84028 / 0.47 ( 16) hydrogen bonds : bond 0.04267 / 2.77 ( 763) hydrogen bonds : angle 4.28272 / 3.00 ( 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 157 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: A 196 TYR cc_start: 0.5876 (OUTLIER) cc_final: 0.4668 (m-80) REVERT: A 298 ILE cc_start: 0.8842 (tp) cc_final: 0.8550 (tt) REVERT: A 334 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.8081 (p) REVERT: A 403 GLU cc_start: 0.8071 (tt0) cc_final: 0.7603 (tm-30) REVERT: A 481 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8666 (p) REVERT: A 546 ASP cc_start: 0.8251 (m-30) cc_final: 0.7941 (m-30) REVERT: A 631 MET cc_start: 0.8304 (mmm) cc_final: 0.8059 (mmm) REVERT: A 661 LYS cc_start: 0.9203 (mmtp) cc_final: 0.8855 (mppt) REVERT: A 695 ASN cc_start: 0.8849 (t0) cc_final: 0.8441 (t0) REVERT: A 770 TYR cc_start: 0.7859 (p90) cc_final: 0.7191 (t80) REVERT: A 773 MET cc_start: 0.9333 (mmm) cc_final: 0.8953 (tpp) REVERT: B 73 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: B 196 TYR cc_start: 0.6484 (OUTLIER) cc_final: 0.5228 (m-80) REVERT: B 298 ILE cc_start: 0.8867 (tp) cc_final: 0.8573 (tt) REVERT: B 334 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 403 GLU cc_start: 0.8053 (tt0) cc_final: 0.7548 (tm-30) REVERT: B 407 GLU cc_start: 0.8530 (tt0) cc_final: 0.8290 (tt0) REVERT: B 481 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8698 (p) REVERT: B 546 ASP cc_start: 0.8256 (m-30) cc_final: 0.7920 (m-30) REVERT: B 661 LYS cc_start: 0.9206 (mmtp) cc_final: 0.8863 (mppt) REVERT: B 695 ASN cc_start: 0.8849 (t0) cc_final: 0.8420 (t0) REVERT: B 770 TYR cc_start: 0.7884 (p90) cc_final: 0.7298 (t80) REVERT: B 773 MET cc_start: 0.9323 (mmm) cc_final: 0.8625 (mmt) outliers start: 40 outliers final: 28 residues processed: 146 average time/residue: 0.1097 time to fit residues: 23.5555 Evaluate side-chains 150 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 192 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.080937 restraints weight = 22704.066| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.63 r_work: 0.2937 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12654 Z= 0.155 Angle : 0.538 9.361 17134 Z= 0.288 Chirality : 0.040 0.132 1854 Planarity : 0.004 0.039 2118 Dihedral : 6.734 59.037 1700 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.85 % Allowed : 10.49 % 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 are not related in a simple way. whole: 1.59 (0.22), residues: 1442 helix: 2.19 (0.16), residues: 920 sheet: 0.32 (0.64), residues: 62 loop : -1.27 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.017 0.001 TYR A 138 PHE 0.014 0.001 PHE A 461 TRP 0.011 0.001 TRP B 397 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (12646) covalent geometry : angle 0.53713 / 0.29 (17118) SS BOND : bond 0.00161 / 0.08 ( 8) SS BOND : angle 0.94782 / 0.52 ( 16) hydrogen bonds : bond 0.04379 / 2.84 ( 763) hydrogen bonds : angle 4.31381 / 3.02 ( 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 155 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: A 196 TYR cc_start: 0.5872 (OUTLIER) cc_final: 0.4654 (m-80) REVERT: A 298 ILE cc_start: 0.8859 (tp) cc_final: 0.8563 (tt) REVERT: A 334 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 403 GLU cc_start: 0.8070 (tt0) cc_final: 0.7598 (tm-30) REVERT: A 481 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8669 (p) REVERT: A 546 ASP cc_start: 0.8258 (m-30) cc_final: 0.7961 (m-30) REVERT: A 631 MET cc_start: 0.8299 (mmm) cc_final: 0.8043 (mmm) REVERT: A 661 LYS cc_start: 0.9198 (mmtp) cc_final: 0.8853 (mppt) REVERT: A 695 ASN cc_start: 0.8839 (t0) cc_final: 0.8443 (t0) REVERT: A 770 TYR cc_start: 0.7873 (p90) cc_final: 0.7194 (t80) REVERT: A 773 MET cc_start: 0.9329 (mmm) cc_final: 0.8962 (tpp) REVERT: B 73 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: B 196 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.5189 (m-80) REVERT: B 298 ILE cc_start: 0.8864 (tp) cc_final: 0.8560 (tt) REVERT: B 334 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8062 (p) REVERT: B 403 GLU cc_start: 0.8047 (tt0) cc_final: 0.7535 (tm-30) REVERT: B 407 GLU cc_start: 0.8552 (tt0) cc_final: 0.8311 (tt0) REVERT: B 481 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8699 (p) REVERT: B 546 ASP cc_start: 0.8261 (m-30) cc_final: 0.7944 (m-30) REVERT: B 661 LYS cc_start: 0.9201 (mmtp) cc_final: 0.8861 (mppt) REVERT: B 695 ASN cc_start: 0.8834 (t0) cc_final: 0.8441 (t0) REVERT: B 770 TYR cc_start: 0.7891 (p90) cc_final: 0.7296 (t80) REVERT: B 773 MET cc_start: 0.9270 (mmm) cc_final: 0.8666 (mmt) outliers start: 38 outliers final: 28 residues processed: 145 average time/residue: 0.1085 time to fit residues: 23.1704 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 : 0.406 ------------------------------------------------------------------------------- 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 192 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.080623 restraints weight = 22473.853| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.57 r_work: 0.2933 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12654 Z= 0.164 Angle : 0.548 9.937 17134 Z= 0.294 Chirality : 0.040 0.134 1854 Planarity : 0.004 0.039 2118 Dihedral : 6.731 59.524 1700 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.92 % Allowed : 10.42 % 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 are not related in a simple way. whole: 1.54 (0.22), residues: 1442 helix: 2.14 (0.16), residues: 920 sheet: 0.34 (0.64), residues: 62 loop : -1.28 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 191 TYR 0.017 0.001 TYR A 580 PHE 0.013 0.001 PHE A 125 TRP 0.011 0.001 TRP A 273 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (12646) covalent geometry : angle 0.54763 / 0.29 (17118) SS BOND : bond 0.00157 / 0.08 ( 8) SS BOND : angle 0.98100 / 0.54 ( 16) hydrogen bonds : bond 0.04435 / 2.88 ( 763) hydrogen bonds : angle 4.33884 / 3.03 ( 2229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.85 seconds wall clock time: 43 minutes 3.04 seconds (2583.04 seconds total)