Starting phenix.real_space_refine on Wed Jul 30 17:32:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8k_15916/07_2025/8b8k_15916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8k_15916/07_2025/8b8k_15916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b8k_15916/07_2025/8b8k_15916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8k_15916/07_2025/8b8k_15916.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8k_15916/07_2025/8b8k_15916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8k_15916/07_2025/8b8k_15916.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 2 5.49 5 S 80 5.16 5 C 8098 2.51 5 N 1976 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.57, per 1000 atoms: 0.61 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: 3.19 Conformation dependent library (CDL) restraints added in 1.5 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: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 89 through 109 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.560A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.526A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 342 through 345 Processing helix chain 'A' and resid 364 through 375 removed outlier: 4.032A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.934A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.694A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 488 removed outlier: 4.484A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.706A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.015A pdb=" N SER A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.835A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 3.982A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 3.815A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.407A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 875 Processing helix chain 'B' and resid 89 through 108 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.557A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.531A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 342 through 345 Processing helix chain 'B' and resid 364 through 375 removed outlier: 4.038A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.934A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 removed outlier: 3.720A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 488 removed outlier: 4.462A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.715A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.019A pdb=" N SER B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.837A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 3.992A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.811A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 796 through 802 removed outlier: 4.411A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 875 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.543A pdb=" N SER A 190 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.554A pdb=" N SER B 190 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 785 763 hydrogen bonds defined for protein. 2229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2011 1.32 - 1.45: 3570 1.45 - 1.57: 6941 1.57 - 1.69: 4 1.69 - 1.81: 120 Bond restraints: 12646 Sorted by residual: bond pdb=" CA ASP B 583 " pdb=" CB ASP B 583 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.27e+00 bond pdb=" CA ASP A 375 " pdb=" CB ASP A 375 " ideal model delta sigma weight residual 1.531 1.565 -0.034 3.28e-02 9.30e+02 1.09e+00 bond pdb=" CA ASP B 375 " pdb=" CB ASP B 375 " ideal model delta sigma weight residual 1.531 1.564 -0.033 3.28e-02 9.30e+02 1.03e+00 bond pdb=" CB VAL A 702 " pdb=" CG1 VAL A 702 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.17e-01 bond pdb=" CB VAL B 702 " pdb=" CG1 VAL B 702 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.15e-01 ... (remaining 12641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 16606 1.22 - 2.44: 398 2.44 - 3.67: 100 3.67 - 4.89: 10 4.89 - 6.11: 4 Bond angle restraints: 17118 Sorted by residual: angle pdb=" N VAL B 578 " pdb=" CA VAL B 578 " pdb=" C VAL B 578 " ideal model delta sigma weight residual 113.71 110.39 3.32 9.50e-01 1.11e+00 1.22e+01 angle pdb=" CA GLY B 600 " pdb=" C GLY B 600 " pdb=" O GLY B 600 " ideal model delta sigma weight residual 122.45 120.32 2.13 7.20e-01 1.93e+00 8.71e+00 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 114.12 -3.42 1.22e+00 6.72e-01 7.86e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 114.06 -3.36 1.22e+00 6.72e-01 7.59e+00 angle pdb=" CA GLY A 600 " pdb=" C GLY A 600 " pdb=" O GLY A 600 " ideal model delta sigma weight residual 122.37 120.37 2.00 7.30e-01 1.88e+00 7.47e+00 ... (remaining 17113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.03: 7354 32.03 - 64.06: 125 64.06 - 96.09: 5 96.09 - 128.12: 0 128.12 - 160.14: 2 Dihedral angle restraints: 7486 sinusoidal: 3104 harmonic: 4382 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.81 -40.81 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.43 -40.43 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" O5 P1O A1003 " pdb=" C7 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " ideal model delta sinusoidal sigma weight residual 56.91 -142.95 -160.14 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 7483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 997 0.025 - 0.050: 483 0.050 - 0.075: 255 0.075 - 0.099: 88 0.099 - 0.124: 31 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CA VAL A 715 " pdb=" N VAL A 715 " pdb=" C VAL A 715 " pdb=" CB VAL A 715 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL B 715 " pdb=" N VAL B 715 " pdb=" C VAL B 715 " pdb=" CB VAL B 715 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1851 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 597 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 598 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 597 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 598 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 580 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO B 581 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 581 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 581 " -0.023 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 195 2.67 - 3.23: 12052 3.23 - 3.78: 19675 3.78 - 4.34: 26171 4.34 - 4.90: 43669 Nonbonded interactions: 101762 Sorted by model distance: nonbonded pdb=" OG SER B 190 " pdb=" OD2 ASP B 194 " model vdw 2.111 3.040 nonbonded pdb=" OG SER A 190 " pdb=" OD2 ASP A 194 " model vdw 2.121 3.040 nonbonded pdb=" OD2 ASP B 749 " pdb=" OH TYR B 776 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASP A 749 " pdb=" OH TYR A 776 " model vdw 2.245 3.040 nonbonded pdb=" OE2 GLU A 699 " pdb="CA CA A1002 " model vdw 2.256 2.510 ... (remaining 101757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.060 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12654 Z= 0.138 Angle : 0.499 6.111 17134 Z= 0.283 Chirality : 0.039 0.124 1854 Planarity : 0.004 0.047 2118 Dihedral : 11.832 160.144 4638 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.92 % Allowed : 4.95 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1442 helix: 2.16 (0.16), residues: 920 sheet: 0.40 (0.66), residues: 62 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.003 0.001 HIS A 275 PHE 0.012 0.001 PHE A 560 TYR 0.016 0.001 TYR A 580 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.07660 ( 763) hydrogen bonds : angle 4.72890 ( 2229) SS BOND : bond 0.00127 ( 8) SS BOND : angle 0.37817 ( 16) covalent geometry : bond 0.00290 (12646) covalent geometry : angle 0.49955 (17118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.296 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: 0.2485 time to fit residues: 87.4072 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 : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 99 GLN A 104 ASN A 234 ASN A 525 ASN A 559 GLN A 632 ASN A 710 GLN A 730 GLN B 44 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 234 ASN B 525 ASN B 559 GLN B 632 ASN B 674 GLN B 695 ASN B 710 GLN B 730 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.082725 restraints weight = 21995.676| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.63 r_work: 0.2985 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12654 Z= 0.134 Angle : 0.524 7.917 17134 Z= 0.284 Chirality : 0.039 0.136 1854 Planarity : 0.005 0.046 2118 Dihedral : 10.057 159.497 1732 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.47 % Allowed : 9.00 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.22), residues: 1442 helix: 2.16 (0.16), residues: 922 sheet: 0.33 (0.65), residues: 62 loop : -1.31 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 PHE 0.013 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.006 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 763) hydrogen bonds : angle 4.43938 ( 2229) SS BOND : bond 0.00101 ( 8) SS BOND : angle 0.37633 ( 16) covalent geometry : bond 0.00296 (12646) covalent geometry : angle 0.52386 (17118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: A 196 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.4582 (m-80) REVERT: A 255 TYR cc_start: 0.8258 (m-80) cc_final: 0.7935 (m-10) REVERT: A 298 ILE cc_start: 0.8929 (tp) cc_final: 0.8616 (tt) REVERT: A 403 GLU cc_start: 0.8120 (tt0) cc_final: 0.7694 (tm-30) REVERT: A 407 GLU cc_start: 0.8480 (tt0) cc_final: 0.8247 (tt0) REVERT: A 546 ASP cc_start: 0.8291 (m-30) cc_final: 0.7942 (m-30) REVERT: A 631 MET cc_start: 0.8324 (mmm) cc_final: 0.8003 (mmm) REVERT: A 695 ASN cc_start: 0.8808 (t0) cc_final: 0.8353 (t0) REVERT: A 770 TYR cc_start: 0.7967 (p90) cc_final: 0.7413 (t80) REVERT: A 773 MET cc_start: 0.9475 (mmm) cc_final: 0.8714 (mmt) REVERT: A 826 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8830 (tt) REVERT: B 73 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: B 142 MET cc_start: 0.8475 (ptt) cc_final: 0.8046 (ptt) REVERT: B 196 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.4468 (m-80) REVERT: B 298 ILE cc_start: 0.8926 (tp) cc_final: 0.8611 (tt) REVERT: B 334 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8287 (p) REVERT: B 403 GLU cc_start: 0.8138 (tt0) cc_final: 0.7653 (tm-30) REVERT: B 407 GLU cc_start: 0.8496 (tt0) cc_final: 0.8284 (tt0) REVERT: B 461 PHE cc_start: 0.6230 (m-80) cc_final: 0.5562 (t80) REVERT: B 546 ASP cc_start: 0.8300 (m-30) cc_final: 0.7958 (m-30) REVERT: B 695 ASN cc_start: 0.8837 (t0) cc_final: 0.8391 (t0) REVERT: B 749 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7145 (t0) REVERT: B 770 TYR cc_start: 0.7922 (p90) cc_final: 0.7510 (t80) REVERT: B 773 MET cc_start: 0.9439 (mmm) cc_final: 0.8680 (mmt) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.2436 time to fit residues: 63.1546 Evaluate side-chains 151 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 120 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.081424 restraints weight = 22481.213| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.63 r_work: 0.2959 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12654 Z= 0.161 Angle : 0.535 7.037 17134 Z= 0.290 Chirality : 0.040 0.153 1854 Planarity : 0.004 0.043 2118 Dihedral : 9.757 159.260 1723 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.85 % Allowed : 9.60 % 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: 1.55 (0.22), residues: 1442 helix: 2.16 (0.16), residues: 922 sheet: 0.32 (0.66), residues: 62 loop : -1.29 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.004 0.001 HIS A 143 PHE 0.019 0.001 PHE A 461 TYR 0.016 0.001 TYR A 580 ARG 0.004 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 763) hydrogen bonds : angle 4.44641 ( 2229) SS BOND : bond 0.00466 ( 8) SS BOND : angle 0.93017 ( 16) covalent geometry : bond 0.00367 (12646) covalent geometry : angle 0.53458 (17118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: A 196 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.4730 (m-80) REVERT: A 255 TYR cc_start: 0.8289 (m-80) cc_final: 0.7986 (m-10) REVERT: A 298 ILE cc_start: 0.8922 (tp) cc_final: 0.8629 (tt) REVERT: A 334 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8386 (p) REVERT: A 403 GLU cc_start: 0.8148 (tt0) cc_final: 0.7712 (tm-30) REVERT: A 481 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 546 ASP cc_start: 0.8279 (m-30) cc_final: 0.7929 (m-30) REVERT: A 695 ASN cc_start: 0.8913 (t0) cc_final: 0.8488 (t0) REVERT: A 770 TYR cc_start: 0.8027 (p90) cc_final: 0.7446 (t80) REVERT: A 773 MET cc_start: 0.9425 (mmm) cc_final: 0.8677 (mmt) REVERT: A 826 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 73 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: B 196 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.4546 (m-80) REVERT: B 298 ILE cc_start: 0.8911 (tp) cc_final: 0.8619 (tt) REVERT: B 334 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8289 (p) REVERT: B 403 GLU cc_start: 0.8160 (tt0) cc_final: 0.7662 (tm-30) REVERT: B 407 GLU cc_start: 0.8493 (tt0) cc_final: 0.8288 (tt0) REVERT: B 461 PHE cc_start: 0.6444 (m-80) cc_final: 0.6176 (t80) REVERT: B 481 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8788 (p) REVERT: B 543 THR cc_start: 0.8377 (p) cc_final: 0.7980 (p) REVERT: B 546 ASP cc_start: 0.8318 (m-30) cc_final: 0.8038 (m-30) REVERT: B 695 ASN cc_start: 0.8922 (t0) cc_final: 0.8473 (t0) REVERT: B 749 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7265 (t0) REVERT: B 770 TYR cc_start: 0.8067 (p90) cc_final: 0.7566 (t80) REVERT: B 773 MET cc_start: 0.9390 (mmm) cc_final: 0.8645 (mmt) outliers start: 38 outliers final: 22 residues processed: 161 average time/residue: 0.2534 time to fit residues: 59.9096 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 : 1.452 ------------------------------------------------------------------------------- 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 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 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 525 ASN A 549 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 401 GLN B 525 ASN B 549 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080029 restraints weight = 22380.057| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.62 r_work: 0.2930 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12654 Z= 0.190 Angle : 0.552 6.831 17134 Z= 0.297 Chirality : 0.041 0.144 1854 Planarity : 0.005 0.044 2118 Dihedral : 9.566 158.466 1723 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.45 % Allowed : 9.52 % 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: 1.47 (0.22), residues: 1442 helix: 2.12 (0.16), residues: 910 sheet: 0.43 (0.67), residues: 62 loop : -1.30 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 273 HIS 0.003 0.001 HIS A 143 PHE 0.023 0.002 PHE A 461 TYR 0.017 0.002 TYR B 580 ARG 0.004 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 763) hydrogen bonds : angle 4.47972 ( 2229) SS BOND : bond 0.00189 ( 8) SS BOND : angle 1.04180 ( 16) covalent geometry : bond 0.00441 (12646) covalent geometry : angle 0.55156 (17118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: A 196 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.4652 (m-80) REVERT: A 255 TYR cc_start: 0.8327 (m-80) cc_final: 0.8107 (m-10) REVERT: A 298 ILE cc_start: 0.8930 (tp) cc_final: 0.8617 (tt) REVERT: A 334 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 403 GLU cc_start: 0.8191 (tt0) cc_final: 0.7710 (tm-30) REVERT: A 481 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8803 (p) REVERT: A 546 ASP cc_start: 0.8312 (m-30) cc_final: 0.7973 (m-30) REVERT: A 695 ASN cc_start: 0.8920 (t0) cc_final: 0.8514 (t0) REVERT: A 770 TYR cc_start: 0.8041 (p90) cc_final: 0.7523 (t80) REVERT: A 773 MET cc_start: 0.9432 (mmm) cc_final: 0.8709 (mmt) REVERT: B 73 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: B 191 ARG cc_start: 0.6915 (ptt90) cc_final: 0.6617 (ptt90) REVERT: B 196 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.4472 (m-80) REVERT: B 298 ILE cc_start: 0.8922 (tp) cc_final: 0.8612 (tt) REVERT: B 403 GLU cc_start: 0.8164 (tt0) cc_final: 0.7645 (tm-30) REVERT: B 407 GLU cc_start: 0.8569 (tt0) cc_final: 0.8361 (tt0) REVERT: B 461 PHE cc_start: 0.6500 (m-80) cc_final: 0.6237 (t80) REVERT: B 481 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 546 ASP cc_start: 0.8345 (m-30) cc_final: 0.7957 (m-30) REVERT: B 695 ASN cc_start: 0.8941 (t0) cc_final: 0.8506 (t0) REVERT: B 770 TYR cc_start: 0.8089 (p90) cc_final: 0.7581 (t80) REVERT: B 773 MET cc_start: 0.9403 (mmm) cc_final: 0.8701 (mmt) outliers start: 46 outliers final: 29 residues processed: 163 average time/residue: 0.2483 time to fit residues: 59.0318 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 93 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 111 optimal weight: 0.0570 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 559 GLN A 674 GLN A 695 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS B 234 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 674 GLN B 695 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081296 restraints weight = 22261.874| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.67 r_work: 0.2945 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12654 Z= 0.139 Angle : 0.518 6.730 17134 Z= 0.279 Chirality : 0.039 0.134 1854 Planarity : 0.004 0.043 2118 Dihedral : 9.375 162.445 1721 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.45 % Allowed : 9.52 % 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: 1.55 (0.22), residues: 1442 helix: 2.13 (0.16), residues: 922 sheet: 0.47 (0.67), residues: 62 loop : -1.28 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 275 PHE 0.017 0.001 PHE A 461 TYR 0.015 0.001 TYR A 580 ARG 0.002 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 763) hydrogen bonds : angle 4.37719 ( 2229) SS BOND : bond 0.00467 ( 8) SS BOND : angle 1.03629 ( 16) covalent geometry : bond 0.00315 (12646) covalent geometry : angle 0.51695 (17118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: A 196 TYR cc_start: 0.5997 (OUTLIER) cc_final: 0.4516 (m-80) REVERT: A 255 TYR cc_start: 0.8285 (m-80) cc_final: 0.8025 (m-10) REVERT: A 298 ILE cc_start: 0.8890 (tp) cc_final: 0.8586 (tt) REVERT: A 334 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8301 (p) REVERT: A 403 GLU cc_start: 0.8148 (tt0) cc_final: 0.7669 (tm-30) REVERT: A 481 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8684 (p) REVERT: A 546 ASP cc_start: 0.8251 (m-30) cc_final: 0.7903 (m-30) REVERT: A 695 ASN cc_start: 0.8829 (t0) cc_final: 0.8434 (t0) REVERT: A 770 TYR cc_start: 0.7876 (p90) cc_final: 0.7216 (t80) REVERT: A 773 MET cc_start: 0.9434 (mmm) cc_final: 0.8699 (mmt) REVERT: B 73 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: B 196 TYR cc_start: 0.5874 (OUTLIER) cc_final: 0.4907 (m-80) REVERT: B 298 ILE cc_start: 0.8885 (tp) cc_final: 0.8581 (tt) REVERT: B 334 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8286 (p) REVERT: B 403 GLU cc_start: 0.8106 (tt0) cc_final: 0.7590 (tm-30) REVERT: B 461 PHE cc_start: 0.6374 (m-80) cc_final: 0.6125 (t80) REVERT: B 481 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8729 (p) REVERT: B 546 ASP cc_start: 0.8286 (m-30) cc_final: 0.7892 (m-30) REVERT: B 695 ASN cc_start: 0.8838 (t0) cc_final: 0.8432 (t0) REVERT: B 770 TYR cc_start: 0.8019 (p90) cc_final: 0.7492 (t80) REVERT: B 773 MET cc_start: 0.9408 (mmm) cc_final: 0.8654 (mmt) outliers start: 46 outliers final: 27 residues processed: 165 average time/residue: 0.2397 time to fit residues: 57.9292 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 87 optimal weight: 0.0050 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 205 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082137 restraints weight = 22464.427| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.60 r_work: 0.2959 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12654 Z= 0.130 Angle : 0.512 7.286 17134 Z= 0.277 Chirality : 0.039 0.144 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.289 163.862 1720 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.52 % Allowed : 9.22 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.22), residues: 1442 helix: 2.20 (0.16), residues: 920 sheet: 0.40 (0.66), residues: 62 loop : -1.25 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS A 844 PHE 0.016 0.001 PHE A 461 TYR 0.014 0.001 TYR A 580 ARG 0.002 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 763) hydrogen bonds : angle 4.31240 ( 2229) SS BOND : bond 0.00127 ( 8) SS BOND : angle 0.88306 ( 16) covalent geometry : bond 0.00293 (12646) covalent geometry : angle 0.51169 (17118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: A 196 TYR cc_start: 0.5892 (OUTLIER) cc_final: 0.4423 (m-80) REVERT: A 255 TYR cc_start: 0.8276 (m-80) cc_final: 0.8054 (m-10) REVERT: A 298 ILE cc_start: 0.8861 (tp) cc_final: 0.8577 (tt) REVERT: A 334 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8078 (p) REVERT: A 403 GLU cc_start: 0.8116 (tt0) cc_final: 0.7662 (tm-30) REVERT: A 481 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8637 (p) REVERT: A 546 ASP cc_start: 0.8234 (m-30) cc_final: 0.7887 (m-30) REVERT: A 631 MET cc_start: 0.8338 (mmm) cc_final: 0.8079 (mmm) REVERT: A 695 ASN cc_start: 0.8839 (t0) cc_final: 0.8406 (t0) REVERT: A 770 TYR cc_start: 0.7819 (p90) cc_final: 0.7185 (t80) REVERT: A 773 MET cc_start: 0.9367 (mmm) cc_final: 0.9000 (tpp) REVERT: B 73 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: B 196 TYR cc_start: 0.5877 (OUTLIER) cc_final: 0.4486 (m-80) REVERT: B 298 ILE cc_start: 0.8870 (tp) cc_final: 0.8571 (tt) REVERT: B 334 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8060 (p) REVERT: B 403 GLU cc_start: 0.8059 (tt0) cc_final: 0.7560 (tm-30) REVERT: B 461 PHE cc_start: 0.6368 (m-80) cc_final: 0.6138 (t80) REVERT: B 481 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8697 (p) REVERT: B 546 ASP cc_start: 0.8277 (m-30) cc_final: 0.7885 (m-30) REVERT: B 661 LYS cc_start: 0.9205 (mmtp) cc_final: 0.8830 (mppt) REVERT: B 695 ASN cc_start: 0.8847 (t0) cc_final: 0.8413 (t0) REVERT: B 770 TYR cc_start: 0.7982 (p90) cc_final: 0.7459 (t80) REVERT: B 773 MET cc_start: 0.9365 (mmm) cc_final: 0.8604 (mmt) outliers start: 47 outliers final: 30 residues processed: 156 average time/residue: 0.2375 time to fit residues: 54.6989 Evaluate side-chains 153 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 146 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080734 restraints weight = 22390.116| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.61 r_work: 0.2932 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12654 Z= 0.169 Angle : 0.540 7.001 17134 Z= 0.291 Chirality : 0.040 0.133 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.271 164.657 1718 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 9.60 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1442 helix: 2.14 (0.16), residues: 922 sheet: 0.40 (0.65), residues: 62 loop : -1.29 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.001 0.001 HIS A 830 PHE 0.015 0.001 PHE A 461 TYR 0.019 0.001 TYR A 580 ARG 0.005 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04468 ( 763) hydrogen bonds : angle 4.35488 ( 2229) SS BOND : bond 0.00175 ( 8) SS BOND : angle 0.97908 ( 16) covalent geometry : bond 0.00393 (12646) covalent geometry : angle 0.53930 (17118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: A 196 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.4731 (m-80) REVERT: A 298 ILE cc_start: 0.8865 (tp) cc_final: 0.8553 (tt) REVERT: A 334 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8082 (p) REVERT: A 403 GLU cc_start: 0.8124 (tt0) cc_final: 0.7659 (tm-30) REVERT: A 481 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8678 (p) REVERT: A 546 ASP cc_start: 0.8259 (m-30) cc_final: 0.7944 (m-30) REVERT: A 695 ASN cc_start: 0.8868 (t0) cc_final: 0.8461 (t0) REVERT: A 770 TYR cc_start: 0.7876 (p90) cc_final: 0.7301 (t80) REVERT: A 773 MET cc_start: 0.9319 (mmm) cc_final: 0.8992 (tpp) REVERT: B 73 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: B 196 TYR cc_start: 0.5890 (OUTLIER) cc_final: 0.4744 (m-80) REVERT: B 298 ILE cc_start: 0.8883 (tp) cc_final: 0.8573 (tt) REVERT: B 334 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8068 (p) REVERT: B 403 GLU cc_start: 0.8058 (tt0) cc_final: 0.7530 (tm-30) REVERT: B 461 PHE cc_start: 0.6570 (m-80) cc_final: 0.6342 (t80) REVERT: B 481 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8715 (p) REVERT: B 546 ASP cc_start: 0.8236 (m-30) cc_final: 0.7859 (m-30) REVERT: B 661 LYS cc_start: 0.9210 (mmtp) cc_final: 0.8840 (mppt) REVERT: B 695 ASN cc_start: 0.8878 (t0) cc_final: 0.8472 (t0) REVERT: B 770 TYR cc_start: 0.7898 (p90) cc_final: 0.7321 (t80) REVERT: B 773 MET cc_start: 0.9305 (mmm) cc_final: 0.8610 (mmt) outliers start: 42 outliers final: 29 residues processed: 148 average time/residue: 0.2382 time to fit residues: 52.2639 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 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 108 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 720 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.079133 restraints weight = 22613.553| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.57 r_work: 0.2905 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12654 Z= 0.212 Angle : 0.577 7.246 17134 Z= 0.310 Chirality : 0.041 0.132 1854 Planarity : 0.004 0.040 2118 Dihedral : 9.320 163.311 1718 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.37 % Allowed : 9.52 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.22), residues: 1442 helix: 2.08 (0.16), residues: 910 sheet: 0.31 (0.64), residues: 62 loop : -1.36 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 273 HIS 0.003 0.001 HIS B 143 PHE 0.015 0.002 PHE A 461 TYR 0.016 0.002 TYR B 580 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 763) hydrogen bonds : angle 4.46678 ( 2229) SS BOND : bond 0.00260 ( 8) SS BOND : angle 1.10901 ( 16) covalent geometry : bond 0.00494 (12646) covalent geometry : angle 0.57584 (17118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: A 196 TYR cc_start: 0.5873 (OUTLIER) cc_final: 0.4660 (m-80) REVERT: A 298 ILE cc_start: 0.8868 (tp) cc_final: 0.8531 (tt) REVERT: A 334 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8066 (p) REVERT: A 403 GLU cc_start: 0.8126 (tt0) cc_final: 0.7613 (tm-30) REVERT: A 481 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8709 (p) REVERT: A 546 ASP cc_start: 0.8274 (m-30) cc_final: 0.8013 (m-30) REVERT: A 695 ASN cc_start: 0.8886 (t0) cc_final: 0.8510 (t0) REVERT: A 770 TYR cc_start: 0.7900 (p90) cc_final: 0.7323 (t80) REVERT: A 773 MET cc_start: 0.9316 (mmm) cc_final: 0.8845 (tpp) REVERT: B 73 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: B 196 TYR cc_start: 0.5969 (OUTLIER) cc_final: 0.4840 (m-80) REVERT: B 298 ILE cc_start: 0.8821 (tp) cc_final: 0.8469 (tt) REVERT: B 334 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8068 (p) REVERT: B 403 GLU cc_start: 0.8071 (tt0) cc_final: 0.7519 (tm-30) REVERT: B 481 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 546 ASP cc_start: 0.8262 (m-30) cc_final: 0.7945 (m-30) REVERT: B 661 LYS cc_start: 0.9200 (mmtp) cc_final: 0.8866 (mppt) REVERT: B 695 ASN cc_start: 0.8896 (t0) cc_final: 0.8522 (t0) REVERT: B 770 TYR cc_start: 0.8044 (p90) cc_final: 0.7481 (t80) REVERT: B 773 MET cc_start: 0.9294 (mmm) cc_final: 0.8640 (mmt) outliers start: 45 outliers final: 28 residues processed: 151 average time/residue: 0.2383 time to fit residues: 53.2326 Evaluate side-chains 145 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 96 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN A 720 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.081118 restraints weight = 22473.409| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.59 r_work: 0.2939 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12654 Z= 0.140 Angle : 0.529 7.905 17134 Z= 0.284 Chirality : 0.039 0.132 1854 Planarity : 0.004 0.039 2118 Dihedral : 9.265 165.929 1718 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.92 % Allowed : 9.97 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.65), residues: 62 loop : -1.34 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 844 PHE 0.014 0.001 PHE A 461 TYR 0.016 0.001 TYR A 580 ARG 0.005 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 763) hydrogen bonds : angle 4.33829 ( 2229) SS BOND : bond 0.00156 ( 8) SS BOND : angle 0.91204 ( 16) covalent geometry : bond 0.00317 (12646) covalent geometry : angle 0.52809 (17118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: A 196 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.4585 (m-80) REVERT: A 298 ILE cc_start: 0.8857 (tp) cc_final: 0.8550 (tt) REVERT: A 334 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 403 GLU cc_start: 0.8109 (tt0) cc_final: 0.7614 (tm-30) REVERT: A 481 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8722 (p) REVERT: A 546 ASP cc_start: 0.8256 (m-30) cc_final: 0.7986 (m-30) REVERT: A 661 LYS cc_start: 0.9219 (mmtp) cc_final: 0.8865 (mppt) REVERT: A 695 ASN cc_start: 0.8821 (t0) cc_final: 0.8411 (t0) REVERT: A 770 TYR cc_start: 0.7875 (p90) cc_final: 0.7193 (t80) REVERT: A 773 MET cc_start: 0.9349 (mmm) cc_final: 0.8981 (tpp) REVERT: B 73 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7250 (m-80) REVERT: B 196 TYR cc_start: 0.5877 (OUTLIER) cc_final: 0.5143 (m-80) REVERT: B 298 ILE cc_start: 0.8850 (tp) cc_final: 0.8533 (tt) REVERT: B 334 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8073 (p) REVERT: B 403 GLU cc_start: 0.8054 (tt0) cc_final: 0.7523 (tm-30) REVERT: B 481 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 546 ASP cc_start: 0.8252 (m-30) cc_final: 0.7934 (m-30) REVERT: B 661 LYS cc_start: 0.9196 (mmtp) cc_final: 0.8853 (mppt) REVERT: B 695 ASN cc_start: 0.8833 (t0) cc_final: 0.8404 (t0) REVERT: B 770 TYR cc_start: 0.7894 (p90) cc_final: 0.7329 (t80) REVERT: B 773 MET cc_start: 0.9341 (mmm) cc_final: 0.8659 (mmt) outliers start: 39 outliers final: 28 residues processed: 149 average time/residue: 0.2412 time to fit residues: 53.0941 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 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 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 142 optimal weight: 0.0170 chunk 146 optimal weight: 0.0070 chunk 65 optimal weight: 4.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 674 GLN A 695 ASN A 720 GLN B 205 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.111518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084062 restraints weight = 22213.783| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.74 r_work: 0.2988 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 12654 Z= 0.109 Angle : 0.505 8.782 17134 Z= 0.269 Chirality : 0.039 0.137 1854 Planarity : 0.004 0.039 2118 Dihedral : 9.116 167.453 1718 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.55 % Allowed : 10.34 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.22), residues: 1442 helix: 2.33 (0.16), residues: 920 sheet: 1.38 (0.79), residues: 42 loop : -1.33 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 397 HIS 0.002 0.000 HIS A 768 PHE 0.014 0.001 PHE A 461 TYR 0.016 0.001 TYR B 528 ARG 0.005 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 763) hydrogen bonds : angle 4.19462 ( 2229) SS BOND : bond 0.00165 ( 8) SS BOND : angle 0.75683 ( 16) covalent geometry : bond 0.00233 (12646) covalent geometry : angle 0.50469 (17118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: A 191 ARG cc_start: 0.6781 (ptt90) cc_final: 0.6442 (ptm-80) REVERT: A 196 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4846 (m-80) REVERT: A 298 ILE cc_start: 0.8852 (tp) cc_final: 0.8596 (tt) REVERT: A 334 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8089 (p) REVERT: A 374 PHE cc_start: 0.8535 (m-80) cc_final: 0.8295 (m-80) REVERT: A 403 GLU cc_start: 0.8051 (tt0) cc_final: 0.7605 (tm-30) REVERT: A 418 GLN cc_start: 0.8204 (tt0) cc_final: 0.7907 (tt0) REVERT: A 481 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 546 ASP cc_start: 0.8237 (m-30) cc_final: 0.7914 (m-30) REVERT: A 661 LYS cc_start: 0.9192 (mmtp) cc_final: 0.8850 (mppt) REVERT: A 695 ASN cc_start: 0.8726 (t0) cc_final: 0.8297 (t0) REVERT: A 770 TYR cc_start: 0.7943 (p90) cc_final: 0.7325 (t80) REVERT: A 773 MET cc_start: 0.9322 (mmm) cc_final: 0.8650 (mmt) REVERT: B 73 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: B 196 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5324 (m-80) REVERT: B 298 ILE cc_start: 0.8857 (tp) cc_final: 0.8588 (tt) REVERT: B 334 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 374 PHE cc_start: 0.8557 (m-80) cc_final: 0.8314 (m-80) REVERT: B 403 GLU cc_start: 0.8051 (tt0) cc_final: 0.7589 (tm-30) REVERT: B 481 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8691 (p) REVERT: B 546 ASP cc_start: 0.8237 (m-30) cc_final: 0.7893 (m-30) REVERT: B 631 MET cc_start: 0.8326 (mmm) cc_final: 0.8106 (mmm) REVERT: B 661 LYS cc_start: 0.9191 (mmtp) cc_final: 0.8867 (mppt) REVERT: B 695 ASN cc_start: 0.8745 (t0) cc_final: 0.8317 (t0) REVERT: B 770 TYR cc_start: 0.7989 (p90) cc_final: 0.7329 (t80) REVERT: B 773 MET cc_start: 0.9324 (mmm) cc_final: 0.8633 (mmt) outliers start: 34 outliers final: 21 residues processed: 157 average time/residue: 0.2382 time to fit residues: 54.8070 Evaluate side-chains 149 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 42 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 720 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080734 restraints weight = 22618.753| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.62 r_work: 0.2929 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12654 Z= 0.185 Angle : 0.564 10.417 17134 Z= 0.299 Chirality : 0.041 0.157 1854 Planarity : 0.004 0.039 2118 Dihedral : 9.179 166.339 1718 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.85 % Allowed : 10.12 % 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: 1.57 (0.22), residues: 1442 helix: 2.18 (0.16), residues: 922 sheet: 0.32 (0.65), 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 0.002 0.001 HIS A 830 PHE 0.012 0.002 PHE A 560 TYR 0.021 0.001 TYR B 138 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04428 ( 763) hydrogen bonds : angle 4.32625 ( 2229) SS BOND : bond 0.00115 ( 8) SS BOND : angle 1.46692 ( 16) covalent geometry : bond 0.00433 (12646) covalent geometry : angle 0.56218 (17118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5837.14 seconds wall clock time: 101 minutes 5.79 seconds (6065.79 seconds total)