Starting phenix.real_space_refine on Mon Dec 30 07:59:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8k_15916/12_2024/8b8k_15916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8k_15916/12_2024/8b8k_15916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b8k_15916/12_2024/8b8k_15916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8k_15916/12_2024/8b8k_15916.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8k_15916/12_2024/8b8k_15916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8k_15916/12_2024/8b8k_15916.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 2 5.49 5 S 80 5.16 5 C 8098 2.51 5 N 1976 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12324 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6121 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "B" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6121 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.45, per 1000 atoms: 0.60 Number of scatterers: 12324 At special positions: 0 Unit cell: (118.482, 108.066, 113.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 80 16.00 P 2 15.00 O 2162 8.00 N 1976 7.00 C 8098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 65.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 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: 4.23 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2011 1.32 - 1.45: 3570 1.45 - 1.57: 6941 1.57 - 1.69: 4 1.69 - 1.81: 120 Bond restraints: 12646 Sorted by residual: bond pdb=" CA ASP B 583 " pdb=" CB ASP B 583 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.27e+00 bond pdb=" CA ASP A 375 " pdb=" CB ASP A 375 " ideal model delta sigma weight residual 1.531 1.565 -0.034 3.28e-02 9.30e+02 1.09e+00 bond pdb=" CA ASP B 375 " pdb=" CB ASP B 375 " ideal model delta sigma weight residual 1.531 1.564 -0.033 3.28e-02 9.30e+02 1.03e+00 bond pdb=" CB VAL A 702 " pdb=" CG1 VAL A 702 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.17e-01 bond pdb=" CB VAL B 702 " pdb=" CG1 VAL B 702 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.15e-01 ... (remaining 12641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 16606 1.22 - 2.44: 398 2.44 - 3.67: 100 3.67 - 4.89: 10 4.89 - 6.11: 4 Bond angle restraints: 17118 Sorted by residual: angle pdb=" N VAL B 578 " pdb=" CA VAL B 578 " pdb=" C VAL B 578 " ideal model delta sigma weight residual 113.71 110.39 3.32 9.50e-01 1.11e+00 1.22e+01 angle pdb=" CA GLY B 600 " pdb=" C GLY B 600 " pdb=" O GLY B 600 " ideal model delta sigma weight residual 122.45 120.32 2.13 7.20e-01 1.93e+00 8.71e+00 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 114.12 -3.42 1.22e+00 6.72e-01 7.86e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 114.06 -3.36 1.22e+00 6.72e-01 7.59e+00 angle pdb=" CA GLY A 600 " pdb=" C GLY A 600 " pdb=" O GLY A 600 " ideal model delta sigma weight residual 122.37 120.37 2.00 7.30e-01 1.88e+00 7.47e+00 ... (remaining 17113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.03: 7354 32.03 - 64.06: 125 64.06 - 96.09: 5 96.09 - 128.12: 0 128.12 - 160.14: 2 Dihedral angle restraints: 7486 sinusoidal: 3104 harmonic: 4382 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.81 -40.81 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.43 -40.43 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" O5 P1O A1003 " pdb=" C7 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " ideal model delta sinusoidal sigma weight residual 56.91 -142.95 -160.14 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 7483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 997 0.025 - 0.050: 483 0.050 - 0.075: 255 0.075 - 0.099: 88 0.099 - 0.124: 31 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CA VAL A 715 " pdb=" N VAL A 715 " pdb=" C VAL A 715 " pdb=" CB VAL A 715 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL B 715 " pdb=" N VAL B 715 " pdb=" C VAL B 715 " pdb=" CB VAL B 715 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1851 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 597 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 598 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 597 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 598 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 580 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO B 581 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 581 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 581 " -0.023 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 195 2.67 - 3.23: 12052 3.23 - 3.78: 19675 3.78 - 4.34: 26171 4.34 - 4.90: 43669 Nonbonded interactions: 101762 Sorted by model distance: nonbonded pdb=" OG SER B 190 " pdb=" OD2 ASP B 194 " model vdw 2.111 3.040 nonbonded pdb=" OG SER A 190 " pdb=" OD2 ASP A 194 " model vdw 2.121 3.040 nonbonded pdb=" OD2 ASP B 749 " pdb=" OH TYR B 776 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASP A 749 " pdb=" OH TYR A 776 " model vdw 2.245 3.040 nonbonded pdb=" OE2 GLU A 699 " pdb="CA CA A1002 " model vdw 2.256 2.510 ... (remaining 101757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.060 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12646 Z= 0.186 Angle : 0.500 6.111 17118 Z= 0.283 Chirality : 0.039 0.124 1854 Planarity : 0.004 0.047 2118 Dihedral : 11.832 160.144 4638 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.92 % Allowed : 4.95 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1442 helix: 2.16 (0.16), residues: 920 sheet: 0.40 (0.66), residues: 62 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.003 0.001 HIS A 275 PHE 0.012 0.001 PHE A 560 TYR 0.016 0.001 TYR A 580 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: A 196 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.4759 (m-80) REVERT: A 236 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 255 TYR cc_start: 0.8186 (m-80) cc_final: 0.7805 (m-10) REVERT: A 298 ILE cc_start: 0.9013 (tp) cc_final: 0.8701 (tt) REVERT: A 370 LYS cc_start: 0.8293 (ptpp) cc_final: 0.8045 (mmtm) REVERT: A 403 GLU cc_start: 0.8060 (tt0) cc_final: 0.7610 (tm-30) REVERT: A 407 GLU cc_start: 0.8457 (tt0) cc_final: 0.8170 (tt0) REVERT: A 413 LEU cc_start: 0.8981 (tt) cc_final: 0.8723 (tt) REVERT: A 546 ASP cc_start: 0.8391 (m-30) cc_final: 0.8048 (m-30) REVERT: A 695 ASN cc_start: 0.8767 (t0) cc_final: 0.8397 (t0) REVERT: A 749 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7203 (t0) REVERT: A 770 TYR cc_start: 0.7937 (p90) cc_final: 0.7404 (t80) REVERT: A 773 MET cc_start: 0.9525 (mmm) cc_final: 0.9201 (tpp) REVERT: A 826 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8952 (tt) REVERT: B 73 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: B 196 TYR cc_start: 0.5988 (OUTLIER) cc_final: 0.4639 (m-80) REVERT: B 289 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8111 (ttt-90) REVERT: B 298 ILE cc_start: 0.9047 (tp) cc_final: 0.8705 (tt) REVERT: B 370 LYS cc_start: 0.8262 (ptpp) cc_final: 0.8018 (mmtm) REVERT: B 403 GLU cc_start: 0.8111 (tt0) cc_final: 0.7637 (tm-30) REVERT: B 407 GLU cc_start: 0.8457 (tt0) cc_final: 0.8157 (tt0) REVERT: B 413 LEU cc_start: 0.9136 (tt) cc_final: 0.8915 (tt) REVERT: B 546 ASP cc_start: 0.8310 (m-30) cc_final: 0.7991 (m-30) REVERT: B 695 ASN cc_start: 0.8770 (t0) cc_final: 0.8395 (t0) REVERT: B 749 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7171 (t0) REVERT: B 770 TYR cc_start: 0.7884 (p90) cc_final: 0.7486 (t80) REVERT: B 773 MET cc_start: 0.9502 (mmm) cc_final: 0.9161 (tpp) outliers start: 39 outliers final: 13 residues processed: 248 average time/residue: 0.2695 time to fit residues: 94.2913 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 99 GLN A 104 ASN A 234 ASN A 525 ASN A 559 GLN A 632 ASN A 710 GLN A 730 GLN B 44 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 234 ASN B 525 ASN B 559 GLN B 632 ASN B 674 GLN B 695 ASN B 710 GLN B 730 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12646 Z= 0.197 Angle : 0.524 7.917 17118 Z= 0.284 Chirality : 0.039 0.136 1854 Planarity : 0.005 0.046 2118 Dihedral : 10.057 159.497 1732 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.47 % Allowed : 9.00 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.22), residues: 1442 helix: 2.16 (0.16), residues: 922 sheet: 0.33 (0.65), residues: 62 loop : -1.31 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 PHE 0.013 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.006 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: A 196 TYR cc_start: 0.5945 (OUTLIER) cc_final: 0.4471 (m-80) REVERT: A 255 TYR cc_start: 0.8211 (m-80) cc_final: 0.7882 (m-10) REVERT: A 298 ILE cc_start: 0.9041 (tp) cc_final: 0.8718 (tt) REVERT: A 403 GLU cc_start: 0.8092 (tt0) cc_final: 0.7695 (tm-30) REVERT: A 407 GLU cc_start: 0.8384 (tt0) cc_final: 0.8134 (tt0) REVERT: A 546 ASP cc_start: 0.8334 (m-30) cc_final: 0.7961 (m-30) REVERT: A 631 MET cc_start: 0.8372 (mmm) cc_final: 0.8045 (mmm) REVERT: A 695 ASN cc_start: 0.8849 (t0) cc_final: 0.8397 (t0) REVERT: A 770 TYR cc_start: 0.8052 (p90) cc_final: 0.7517 (t80) REVERT: A 773 MET cc_start: 0.9530 (mmm) cc_final: 0.8767 (mmt) REVERT: A 826 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8960 (tt) REVERT: B 73 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: B 142 MET cc_start: 0.8515 (ptt) cc_final: 0.8152 (ptt) REVERT: B 196 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.4405 (m-80) REVERT: B 298 ILE cc_start: 0.9048 (tp) cc_final: 0.8721 (tt) REVERT: B 334 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8312 (p) REVERT: B 403 GLU cc_start: 0.8133 (tt0) cc_final: 0.7666 (tm-30) REVERT: B 407 GLU cc_start: 0.8413 (tt0) cc_final: 0.8193 (tt0) REVERT: B 461 PHE cc_start: 0.6238 (m-80) cc_final: 0.5571 (t80) REVERT: B 546 ASP cc_start: 0.8342 (m-30) cc_final: 0.7973 (m-30) REVERT: B 695 ASN cc_start: 0.8844 (t0) cc_final: 0.8445 (t0) REVERT: B 714 MET cc_start: 0.8694 (mtp) cc_final: 0.8491 (mtm) REVERT: B 717 GLU cc_start: 0.8165 (mp0) cc_final: 0.7963 (mp0) REVERT: B 749 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7233 (t0) REVERT: B 770 TYR cc_start: 0.8004 (p90) cc_final: 0.7611 (t80) REVERT: B 773 MET cc_start: 0.9495 (mmm) cc_final: 0.8710 (mmt) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.2477 time to fit residues: 63.4904 Evaluate side-chains 152 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 chunk 133 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 549 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12646 Z= 0.260 Angle : 0.543 7.233 17118 Z= 0.293 Chirality : 0.040 0.158 1854 Planarity : 0.004 0.043 2118 Dihedral : 9.759 158.589 1723 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 9.67 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1442 helix: 2.14 (0.16), residues: 922 sheet: 0.32 (0.66), residues: 62 loop : -1.30 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 829 HIS 0.004 0.001 HIS A 143 PHE 0.018 0.002 PHE A 461 TYR 0.016 0.001 TYR B 580 ARG 0.004 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.7518 (m-80) REVERT: A 196 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.4625 (m-80) REVERT: A 255 TYR cc_start: 0.8243 (m-80) cc_final: 0.7935 (m-10) REVERT: A 298 ILE cc_start: 0.9026 (tp) cc_final: 0.8717 (tt) REVERT: A 334 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 403 GLU cc_start: 0.8101 (tt0) cc_final: 0.7642 (tm-30) REVERT: A 407 GLU cc_start: 0.8406 (tt0) cc_final: 0.8189 (tt0) REVERT: A 481 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8757 (p) REVERT: A 546 ASP cc_start: 0.8359 (m-30) cc_final: 0.7983 (m-30) REVERT: A 695 ASN cc_start: 0.8932 (t0) cc_final: 0.8511 (t0) REVERT: A 770 TYR cc_start: 0.8106 (p90) cc_final: 0.7535 (t80) REVERT: A 773 MET cc_start: 0.9470 (mmm) cc_final: 0.8724 (mmt) REVERT: A 826 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9027 (tt) REVERT: B 73 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: B 196 TYR cc_start: 0.5966 (OUTLIER) cc_final: 0.4458 (m-80) REVERT: B 298 ILE cc_start: 0.9032 (tp) cc_final: 0.8719 (tt) REVERT: B 334 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8287 (p) REVERT: B 403 GLU cc_start: 0.8148 (tt0) cc_final: 0.7666 (tm-30) REVERT: B 407 GLU cc_start: 0.8412 (tt0) cc_final: 0.8186 (tt0) REVERT: B 461 PHE cc_start: 0.6406 (m-80) cc_final: 0.6167 (t80) REVERT: B 481 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 546 ASP cc_start: 0.8350 (m-30) cc_final: 0.7984 (m-30) REVERT: B 695 ASN cc_start: 0.8954 (t0) cc_final: 0.8515 (t0) REVERT: B 717 GLU cc_start: 0.8159 (mp0) cc_final: 0.7950 (mp0) REVERT: B 749 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7357 (t0) REVERT: B 770 TYR cc_start: 0.8138 (p90) cc_final: 0.7655 (t80) REVERT: B 773 MET cc_start: 0.9449 (mmm) cc_final: 0.8690 (mmt) outliers start: 40 outliers final: 24 residues processed: 163 average time/residue: 0.2513 time to fit residues: 59.3321 Evaluate side-chains 150 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 525 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 525 ASN B 549 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12646 Z= 0.232 Angle : 0.526 6.819 17118 Z= 0.284 Chirality : 0.040 0.141 1854 Planarity : 0.004 0.044 2118 Dihedral : 9.588 159.935 1723 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.37 % Allowed : 9.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1442 helix: 2.13 (0.16), residues: 922 sheet: 0.43 (0.67), residues: 62 loop : -1.30 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.004 0.001 HIS B 143 PHE 0.023 0.001 PHE A 461 TYR 0.015 0.001 TYR A 580 ARG 0.003 0.000 ARG A 636 *********************** 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 167 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: A 196 TYR cc_start: 0.5986 (OUTLIER) cc_final: 0.4496 (m-80) REVERT: A 255 TYR cc_start: 0.8274 (m-80) cc_final: 0.8030 (m-10) REVERT: A 298 ILE cc_start: 0.9028 (tp) cc_final: 0.8722 (tt) REVERT: A 334 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8409 (p) REVERT: A 403 GLU cc_start: 0.8107 (tt0) cc_final: 0.7642 (tm-30) REVERT: A 407 GLU cc_start: 0.8401 (tt0) cc_final: 0.8187 (tt0) REVERT: A 481 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 546 ASP cc_start: 0.8371 (m-30) cc_final: 0.7986 (m-30) REVERT: A 695 ASN cc_start: 0.8928 (t0) cc_final: 0.8509 (t0) REVERT: A 770 TYR cc_start: 0.7966 (p90) cc_final: 0.7359 (t80) REVERT: A 773 MET cc_start: 0.9479 (mmm) cc_final: 0.8716 (mmt) REVERT: B 73 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: B 196 TYR cc_start: 0.5977 (OUTLIER) cc_final: 0.4388 (m-80) REVERT: B 298 ILE cc_start: 0.9035 (tp) cc_final: 0.8724 (tt) REVERT: B 334 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8318 (p) REVERT: B 403 GLU cc_start: 0.8131 (tt0) cc_final: 0.7636 (tm-30) REVERT: B 407 GLU cc_start: 0.8447 (tt0) cc_final: 0.8246 (tt0) REVERT: B 461 PHE cc_start: 0.6448 (m-80) cc_final: 0.6198 (t80) REVERT: B 481 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8802 (p) REVERT: B 546 ASP cc_start: 0.8360 (m-30) cc_final: 0.7957 (m-30) REVERT: B 695 ASN cc_start: 0.8952 (t0) cc_final: 0.8518 (t0) REVERT: B 770 TYR cc_start: 0.8140 (p90) cc_final: 0.7656 (t80) REVERT: B 773 MET cc_start: 0.9447 (mmm) cc_final: 0.8752 (mmt) outliers start: 45 outliers final: 28 residues processed: 161 average time/residue: 0.2540 time to fit residues: 60.0038 Evaluate side-chains 154 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 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 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 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN A 559 GLN A 674 GLN A 695 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS B 234 ASN B 401 GLN B 559 GLN B 674 GLN B 695 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12646 Z= 0.232 Angle : 0.522 6.778 17118 Z= 0.282 Chirality : 0.040 0.134 1854 Planarity : 0.004 0.042 2118 Dihedral : 9.368 161.554 1721 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.67 % Allowed : 9.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1442 helix: 2.14 (0.16), residues: 922 sheet: 0.43 (0.66), residues: 62 loop : -1.29 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 PHE 0.019 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.003 0.000 ARG A 636 *********************** 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 170 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7514 (m-80) REVERT: A 196 TYR cc_start: 0.5968 (OUTLIER) cc_final: 0.4503 (m-80) REVERT: A 255 TYR cc_start: 0.8268 (m-80) cc_final: 0.8058 (m-10) REVERT: A 298 ILE cc_start: 0.9038 (tp) cc_final: 0.8733 (tt) REVERT: A 334 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8354 (p) REVERT: A 403 GLU cc_start: 0.8159 (tt0) cc_final: 0.7743 (tm-30) REVERT: A 407 GLU cc_start: 0.8405 (tt0) cc_final: 0.8188 (tt0) REVERT: A 481 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (p) REVERT: A 546 ASP cc_start: 0.8385 (m-30) cc_final: 0.8016 (m-30) REVERT: A 695 ASN cc_start: 0.8872 (t0) cc_final: 0.8514 (t0) REVERT: A 770 TYR cc_start: 0.7982 (p90) cc_final: 0.7364 (t80) REVERT: A 773 MET cc_start: 0.9506 (mmm) cc_final: 0.8758 (mmt) REVERT: B 73 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: B 196 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.4319 (m-80) REVERT: B 298 ILE cc_start: 0.9038 (tp) cc_final: 0.8731 (tt) REVERT: B 403 GLU cc_start: 0.8129 (tt0) cc_final: 0.7637 (tm-30) REVERT: B 461 PHE cc_start: 0.6441 (m-80) cc_final: 0.6217 (t80) REVERT: B 481 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8805 (p) REVERT: B 546 ASP cc_start: 0.8376 (m-30) cc_final: 0.7964 (m-30) REVERT: B 695 ASN cc_start: 0.8894 (t0) cc_final: 0.8533 (t0) REVERT: B 770 TYR cc_start: 0.8136 (p90) cc_final: 0.7639 (t80) REVERT: B 773 MET cc_start: 0.9478 (mmm) cc_final: 0.8716 (mmt) outliers start: 49 outliers final: 29 residues processed: 165 average time/residue: 0.2576 time to fit residues: 62.0390 Evaluate side-chains 149 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 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 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 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 48 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 525 ASN A 559 GLN A 674 GLN A 695 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 559 GLN B 674 GLN B 695 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12646 Z= 0.228 Angle : 0.523 7.316 17118 Z= 0.283 Chirality : 0.040 0.151 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.325 163.172 1720 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.07 % Allowed : 9.45 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1442 helix: 2.14 (0.16), residues: 922 sheet: 0.34 (0.65), residues: 62 loop : -1.27 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 PHE 0.018 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.003 0.000 ARG A 636 *********************** 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 162 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: A 196 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.4478 (m-80) REVERT: A 255 TYR cc_start: 0.8265 (m-80) cc_final: 0.8039 (m-10) REVERT: A 298 ILE cc_start: 0.9039 (tp) cc_final: 0.8737 (tt) REVERT: A 334 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 403 GLU cc_start: 0.8148 (tt0) cc_final: 0.7688 (tm-30) REVERT: A 407 GLU cc_start: 0.8412 (tt0) cc_final: 0.8190 (tt0) REVERT: A 481 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 546 ASP cc_start: 0.8392 (m-30) cc_final: 0.8041 (m-30) REVERT: A 695 ASN cc_start: 0.8939 (t0) cc_final: 0.8510 (t0) REVERT: A 770 TYR cc_start: 0.7986 (p90) cc_final: 0.7366 (t80) REVERT: A 773 MET cc_start: 0.9486 (mmm) cc_final: 0.8740 (mmt) REVERT: B 73 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: B 196 TYR cc_start: 0.5898 (OUTLIER) cc_final: 0.4892 (m-80) REVERT: B 298 ILE cc_start: 0.9048 (tp) cc_final: 0.8742 (tt) REVERT: B 403 GLU cc_start: 0.8123 (tt0) cc_final: 0.7635 (tm-30) REVERT: B 461 PHE cc_start: 0.6438 (m-80) cc_final: 0.6222 (t80) REVERT: B 481 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8808 (p) REVERT: B 546 ASP cc_start: 0.8387 (m-30) cc_final: 0.7965 (m-30) REVERT: B 661 LYS cc_start: 0.9058 (mmtp) cc_final: 0.8768 (mppt) REVERT: B 695 ASN cc_start: 0.8946 (t0) cc_final: 0.8515 (t0) REVERT: B 770 TYR cc_start: 0.8136 (p90) cc_final: 0.7638 (t80) REVERT: B 773 MET cc_start: 0.9460 (mmm) cc_final: 0.8685 (mmt) outliers start: 41 outliers final: 28 residues processed: 157 average time/residue: 0.2421 time to fit residues: 56.4175 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 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 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12646 Z= 0.313 Angle : 0.565 7.413 17118 Z= 0.307 Chirality : 0.041 0.155 1854 Planarity : 0.004 0.039 2118 Dihedral : 9.354 163.684 1719 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.45 % Allowed : 9.22 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.22), residues: 1442 helix: 2.06 (0.16), residues: 912 sheet: 0.34 (0.65), residues: 62 loop : -1.29 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.003 0.001 HIS A 275 PHE 0.016 0.002 PHE A 461 TYR 0.020 0.002 TYR A 580 ARG 0.003 0.000 ARG B 753 *********************** 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 157 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7455 (m-80) REVERT: A 196 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.4811 (m-80) REVERT: A 298 ILE cc_start: 0.9038 (tp) cc_final: 0.8709 (tt) REVERT: A 334 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 403 GLU cc_start: 0.8159 (tt0) cc_final: 0.7679 (tm-30) REVERT: A 407 GLU cc_start: 0.8449 (tt0) cc_final: 0.8193 (tt0) REVERT: A 481 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8841 (p) REVERT: A 546 ASP cc_start: 0.8414 (m-30) cc_final: 0.8116 (m-30) REVERT: A 695 ASN cc_start: 0.8958 (t0) cc_final: 0.8583 (t0) REVERT: A 770 TYR cc_start: 0.8022 (p90) cc_final: 0.7493 (t80) REVERT: A 773 MET cc_start: 0.9428 (mmm) cc_final: 0.9079 (tpp) REVERT: B 73 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: B 196 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.4834 (m-80) REVERT: B 298 ILE cc_start: 0.9037 (tp) cc_final: 0.8704 (tt) REVERT: B 334 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 403 GLU cc_start: 0.8135 (tt0) cc_final: 0.7624 (tm-30) REVERT: B 481 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8824 (p) REVERT: B 546 ASP cc_start: 0.8411 (m-30) cc_final: 0.8052 (m-30) REVERT: B 695 ASN cc_start: 0.8969 (t0) cc_final: 0.8590 (t0) REVERT: B 770 TYR cc_start: 0.8167 (p90) cc_final: 0.7644 (t80) REVERT: B 773 MET cc_start: 0.9403 (mmm) cc_final: 0.8710 (mmt) outliers start: 46 outliers final: 31 residues processed: 152 average time/residue: 0.2475 time to fit residues: 55.1124 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL 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 56 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 0.0070 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 525 ASN A 674 GLN A 695 ASN B 111 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12646 Z= 0.176 Angle : 0.513 7.018 17118 Z= 0.276 Chirality : 0.039 0.132 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.257 166.235 1719 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.92 % Allowed : 9.60 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1442 helix: 2.22 (0.16), residues: 920 sheet: 0.37 (0.66), residues: 62 loop : -1.31 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 PHE 0.015 0.001 PHE A 461 TYR 0.015 0.001 TYR A 528 ARG 0.002 0.000 ARG A 636 *********************** 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 159 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: A 196 TYR cc_start: 0.5852 (OUTLIER) cc_final: 0.4690 (m-80) REVERT: A 298 ILE cc_start: 0.9016 (tp) cc_final: 0.8727 (tt) REVERT: A 334 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8159 (p) REVERT: A 403 GLU cc_start: 0.8158 (tt0) cc_final: 0.7743 (tm-30) REVERT: A 407 GLU cc_start: 0.8362 (tt0) cc_final: 0.8141 (tt0) REVERT: A 481 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8784 (p) REVERT: A 546 ASP cc_start: 0.8409 (m-30) cc_final: 0.8091 (m-30) REVERT: A 631 MET cc_start: 0.8448 (mmm) cc_final: 0.8193 (mmm) REVERT: A 661 LYS cc_start: 0.9060 (mmtp) cc_final: 0.8759 (mppt) REVERT: A 695 ASN cc_start: 0.8861 (t0) cc_final: 0.8472 (t0) REVERT: A 770 TYR cc_start: 0.7961 (p90) cc_final: 0.7367 (t80) REVERT: A 773 MET cc_start: 0.9453 (mmm) cc_final: 0.8674 (mmt) REVERT: B 73 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: B 196 TYR cc_start: 0.5848 (OUTLIER) cc_final: 0.5200 (m-80) REVERT: B 298 ILE cc_start: 0.9038 (tp) cc_final: 0.8743 (tt) REVERT: B 334 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8156 (p) REVERT: B 403 GLU cc_start: 0.8123 (tt0) cc_final: 0.7628 (tm-30) REVERT: B 407 GLU cc_start: 0.8407 (tt0) cc_final: 0.8168 (tt0) REVERT: B 481 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 546 ASP cc_start: 0.8413 (m-30) cc_final: 0.8041 (m-30) REVERT: B 661 LYS cc_start: 0.9053 (mmtp) cc_final: 0.8764 (mppt) REVERT: B 695 ASN cc_start: 0.8867 (t0) cc_final: 0.8481 (t0) REVERT: B 770 TYR cc_start: 0.8130 (p90) cc_final: 0.7533 (t80) REVERT: B 773 MET cc_start: 0.9426 (mmm) cc_final: 0.8717 (mmt) REVERT: B 872 LYS cc_start: 0.8395 (pttm) cc_final: 0.8151 (ptpp) outliers start: 39 outliers final: 28 residues processed: 152 average time/residue: 0.2740 time to fit residues: 60.6687 Evaluate side-chains 149 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 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 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 480 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL 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 136 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 87 optimal weight: 0.0170 chunk 140 optimal weight: 0.2980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN B 205 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12646 Z= 0.169 Angle : 0.507 8.325 17118 Z= 0.272 Chirality : 0.039 0.133 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.130 166.069 1718 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.00 % Allowed : 9.67 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1442 helix: 2.29 (0.16), residues: 920 sheet: 0.42 (0.65), residues: 62 loop : -1.28 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 249 PHE 0.015 0.001 PHE A 461 TYR 0.016 0.001 TYR A 580 ARG 0.003 0.000 ARG A 191 *********************** 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 158 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: A 191 ARG cc_start: 0.6582 (ptt90) cc_final: 0.6231 (ptm-80) REVERT: A 196 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.4630 (m-80) REVERT: A 290 LYS cc_start: 0.9223 (ptmt) cc_final: 0.9007 (ptmm) REVERT: A 298 ILE cc_start: 0.9024 (tp) cc_final: 0.8760 (tt) REVERT: A 334 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 403 GLU cc_start: 0.8108 (tt0) cc_final: 0.7697 (tm-30) REVERT: A 407 GLU cc_start: 0.8367 (tt0) cc_final: 0.8163 (tt0) REVERT: A 481 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8756 (p) REVERT: A 546 ASP cc_start: 0.8410 (m-30) cc_final: 0.8071 (m-30) REVERT: A 631 MET cc_start: 0.8472 (mmm) cc_final: 0.8230 (mmm) REVERT: A 661 LYS cc_start: 0.9117 (mmtp) cc_final: 0.8785 (mppt) REVERT: A 695 ASN cc_start: 0.8843 (t0) cc_final: 0.8417 (t0) REVERT: A 770 TYR cc_start: 0.7965 (p90) cc_final: 0.7365 (t80) REVERT: A 773 MET cc_start: 0.9430 (mmm) cc_final: 0.8649 (mmt) REVERT: B 73 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: B 196 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: B 298 ILE cc_start: 0.9031 (tp) cc_final: 0.8761 (tt) REVERT: B 334 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8152 (p) REVERT: B 403 GLU cc_start: 0.8128 (tt0) cc_final: 0.7686 (tm-30) REVERT: B 407 GLU cc_start: 0.8388 (tt0) cc_final: 0.8158 (tt0) REVERT: B 546 ASP cc_start: 0.8415 (m-30) cc_final: 0.8044 (m-30) REVERT: B 631 MET cc_start: 0.8511 (mmm) cc_final: 0.8251 (mmm) REVERT: B 661 LYS cc_start: 0.9117 (mmtp) cc_final: 0.8801 (mppt) REVERT: B 695 ASN cc_start: 0.8910 (t0) cc_final: 0.8475 (t0) REVERT: B 770 TYR cc_start: 0.8128 (p90) cc_final: 0.7593 (t80) REVERT: B 773 MET cc_start: 0.9402 (mmm) cc_final: 0.8692 (mmt) REVERT: B 872 LYS cc_start: 0.8399 (pttm) cc_final: 0.8156 (ptpp) outliers start: 40 outliers final: 25 residues processed: 148 average time/residue: 0.2596 time to fit residues: 56.1724 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 0.0980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12646 Z= 0.173 Angle : 0.525 9.658 17118 Z= 0.276 Chirality : 0.039 0.228 1854 Planarity : 0.004 0.039 2118 Dihedral : 8.958 166.271 1716 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.47 % Allowed : 9.90 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1442 helix: 2.30 (0.16), residues: 920 sheet: 0.30 (0.65), residues: 62 loop : -1.29 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.019 0.001 PHE A 461 TYR 0.015 0.001 TYR A 580 ARG 0.003 0.000 ARG A 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: A 196 TYR cc_start: 0.5685 (OUTLIER) cc_final: 0.4715 (m-80) REVERT: A 290 LYS cc_start: 0.9236 (ptmt) cc_final: 0.9001 (ptmm) REVERT: A 298 ILE cc_start: 0.9035 (tp) cc_final: 0.8766 (tt) REVERT: A 334 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 403 GLU cc_start: 0.8104 (tt0) cc_final: 0.7698 (tm-30) REVERT: A 481 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 546 ASP cc_start: 0.8416 (m-30) cc_final: 0.8059 (m-30) REVERT: A 631 MET cc_start: 0.8465 (mmm) cc_final: 0.8230 (mmm) REVERT: A 661 LYS cc_start: 0.9116 (mmtp) cc_final: 0.8787 (mppt) REVERT: A 695 ASN cc_start: 0.8828 (t0) cc_final: 0.8465 (t0) REVERT: A 770 TYR cc_start: 0.7965 (p90) cc_final: 0.7363 (t80) REVERT: A 773 MET cc_start: 0.9422 (mmm) cc_final: 0.8724 (mmt) REVERT: B 73 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: B 196 TYR cc_start: 0.6309 (OUTLIER) cc_final: 0.5095 (m-80) REVERT: B 298 ILE cc_start: 0.9042 (tp) cc_final: 0.8773 (tt) REVERT: B 334 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8151 (p) REVERT: B 403 GLU cc_start: 0.8126 (tt0) cc_final: 0.7688 (tm-30) REVERT: B 407 GLU cc_start: 0.8389 (tt0) cc_final: 0.8163 (tt0) REVERT: B 543 THR cc_start: 0.8529 (p) cc_final: 0.8216 (p) REVERT: B 546 ASP cc_start: 0.8418 (m-30) cc_final: 0.8103 (m-30) REVERT: B 631 MET cc_start: 0.8506 (mmm) cc_final: 0.8249 (mmm) REVERT: B 661 LYS cc_start: 0.9118 (mmtp) cc_final: 0.8807 (mppt) REVERT: B 695 ASN cc_start: 0.8835 (t0) cc_final: 0.8475 (t0) REVERT: B 770 TYR cc_start: 0.8119 (p90) cc_final: 0.7589 (t80) REVERT: B 773 MET cc_start: 0.9396 (mmm) cc_final: 0.8683 (mmt) outliers start: 33 outliers final: 23 residues processed: 143 average time/residue: 0.2559 time to fit residues: 54.0240 Evaluate side-chains 151 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.108287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081182 restraints weight = 22455.894| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.58 r_work: 0.2938 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12646 Z= 0.249 Angle : 0.557 11.087 17118 Z= 0.294 Chirality : 0.040 0.195 1854 Planarity : 0.004 0.039 2118 Dihedral : 8.996 165.746 1716 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.77 % Allowed : 9.67 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.22), residues: 1442 helix: 2.19 (0.16), residues: 920 sheet: 0.29 (0.65), residues: 62 loop : -1.29 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.001 HIS B 830 PHE 0.034 0.002 PHE B 461 TYR 0.017 0.001 TYR A 580 ARG 0.006 0.000 ARG A 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2408.97 seconds wall clock time: 45 minutes 29.42 seconds (2729.42 seconds total)