Starting phenix.real_space_refine on Sat Sep 12 21:22:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oeg_20020/09_2026/6oeg_20020_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oeg_20020/09_2026/6oeg_20020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oeg_20020/09_2026/6oeg_20020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oeg_20020/09_2026/6oeg_20020.map" model { file = "/net/cci-nas-00/data/ceres_data/6oeg_20020/09_2026/6oeg_20020_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oeg_20020/09_2026/6oeg_20020_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 11872 2.51 5 N 3206 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18564 Number of models: 1 Model: "" Number of chains: 1 Chain: "N" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Restraints were copied for chains: O, P, Q, R, S, T, U, V, W, X, Y, Z, a Time building chain proxies: 2.10, per 1000 atoms: 0.11 Number of scatterers: 18564 At special positions: 0 Unit cell: (188.6, 188.6, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 3416 8.00 N 3206 7.00 C 11872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 720.0 milliseconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4340 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 28 sheets defined 27.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'N' and resid 351 through 356 Processing helix chain 'N' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE N 363 " --> pdb=" O ASN N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 464 removed outlier: 3.504A pdb=" N GLY N 463 " --> pdb=" O THR N 460 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 356 Processing helix chain 'O' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE O 363 " --> pdb=" O ASN O 359 " (cutoff:3.500A) Processing helix chain 'O' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY O 463 " --> pdb=" O THR O 460 " (cutoff:3.500A) Processing helix chain 'P' and resid 351 through 356 Processing helix chain 'P' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE P 363 " --> pdb=" O ASN P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY P 463 " --> pdb=" O THR P 460 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 356 Processing helix chain 'Q' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE Q 363 " --> pdb=" O ASN Q 359 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY Q 463 " --> pdb=" O THR Q 460 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 356 Processing helix chain 'R' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE R 363 " --> pdb=" O ASN R 359 " (cutoff:3.500A) Processing helix chain 'R' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY R 463 " --> pdb=" O THR R 460 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 356 Processing helix chain 'S' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE S 363 " --> pdb=" O ASN S 359 " (cutoff:3.500A) Processing helix chain 'S' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY S 463 " --> pdb=" O THR S 460 " (cutoff:3.500A) Processing helix chain 'T' and resid 351 through 356 Processing helix chain 'T' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE T 363 " --> pdb=" O ASN T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY T 463 " --> pdb=" O THR T 460 " (cutoff:3.500A) Processing helix chain 'U' and resid 351 through 356 Processing helix chain 'U' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE U 363 " --> pdb=" O ASN U 359 " (cutoff:3.500A) Processing helix chain 'U' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY U 463 " --> pdb=" O THR U 460 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 356 Processing helix chain 'V' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE V 363 " --> pdb=" O ASN V 359 " (cutoff:3.500A) Processing helix chain 'V' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY V 463 " --> pdb=" O THR V 460 " (cutoff:3.500A) Processing helix chain 'W' and resid 351 through 356 Processing helix chain 'W' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE W 363 " --> pdb=" O ASN W 359 " (cutoff:3.500A) Processing helix chain 'W' and resid 460 through 464 removed outlier: 3.504A pdb=" N GLY W 463 " --> pdb=" O THR W 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 351 through 356 Processing helix chain 'X' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE X 363 " --> pdb=" O ASN X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY X 463 " --> pdb=" O THR X 460 " (cutoff:3.500A) Processing helix chain 'Y' and resid 351 through 356 Processing helix chain 'Y' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE Y 363 " --> pdb=" O ASN Y 359 " (cutoff:3.500A) Processing helix chain 'Y' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY Y 463 " --> pdb=" O THR Y 460 " (cutoff:3.500A) Processing helix chain 'Z' and resid 351 through 356 Processing helix chain 'Z' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE Z 363 " --> pdb=" O ASN Z 359 " (cutoff:3.500A) Processing helix chain 'Z' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY Z 463 " --> pdb=" O THR Z 460 " (cutoff:3.500A) Processing helix chain 'a' and resid 351 through 356 Processing helix chain 'a' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE a 363 " --> pdb=" O ASN a 359 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 464 removed outlier: 3.504A pdb=" N GLY a 463 " --> pdb=" O THR a 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS N 475 " --> pdb=" O VAL N 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 420 through 421 Processing sheet with id=AA3, first strand: chain 'O' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS O 475 " --> pdb=" O VAL O 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 420 through 421 Processing sheet with id=AA5, first strand: chain 'P' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS P 475 " --> pdb=" O VAL P 442 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 420 through 421 Processing sheet with id=AA7, first strand: chain 'Q' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS Q 475 " --> pdb=" O VAL Q 442 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 420 through 421 Processing sheet with id=AA9, first strand: chain 'R' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS R 475 " --> pdb=" O VAL R 442 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 420 through 421 Processing sheet with id=AB2, first strand: chain 'S' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS S 475 " --> pdb=" O VAL S 442 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 420 through 421 Processing sheet with id=AB4, first strand: chain 'T' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS T 475 " --> pdb=" O VAL T 442 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 420 through 421 Processing sheet with id=AB6, first strand: chain 'U' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS U 475 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 420 through 421 Processing sheet with id=AB8, first strand: chain 'V' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS V 475 " --> pdb=" O VAL V 442 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'V' and resid 420 through 421 Processing sheet with id=AC1, first strand: chain 'W' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS W 475 " --> pdb=" O VAL W 442 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 420 through 421 Processing sheet with id=AC3, first strand: chain 'X' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS X 475 " --> pdb=" O VAL X 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 420 through 421 Processing sheet with id=AC5, first strand: chain 'Y' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS Y 475 " --> pdb=" O VAL Y 442 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 420 through 421 Processing sheet with id=AC7, first strand: chain 'Z' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS Z 475 " --> pdb=" O VAL Z 442 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 420 through 421 Processing sheet with id=AC9, first strand: chain 'a' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS a 475 " --> pdb=" O VAL a 442 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 420 through 421 784 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5739 1.34 - 1.45: 3274 1.45 - 1.57: 9775 1.57 - 1.69: 14 1.69 - 1.81: 140 Bond restraints: 18942 Sorted by residual: bond pdb=" CB GLU X 418 " pdb=" CG GLU X 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.30e+00 bond pdb=" CB GLU W 418 " pdb=" CG GLU W 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.25e+00 bond pdb=" CB GLU Y 418 " pdb=" CG GLU Y 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.23e+00 bond pdb=" CB GLU R 418 " pdb=" CG GLU R 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.21e+00 bond pdb=" CB GLU a 418 " pdb=" CG GLU a 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.18e+00 ... (remaining 18937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 24528 2.42 - 4.84: 835 4.84 - 7.26: 131 7.26 - 9.68: 14 9.68 - 12.10: 28 Bond angle restraints: 25536 Sorted by residual: angle pdb=" CB GLU P 418 " pdb=" CG GLU P 418 " pdb=" CD GLU P 418 " ideal model delta sigma weight residual 112.60 123.51 -10.91 1.70e+00 3.46e-01 4.12e+01 angle pdb=" CB GLU Q 418 " pdb=" CG GLU Q 418 " pdb=" CD GLU Q 418 " ideal model delta sigma weight residual 112.60 123.51 -10.91 1.70e+00 3.46e-01 4.12e+01 angle pdb=" CB GLU a 418 " pdb=" CG GLU a 418 " pdb=" CD GLU a 418 " ideal model delta sigma weight residual 112.60 123.50 -10.90 1.70e+00 3.46e-01 4.11e+01 angle pdb=" CB GLU S 418 " pdb=" CG GLU S 418 " pdb=" CD GLU S 418 " ideal model delta sigma weight residual 112.60 123.49 -10.89 1.70e+00 3.46e-01 4.11e+01 angle pdb=" CB GLU T 418 " pdb=" CG GLU T 418 " pdb=" CD GLU T 418 " ideal model delta sigma weight residual 112.60 123.49 -10.89 1.70e+00 3.46e-01 4.10e+01 ... (remaining 25531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 10766 17.54 - 35.07: 672 35.07 - 52.61: 224 52.61 - 70.15: 28 70.15 - 87.68: 14 Dihedral angle restraints: 11704 sinusoidal: 4970 harmonic: 6734 Sorted by residual: dihedral pdb=" CA ILE V 479 " pdb=" C ILE V 479 " pdb=" N LYS V 480 " pdb=" CA LYS V 480 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE T 479 " pdb=" C ILE T 479 " pdb=" N LYS T 480 " pdb=" CA LYS T 480 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE R 479 " pdb=" C ILE R 479 " pdb=" N LYS R 480 " pdb=" CA LYS R 480 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 11701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1640 0.050 - 0.100: 827 0.100 - 0.150: 249 0.150 - 0.200: 14 0.200 - 0.250: 14 Chirality restraints: 2744 Sorted by residual: chirality pdb=" CB ILE Q 503 " pdb=" CA ILE Q 503 " pdb=" CG1 ILE Q 503 " pdb=" CG2 ILE Q 503 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE W 503 " pdb=" CA ILE W 503 " pdb=" CG1 ILE W 503 " pdb=" CG2 ILE W 503 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE T 503 " pdb=" CA ILE T 503 " pdb=" CG1 ILE T 503 " pdb=" CG2 ILE T 503 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2741 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 376 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C ILE P 376 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE P 376 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU P 377 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE V 376 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ILE V 376 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE V 376 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU V 377 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Y 376 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C ILE Y 376 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE Y 376 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU Y 377 " 0.012 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 6587 2.88 - 3.38: 17093 3.38 - 3.89: 29490 3.89 - 4.39: 31340 4.39 - 4.90: 53217 Nonbonded interactions: 137727 Sorted by model distance: nonbonded pdb=" O MET T 355 " pdb=" OG SER T 358 " model vdw 2.370 3.040 nonbonded pdb=" O MET Y 355 " pdb=" OG SER Y 358 " model vdw 2.370 3.040 nonbonded pdb=" O MET S 355 " pdb=" OG SER S 358 " model vdw 2.370 3.040 nonbonded pdb=" O MET U 355 " pdb=" OG SER U 358 " model vdw 2.370 3.040 nonbonded pdb=" O MET a 355 " pdb=" OG SER a 358 " model vdw 2.370 3.040 ... (remaining 137722 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: 0.07 Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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 group one per residue 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: 9.290 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.100 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.008 0.075 18942 Z= 0.354 Angle : 1.117 12.097 25536 Z= 0.623 Chirality : 0.061 0.250 2744 Planarity : 0.008 0.052 3304 Dihedral : 13.456 87.684 7364 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.56 % Allowed : 4.17 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.92 (0.12), residues: 2240 helix: -2.82 (0.17), residues: 560 sheet: -2.75 (0.17), residues: 434 loop : -3.81 (0.12), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 399 TYR 0.018 0.003 TYR R 467 PHE 0.022 0.004 PHE X 420 TRP 0.015 0.004 TRP U 466 HIS 0.002 0.001 HIS P 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.35 (18942) covalent geometry : angle 1.11676 / 0.62 (25536) hydrogen bonds : bond 0.11041 / 7.19 ( 784) hydrogen bonds : angle 6.73162 / 4.48 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 841 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 373 GLN cc_start: 0.8632 (tp40) cc_final: 0.8379 (tp40) REVERT: N 379 GLN cc_start: 0.8787 (tt0) cc_final: 0.8450 (tm-30) REVERT: N 384 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: N 404 TYR cc_start: 0.8339 (m-10) cc_final: 0.4589 (t80) REVERT: N 405 GLN cc_start: 0.8704 (pt0) cc_final: 0.8190 (pt0) REVERT: N 415 MET cc_start: 0.8081 (ttm) cc_final: 0.7830 (ttm) REVERT: N 449 SER cc_start: 0.8969 (t) cc_final: 0.8694 (p) REVERT: N 450 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6226 (ptp) REVERT: O 379 GLN cc_start: 0.8903 (tt0) cc_final: 0.8442 (tm-30) REVERT: O 404 TYR cc_start: 0.8148 (m-10) cc_final: 0.5684 (t80) REVERT: O 405 GLN cc_start: 0.8791 (pt0) cc_final: 0.8442 (pt0) REVERT: O 415 MET cc_start: 0.7742 (ttm) cc_final: 0.7415 (ttm) REVERT: O 450 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.6721 (ptp) REVERT: P 364 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8477 (t0) REVERT: P 367 LYS cc_start: 0.8501 (ptmt) cc_final: 0.8267 (pttm) REVERT: P 379 GLN cc_start: 0.8753 (tt0) cc_final: 0.7994 (tm-30) REVERT: P 387 TYR cc_start: 0.8924 (t80) cc_final: 0.8713 (t80) REVERT: P 404 TYR cc_start: 0.8104 (m-10) cc_final: 0.5385 (t80) REVERT: P 415 MET cc_start: 0.7759 (ttm) cc_final: 0.7540 (ttm) REVERT: P 450 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6715 (ttt) REVERT: P 456 ASP cc_start: 0.8783 (t0) cc_final: 0.8512 (t0) REVERT: P 464 LEU cc_start: 0.9307 (mp) cc_final: 0.9013 (mm) REVERT: Q 383 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7566 (mt) REVERT: Q 404 TYR cc_start: 0.8737 (m-10) cc_final: 0.5699 (t80) REVERT: Q 421 ASP cc_start: 0.8568 (p0) cc_final: 0.8155 (p0) REVERT: Q 427 TYR cc_start: 0.8761 (m-80) cc_final: 0.8455 (m-80) REVERT: Q 452 ASP cc_start: 0.7911 (p0) cc_final: 0.7663 (p0) REVERT: R 481 ASP cc_start: 0.7718 (p0) cc_final: 0.7492 (p0) REVERT: S 383 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7176 (mt) REVERT: S 384 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: S 404 TYR cc_start: 0.8072 (m-10) cc_final: 0.5835 (t80) REVERT: S 422 ASP cc_start: 0.8663 (p0) cc_final: 0.8398 (p0) REVERT: S 450 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7053 (ptp) REVERT: S 452 ASP cc_start: 0.8033 (p0) cc_final: 0.7795 (p0) REVERT: S 478 LEU cc_start: 0.9318 (mp) cc_final: 0.9082 (mp) REVERT: T 364 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7924 (t0) REVERT: T 379 GLN cc_start: 0.8477 (tt0) cc_final: 0.7663 (tm-30) REVERT: T 404 TYR cc_start: 0.7904 (m-10) cc_final: 0.5477 (t80) REVERT: T 405 GLN cc_start: 0.8588 (pt0) cc_final: 0.8064 (pt0) REVERT: T 456 ASP cc_start: 0.8828 (t0) cc_final: 0.8407 (t0) REVERT: U 367 LYS cc_start: 0.8713 (ptmt) cc_final: 0.8473 (pttm) REVERT: U 379 GLN cc_start: 0.9016 (tt0) cc_final: 0.8175 (tm-30) REVERT: U 404 TYR cc_start: 0.8317 (m-10) cc_final: 0.4863 (t80) REVERT: U 414 ILE cc_start: 0.9539 (tp) cc_final: 0.9337 (tt) REVERT: U 415 MET cc_start: 0.8070 (ttm) cc_final: 0.7854 (ttm) REVERT: U 434 THR cc_start: 0.8577 (t) cc_final: 0.8370 (t) REVERT: U 449 SER cc_start: 0.9326 (t) cc_final: 0.9046 (m) REVERT: U 450 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.6712 (ptp) REVERT: V 366 GLU cc_start: 0.8517 (pp20) cc_final: 0.8298 (tm-30) REVERT: V 408 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5901 (mm-30) REVERT: V 411 SER cc_start: 0.9173 (m) cc_final: 0.8943 (m) REVERT: V 450 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.6105 (ptp) REVERT: W 379 GLN cc_start: 0.8973 (tt0) cc_final: 0.8207 (tm-30) REVERT: W 417 SER cc_start: 0.9016 (t) cc_final: 0.8815 (t) REVERT: W 450 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6810 (ptp) REVERT: X 384 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: X 404 TYR cc_start: 0.8106 (m-10) cc_final: 0.5678 (t80) REVERT: X 414 ILE cc_start: 0.9140 (tp) cc_final: 0.8921 (tp) REVERT: X 421 ASP cc_start: 0.8751 (p0) cc_final: 0.8300 (p0) REVERT: X 427 TYR cc_start: 0.8788 (m-80) cc_final: 0.8500 (m-80) REVERT: X 450 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.5807 (ptp) REVERT: X 501 TYR cc_start: 0.7631 (t80) cc_final: 0.7379 (t80) REVERT: Y 364 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8192 (t0) REVERT: Y 372 LYS cc_start: 0.9185 (pptt) cc_final: 0.8913 (mmmt) REVERT: Y 377 LEU cc_start: 0.8759 (tp) cc_final: 0.8549 (tp) REVERT: Y 379 GLN cc_start: 0.8839 (tt0) cc_final: 0.8475 (tm-30) REVERT: Y 384 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: Y 387 TYR cc_start: 0.8999 (t80) cc_final: 0.8746 (t80) REVERT: Y 404 TYR cc_start: 0.8002 (m-10) cc_final: 0.5194 (t80) REVERT: Y 415 MET cc_start: 0.7784 (ttm) cc_final: 0.7512 (ttm) REVERT: Y 421 ASP cc_start: 0.8712 (p0) cc_final: 0.8351 (p0) REVERT: Y 456 ASP cc_start: 0.8886 (t0) cc_final: 0.8683 (t0) REVERT: Z 367 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8203 (pttm) REVERT: Z 372 LYS cc_start: 0.8987 (pptt) cc_final: 0.8621 (mtpt) REVERT: Z 379 GLN cc_start: 0.8790 (tt0) cc_final: 0.8401 (tm-30) REVERT: Z 404 TYR cc_start: 0.8258 (m-10) cc_final: 0.5767 (t80) REVERT: Z 405 GLN cc_start: 0.8755 (pt0) cc_final: 0.8456 (pt0) REVERT: Z 415 MET cc_start: 0.7918 (ttm) cc_final: 0.7684 (ttm) REVERT: Z 432 ASN cc_start: 0.9259 (p0) cc_final: 0.9020 (p0) REVERT: Z 450 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.6712 (ptp) REVERT: Z 456 ASP cc_start: 0.8909 (t0) cc_final: 0.8624 (t0) REVERT: a 371 GLU cc_start: 0.8587 (tp30) cc_final: 0.8357 (tp30) REVERT: a 381 LYS cc_start: 0.8701 (tppt) cc_final: 0.8438 (ttmm) REVERT: a 421 ASP cc_start: 0.8677 (p0) cc_final: 0.8359 (p0) REVERT: a 432 ASN cc_start: 0.9075 (p0) cc_final: 0.8872 (p0) REVERT: a 449 SER cc_start: 0.9223 (t) cc_final: 0.8662 (m) REVERT: a 450 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6481 (ptp) outliers start: 112 outliers final: 30 residues processed: 856 average time/residue: 0.1460 time to fit residues: 185.4498 Evaluate side-chains 684 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 635 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain N residue 384 GLU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 509 LEU Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain O residue 384 GLU Chi-restraints excluded: chain O residue 450 MET Chi-restraints excluded: chain O residue 509 LEU Chi-restraints excluded: chain P residue 364 ASN Chi-restraints excluded: chain P residue 384 GLU Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain P residue 450 MET Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain Q residue 383 LEU Chi-restraints excluded: chain Q residue 384 GLU Chi-restraints excluded: chain Q residue 509 LEU Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain S residue 383 LEU Chi-restraints excluded: chain S residue 384 GLU Chi-restraints excluded: chain S residue 450 MET Chi-restraints excluded: chain S residue 509 LEU Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 383 LEU Chi-restraints excluded: chain T residue 384 GLU Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 450 MET Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 418 GLU Chi-restraints excluded: chain V residue 450 MET Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain W residue 383 LEU Chi-restraints excluded: chain W residue 418 GLU Chi-restraints excluded: chain W residue 450 MET Chi-restraints excluded: chain W residue 509 LEU Chi-restraints excluded: chain X residue 384 GLU Chi-restraints excluded: chain X residue 418 GLU Chi-restraints excluded: chain X residue 450 MET Chi-restraints excluded: chain X residue 509 LEU Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 384 GLU Chi-restraints excluded: chain Y residue 418 GLU Chi-restraints excluded: chain Y residue 509 LEU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 450 MET Chi-restraints excluded: chain Z residue 509 LEU Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 450 MET Chi-restraints excluded: chain a residue 509 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.789 > 50:) chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.3980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 505 ASN O 505 ASN P 373 GLN P 505 ASN Q 500 ASN Q 505 ASN R 364 ASN R 432 ASN R 500 ASN S 505 ASN T 373 GLN T 461 ASN T 505 ASN U 505 ASN V 505 ASN W 505 ASN X 505 ASN Y 373 GLN Y 505 ASN Z 505 ASN a 373 GLN a 505 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097585 restraints weight = 44395.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.099235 restraints weight = 20398.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100200 restraints weight = 12053.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100790 restraints weight = 8680.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101094 restraints weight = 7100.274| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18942 Z= 0.144 Angle : 0.660 8.245 25536 Z= 0.353 Chirality : 0.047 0.149 2744 Planarity : 0.006 0.044 3304 Dihedral : 7.851 50.528 2614 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.97 % Allowed : 13.19 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.14), residues: 2240 helix: -1.46 (0.18), residues: 574 sheet: -2.58 (0.18), residues: 462 loop : -3.34 (0.14), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 369 TYR 0.013 0.001 TYR T 467 PHE 0.025 0.002 PHE R 420 TRP 0.015 0.003 TRP W 466 HIS 0.003 0.001 HIS R 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (18942) covalent geometry : angle 0.66044 / 0.35 (25536) hydrogen bonds : bond 0.03193 / 2.09 ( 784) hydrogen bonds : angle 5.36998 / 3.57 ( 2142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 714 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 373 GLN cc_start: 0.8676 (tp40) cc_final: 0.8426 (tp40) REVERT: N 379 GLN cc_start: 0.8846 (tt0) cc_final: 0.8387 (tm-30) REVERT: N 404 TYR cc_start: 0.8168 (m-10) cc_final: 0.5383 (t80) REVERT: N 405 GLN cc_start: 0.8676 (pt0) cc_final: 0.8148 (pt0) REVERT: N 415 MET cc_start: 0.8031 (ttm) cc_final: 0.7597 (ttm) REVERT: N 449 SER cc_start: 0.9132 (t) cc_final: 0.8515 (p) REVERT: N 450 MET cc_start: 0.7410 (ttp) cc_final: 0.6084 (ptp) REVERT: O 379 GLN cc_start: 0.8843 (tt0) cc_final: 0.8472 (tm-30) REVERT: O 386 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8546 (tm-30) REVERT: O 404 TYR cc_start: 0.8015 (m-10) cc_final: 0.5809 (t80) REVERT: O 405 GLN cc_start: 0.8572 (pt0) cc_final: 0.8317 (pt0) REVERT: O 415 MET cc_start: 0.7626 (ttm) cc_final: 0.7246 (ttm) REVERT: O 418 GLU cc_start: 0.6163 (mp0) cc_final: 0.5817 (mp0) REVERT: O 450 MET cc_start: 0.7558 (ttp) cc_final: 0.6748 (ptp) REVERT: O 461 ASN cc_start: 0.8525 (t0) cc_final: 0.8318 (t0) REVERT: P 367 LYS cc_start: 0.8140 (ptmt) cc_final: 0.7737 (pttm) REVERT: P 372 LYS cc_start: 0.8845 (pptt) cc_final: 0.8392 (mtpt) REVERT: P 379 GLN cc_start: 0.8725 (tt0) cc_final: 0.7912 (tm-30) REVERT: P 384 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7937 (pp20) REVERT: P 386 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: P 387 TYR cc_start: 0.9012 (t80) cc_final: 0.8805 (t80) REVERT: P 404 TYR cc_start: 0.8012 (m-10) cc_final: 0.5532 (t80) REVERT: P 415 MET cc_start: 0.7506 (ttm) cc_final: 0.7162 (ttm) REVERT: P 422 ASP cc_start: 0.8999 (p0) cc_final: 0.8571 (p0) REVERT: P 464 LEU cc_start: 0.9324 (mp) cc_final: 0.9047 (mm) REVERT: Q 404 TYR cc_start: 0.8674 (m-10) cc_final: 0.5758 (t80) REVERT: Q 405 GLN cc_start: 0.8184 (pt0) cc_final: 0.7934 (pt0) REVERT: Q 415 MET cc_start: 0.7483 (ttm) cc_final: 0.7215 (ttm) REVERT: Q 421 ASP cc_start: 0.8410 (p0) cc_final: 0.8073 (p0) REVERT: Q 422 ASP cc_start: 0.8876 (p0) cc_final: 0.8624 (p0) REVERT: Q 427 TYR cc_start: 0.8801 (m-80) cc_final: 0.8470 (m-80) REVERT: Q 448 LEU cc_start: 0.8728 (mt) cc_final: 0.8457 (mt) REVERT: Q 450 MET cc_start: 0.8608 (ppp) cc_final: 0.7503 (ttt) REVERT: Q 459 MET cc_start: 0.7561 (mtp) cc_final: 0.7208 (mtp) REVERT: R 386 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7620 (pp30) REVERT: R 389 HIS cc_start: 0.6962 (t-90) cc_final: 0.6681 (t70) REVERT: R 415 MET cc_start: 0.7769 (ttm) cc_final: 0.7468 (ttm) REVERT: R 421 ASP cc_start: 0.7956 (p0) cc_final: 0.7746 (p0) REVERT: S 364 ASN cc_start: 0.8059 (t0) cc_final: 0.7611 (t0) REVERT: S 383 LEU cc_start: 0.7524 (tm) cc_final: 0.7252 (mt) REVERT: S 404 TYR cc_start: 0.7880 (m-10) cc_final: 0.6007 (t80) REVERT: S 422 ASP cc_start: 0.8831 (p0) cc_final: 0.8262 (p0) REVERT: S 452 ASP cc_start: 0.7816 (p0) cc_final: 0.7587 (p0) REVERT: T 364 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8180 (t0) REVERT: T 379 GLN cc_start: 0.8336 (tt0) cc_final: 0.7485 (tm-30) REVERT: T 404 TYR cc_start: 0.7741 (m-10) cc_final: 0.5552 (t80) REVERT: T 405 GLN cc_start: 0.8516 (pt0) cc_final: 0.8079 (pt0) REVERT: T 456 ASP cc_start: 0.8627 (t0) cc_final: 0.8421 (t0) REVERT: U 379 GLN cc_start: 0.8979 (tt0) cc_final: 0.8339 (tm-30) REVERT: U 404 TYR cc_start: 0.8138 (m-10) cc_final: 0.5615 (t80) REVERT: U 415 MET cc_start: 0.8078 (ttm) cc_final: 0.7805 (ttm) REVERT: U 427 TYR cc_start: 0.8961 (m-80) cc_final: 0.8633 (m-80) REVERT: U 449 SER cc_start: 0.9407 (t) cc_final: 0.9197 (t) REVERT: U 450 MET cc_start: 0.7078 (ttp) cc_final: 0.6484 (ptp) REVERT: U 456 ASP cc_start: 0.8843 (t0) cc_final: 0.8565 (t0) REVERT: V 384 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7114 (tm-30) REVERT: V 418 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6888 (mp0) REVERT: V 450 MET cc_start: 0.6812 (ttp) cc_final: 0.5598 (ptp) REVERT: V 452 ASP cc_start: 0.7981 (p0) cc_final: 0.7521 (m-30) REVERT: W 379 GLN cc_start: 0.8997 (tt0) cc_final: 0.8361 (tm-30) REVERT: W 386 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8648 (tm-30) REVERT: W 402 ASN cc_start: 0.8467 (t0) cc_final: 0.8168 (t0) REVERT: W 450 MET cc_start: 0.7165 (ttp) cc_final: 0.6870 (ptp) REVERT: X 355 MET cc_start: 0.8218 (mmp) cc_final: 0.7131 (tpt) REVERT: X 384 GLU cc_start: 0.7821 (tm-30) cc_final: 0.6894 (tm-30) REVERT: X 386 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8928 (tm-30) REVERT: X 404 TYR cc_start: 0.8052 (m-10) cc_final: 0.6286 (t80) REVERT: X 418 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6684 (mp0) REVERT: X 421 ASP cc_start: 0.8381 (p0) cc_final: 0.8030 (p0) REVERT: X 427 TYR cc_start: 0.8665 (m-80) cc_final: 0.8426 (m-80) REVERT: X 450 MET cc_start: 0.7559 (ttp) cc_final: 0.5875 (ptp) REVERT: X 459 MET cc_start: 0.8308 (mtp) cc_final: 0.8101 (ttm) REVERT: Y 379 GLN cc_start: 0.8858 (tt0) cc_final: 0.8552 (tm-30) REVERT: Y 384 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7485 (tm-30) REVERT: Y 404 TYR cc_start: 0.7900 (m-10) cc_final: 0.5458 (t80) REVERT: Y 415 MET cc_start: 0.7761 (ttm) cc_final: 0.7553 (ttm) REVERT: Y 418 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6540 (mm-30) REVERT: Y 421 ASP cc_start: 0.8510 (p0) cc_final: 0.8278 (p0) REVERT: Y 422 ASP cc_start: 0.8737 (p0) cc_final: 0.8475 (p0) REVERT: Z 367 LYS cc_start: 0.8768 (ptmt) cc_final: 0.8263 (pttm) REVERT: Z 372 LYS cc_start: 0.9021 (pptt) cc_final: 0.8756 (pttm) REVERT: Z 379 GLN cc_start: 0.8722 (tt0) cc_final: 0.8504 (tm-30) REVERT: Z 404 TYR cc_start: 0.8169 (m-10) cc_final: 0.5903 (t80) REVERT: Z 422 ASP cc_start: 0.8772 (p0) cc_final: 0.8547 (p0) REVERT: Z 450 MET cc_start: 0.7565 (ttp) cc_final: 0.6828 (ptp) REVERT: a 355 MET cc_start: 0.8255 (mmp) cc_final: 0.7876 (tpt) REVERT: a 417 SER cc_start: 0.8709 (t) cc_final: 0.8269 (t) REVERT: a 421 ASP cc_start: 0.8497 (p0) cc_final: 0.8255 (p0) REVERT: a 422 ASP cc_start: 0.8363 (p0) cc_final: 0.8151 (p0) REVERT: a 449 SER cc_start: 0.9181 (t) cc_final: 0.8670 (m) REVERT: a 450 MET cc_start: 0.6830 (ttp) cc_final: 0.6417 (ptp) outliers start: 80 outliers final: 50 residues processed: 742 average time/residue: 0.1351 time to fit residues: 153.1951 Evaluate side-chains 688 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 636 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain O residue 364 ASN Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain P residue 354 VAL Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 386 GLN Chi-restraints excluded: chain P residue 424 THR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain Q residue 464 LEU Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 509 LEU Chi-restraints excluded: chain R residue 383 LEU Chi-restraints excluded: chain R residue 417 SER Chi-restraints excluded: chain S residue 354 VAL Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 432 ASN Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 358 SER Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain W residue 358 SER Chi-restraints excluded: chain W residue 364 ASN Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain X residue 364 ASN Chi-restraints excluded: chain X residue 441 VAL Chi-restraints excluded: chain X residue 484 LEU Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Z residue 354 VAL Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 388 VAL Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain a residue 354 VAL Chi-restraints excluded: chain a residue 364 ASN Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 212 optimal weight: 0.0050 chunk 135 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 186 optimal weight: 0.0670 chunk 149 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 124 optimal weight: 0.0050 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 500 ASN O 432 ASN R 389 HIS R 432 ASN U 500 ASN V 443 GLN V 470 ASN X 373 GLN Y 461 ASN Z 413 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099315 restraints weight = 44535.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100998 restraints weight = 20271.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101985 restraints weight = 11898.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102588 restraints weight = 8494.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102886 restraints weight = 6916.065| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18942 Z= 0.117 Angle : 0.659 8.733 25536 Z= 0.336 Chirality : 0.047 0.166 2744 Planarity : 0.005 0.041 3304 Dihedral : 5.479 46.304 2496 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.42 % Allowed : 16.42 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.15), residues: 2240 helix: -0.33 (0.20), residues: 574 sheet: -1.61 (0.19), residues: 434 loop : -3.28 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 468 TYR 0.019 0.001 TYR X 506 PHE 0.029 0.001 PHE R 420 TRP 0.013 0.002 TRP a 466 HIS 0.003 0.001 HIS T 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (18942) covalent geometry : angle 0.65915 / 0.34 (25536) hydrogen bonds : bond 0.02825 / 1.88 ( 784) hydrogen bonds : angle 4.96605 / 3.30 ( 2142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 675 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 373 GLN cc_start: 0.8529 (tp40) cc_final: 0.8323 (tp-100) REVERT: N 379 GLN cc_start: 0.8922 (tt0) cc_final: 0.8463 (tm-30) REVERT: N 404 TYR cc_start: 0.8192 (m-10) cc_final: 0.5367 (t80) REVERT: N 405 GLN cc_start: 0.8497 (pt0) cc_final: 0.7913 (pt0) REVERT: N 415 MET cc_start: 0.8032 (ttm) cc_final: 0.7472 (ttm) REVERT: N 450 MET cc_start: 0.7393 (ttp) cc_final: 0.6140 (ptp) REVERT: O 379 GLN cc_start: 0.8859 (tt0) cc_final: 0.8447 (tm-30) REVERT: O 386 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8608 (tm-30) REVERT: O 404 TYR cc_start: 0.7863 (m-10) cc_final: 0.5507 (t80) REVERT: O 405 GLN cc_start: 0.8442 (pt0) cc_final: 0.8234 (pt0) REVERT: O 415 MET cc_start: 0.7809 (ttm) cc_final: 0.7478 (ttm) REVERT: O 418 GLU cc_start: 0.6304 (mp0) cc_final: 0.6080 (mp0) REVERT: O 450 MET cc_start: 0.7367 (ttp) cc_final: 0.6588 (ptp) REVERT: O 509 LEU cc_start: 0.6691 (mm) cc_final: 0.6381 (mm) REVERT: P 358 SER cc_start: 0.7824 (OUTLIER) cc_final: 0.7363 (p) REVERT: P 367 LYS cc_start: 0.8066 (ptmt) cc_final: 0.7737 (pttm) REVERT: P 379 GLN cc_start: 0.8663 (tt0) cc_final: 0.7968 (tm-30) REVERT: P 384 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7966 (pp20) REVERT: P 387 TYR cc_start: 0.9006 (t80) cc_final: 0.8702 (t80) REVERT: P 404 TYR cc_start: 0.7977 (m-10) cc_final: 0.5446 (t80) REVERT: P 415 MET cc_start: 0.7570 (ttm) cc_final: 0.7263 (ttm) REVERT: P 418 GLU cc_start: 0.5182 (mp0) cc_final: 0.4561 (mp0) REVERT: P 464 LEU cc_start: 0.9258 (mp) cc_final: 0.8871 (mm) REVERT: Q 404 TYR cc_start: 0.8745 (m-10) cc_final: 0.5842 (t80) REVERT: Q 415 MET cc_start: 0.7649 (ttm) cc_final: 0.7137 (ttm) REVERT: Q 421 ASP cc_start: 0.8469 (p0) cc_final: 0.7928 (p0) REVERT: Q 422 ASP cc_start: 0.8896 (p0) cc_final: 0.8670 (p0) REVERT: Q 427 TYR cc_start: 0.8826 (m-80) cc_final: 0.8460 (m-80) REVERT: Q 450 MET cc_start: 0.8647 (ppp) cc_final: 0.7466 (ttt) REVERT: Q 459 MET cc_start: 0.7673 (mtp) cc_final: 0.7367 (mtp) REVERT: R 386 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7711 (pp30) REVERT: R 389 HIS cc_start: 0.7311 (t70) cc_final: 0.6947 (t70) REVERT: R 415 MET cc_start: 0.7962 (ttm) cc_final: 0.7733 (ttm) REVERT: R 418 GLU cc_start: 0.5700 (mp0) cc_final: 0.5313 (mp0) REVERT: S 364 ASN cc_start: 0.7852 (t0) cc_final: 0.7475 (t0) REVERT: S 383 LEU cc_start: 0.7515 (tm) cc_final: 0.7283 (mt) REVERT: S 384 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8348 (pp20) REVERT: S 404 TYR cc_start: 0.7900 (m-10) cc_final: 0.5972 (t80) REVERT: S 422 ASP cc_start: 0.8781 (p0) cc_final: 0.8536 (p0) REVERT: S 436 GLN cc_start: 0.9229 (tp40) cc_final: 0.6402 (pm20) REVERT: T 367 LYS cc_start: 0.8428 (ptmt) cc_final: 0.8006 (pttm) REVERT: T 379 GLN cc_start: 0.8334 (tt0) cc_final: 0.7425 (pp30) REVERT: T 384 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8159 (tm-30) REVERT: T 404 TYR cc_start: 0.7844 (m-10) cc_final: 0.5885 (t80) REVERT: T 405 GLN cc_start: 0.8283 (pt0) cc_final: 0.7628 (pt0) REVERT: T 426 THR cc_start: 0.9320 (m) cc_final: 0.9059 (m) REVERT: U 379 GLN cc_start: 0.8990 (tt0) cc_final: 0.8294 (tm-30) REVERT: U 384 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8018 (pp20) REVERT: U 404 TYR cc_start: 0.8095 (m-10) cc_final: 0.5538 (t80) REVERT: U 422 ASP cc_start: 0.9058 (p0) cc_final: 0.8782 (p0) REVERT: U 450 MET cc_start: 0.7434 (ttp) cc_final: 0.6604 (ptp) REVERT: U 456 ASP cc_start: 0.8751 (t0) cc_final: 0.8535 (t0) REVERT: V 384 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6870 (tm-30) REVERT: V 386 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8898 (tm-30) REVERT: V 417 SER cc_start: 0.8933 (t) cc_final: 0.8651 (t) REVERT: V 418 GLU cc_start: 0.6278 (mm-30) cc_final: 0.6072 (mm-30) REVERT: V 450 MET cc_start: 0.6900 (ttp) cc_final: 0.5774 (ptp) REVERT: W 377 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8602 (pp) REVERT: W 379 GLN cc_start: 0.8995 (tt0) cc_final: 0.8259 (tm-30) REVERT: W 384 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7711 (tm-30) REVERT: W 386 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8500 (tm-30) REVERT: W 410 ARG cc_start: 0.8309 (ptp-110) cc_final: 0.8012 (ptp90) REVERT: X 355 MET cc_start: 0.8096 (mmp) cc_final: 0.7081 (tpt) REVERT: X 361 GLN cc_start: 0.8589 (tt0) cc_final: 0.7788 (tm-30) REVERT: X 384 GLU cc_start: 0.7651 (tm-30) cc_final: 0.6870 (tm-30) REVERT: X 386 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8888 (tm-30) REVERT: X 404 TYR cc_start: 0.6735 (m-10) cc_final: 0.5161 (t80) REVERT: X 421 ASP cc_start: 0.8361 (p0) cc_final: 0.7920 (p0) REVERT: X 427 TYR cc_start: 0.8686 (m-80) cc_final: 0.8402 (m-80) REVERT: X 450 MET cc_start: 0.7522 (ttp) cc_final: 0.5896 (ptp) REVERT: Y 371 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8143 (mm-30) REVERT: Y 379 GLN cc_start: 0.8860 (tt0) cc_final: 0.8504 (tm-30) REVERT: Y 386 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: Y 387 TYR cc_start: 0.8977 (t80) cc_final: 0.8757 (t80) REVERT: Y 404 TYR cc_start: 0.7772 (m-10) cc_final: 0.5257 (t80) REVERT: Y 418 GLU cc_start: 0.6427 (mm-30) cc_final: 0.5868 (mm-30) REVERT: Y 422 ASP cc_start: 0.8726 (p0) cc_final: 0.8400 (p0) REVERT: Z 367 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8529 (pttm) REVERT: Z 372 LYS cc_start: 0.9020 (pptt) cc_final: 0.8716 (pttm) REVERT: Z 373 GLN cc_start: 0.8409 (tp-100) cc_final: 0.8189 (tp40) REVERT: Z 379 GLN cc_start: 0.8722 (tt0) cc_final: 0.8469 (pp30) REVERT: Z 384 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8044 (tm-30) REVERT: Z 404 TYR cc_start: 0.8163 (m-10) cc_final: 0.5849 (t80) REVERT: Z 422 ASP cc_start: 0.8890 (p0) cc_final: 0.8535 (p0) REVERT: Z 450 MET cc_start: 0.7407 (ttp) cc_final: 0.6702 (ptp) REVERT: a 355 MET cc_start: 0.8128 (mmp) cc_final: 0.7819 (tpt) REVERT: a 371 GLU cc_start: 0.8446 (tp30) cc_final: 0.8221 (tp30) REVERT: a 375 ILE cc_start: 0.8787 (mm) cc_final: 0.8522 (mm) REVERT: a 383 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8698 (tt) REVERT: a 418 GLU cc_start: 0.6607 (mp0) cc_final: 0.6208 (mp0) REVERT: a 421 ASP cc_start: 0.8523 (p0) cc_final: 0.8252 (p0) REVERT: a 426 THR cc_start: 0.9327 (m) cc_final: 0.8970 (m) outliers start: 69 outliers final: 41 residues processed: 701 average time/residue: 0.1339 time to fit residues: 143.2437 Evaluate side-chains 677 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 632 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 449 SER Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 424 THR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain Q residue 424 THR Chi-restraints excluded: chain Q residue 464 LEU Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain R residue 432 ASN Chi-restraints excluded: chain R residue 441 VAL Chi-restraints excluded: chain R residue 443 GLN Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 439 ILE Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 358 SER Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 449 SER Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 484 LEU Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 386 GLN Chi-restraints excluded: chain Y residue 449 SER Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 497 LEU Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 179 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 361 GLN R 505 ASN T 461 ASN V 361 GLN V 470 ASN X 373 GLN ** X 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 373 GLN Y 413 HIS Y 461 ASN Z 461 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.096714 restraints weight = 44737.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.098343 restraints weight = 20988.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099319 restraints weight = 12536.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099905 restraints weight = 9006.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100231 restraints weight = 7385.437| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18942 Z= 0.147 Angle : 0.667 9.574 25536 Z= 0.340 Chirality : 0.047 0.167 2744 Planarity : 0.005 0.035 3304 Dihedral : 5.260 20.480 2492 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.27 % Allowed : 18.01 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.15), residues: 2240 helix: 0.35 (0.21), residues: 574 sheet: -1.50 (0.19), residues: 462 loop : -3.14 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 369 TYR 0.013 0.001 TYR a 467 PHE 0.032 0.002 PHE R 420 TRP 0.010 0.002 TRP V 466 HIS 0.002 0.001 HIS R 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (18942) covalent geometry : angle 0.66737 / 0.34 (25536) hydrogen bonds : bond 0.02820 / 1.88 ( 784) hydrogen bonds : angle 4.75718 / 3.15 ( 2142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 653 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 371 GLU cc_start: 0.8660 (tp30) cc_final: 0.8330 (tp30) REVERT: N 379 GLN cc_start: 0.8958 (tt0) cc_final: 0.8442 (tm-30) REVERT: N 404 TYR cc_start: 0.8040 (m-10) cc_final: 0.5079 (t80) REVERT: N 405 GLN cc_start: 0.8521 (pt0) cc_final: 0.7995 (pt0) REVERT: N 415 MET cc_start: 0.7976 (ttm) cc_final: 0.7398 (ttm) REVERT: N 450 MET cc_start: 0.7365 (ttp) cc_final: 0.6117 (ptp) REVERT: O 379 GLN cc_start: 0.8820 (tt0) cc_final: 0.8490 (tm-30) REVERT: O 386 GLN cc_start: 0.9260 (tm-30) cc_final: 0.8511 (tm-30) REVERT: O 404 TYR cc_start: 0.7960 (m-10) cc_final: 0.5490 (t80) REVERT: O 405 GLN cc_start: 0.8470 (pt0) cc_final: 0.8268 (pt0) REVERT: O 450 MET cc_start: 0.7550 (ttp) cc_final: 0.6579 (ptp) REVERT: O 509 LEU cc_start: 0.6980 (mm) cc_final: 0.6713 (mm) REVERT: P 358 SER cc_start: 0.8446 (m) cc_final: 0.7935 (t) REVERT: P 367 LYS cc_start: 0.8324 (ptmt) cc_final: 0.7945 (pttm) REVERT: P 370 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7800 (tm-30) REVERT: P 372 LYS cc_start: 0.8889 (pptt) cc_final: 0.8411 (mtpt) REVERT: P 379 GLN cc_start: 0.8704 (tt0) cc_final: 0.7985 (tm-30) REVERT: P 384 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7586 (tm-30) REVERT: P 387 TYR cc_start: 0.9232 (t80) cc_final: 0.8871 (t80) REVERT: P 404 TYR cc_start: 0.8052 (m-10) cc_final: 0.5415 (t80) REVERT: P 418 GLU cc_start: 0.4918 (mp0) cc_final: 0.4319 (mp0) REVERT: P 422 ASP cc_start: 0.9047 (p0) cc_final: 0.8674 (p0) REVERT: P 464 LEU cc_start: 0.9322 (mp) cc_final: 0.9010 (mt) REVERT: Q 404 TYR cc_start: 0.8821 (m-10) cc_final: 0.5511 (t80) REVERT: Q 421 ASP cc_start: 0.8461 (p0) cc_final: 0.7820 (p0) REVERT: Q 422 ASP cc_start: 0.9008 (p0) cc_final: 0.8753 (p0) REVERT: Q 427 TYR cc_start: 0.8860 (m-80) cc_final: 0.8452 (m-80) REVERT: Q 459 MET cc_start: 0.7827 (mtp) cc_final: 0.7545 (mtp) REVERT: R 386 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8407 (pp30) REVERT: R 415 MET cc_start: 0.7992 (ttm) cc_final: 0.7679 (ttm) REVERT: R 418 GLU cc_start: 0.5794 (mp0) cc_final: 0.5487 (mp0) REVERT: S 364 ASN cc_start: 0.7940 (t0) cc_final: 0.7590 (t0) REVERT: S 404 TYR cc_start: 0.8035 (m-10) cc_final: 0.5943 (t80) REVERT: S 422 ASP cc_start: 0.8792 (p0) cc_final: 0.8569 (p0) REVERT: S 436 GLN cc_start: 0.9353 (tp40) cc_final: 0.6489 (pm20) REVERT: T 379 GLN cc_start: 0.8160 (tt0) cc_final: 0.7524 (pp30) REVERT: T 404 TYR cc_start: 0.7930 (m-10) cc_final: 0.5738 (t80) REVERT: T 405 GLN cc_start: 0.8690 (pt0) cc_final: 0.8128 (pt0) REVERT: U 365 LYS cc_start: 0.8382 (ptpp) cc_final: 0.8125 (ptpt) REVERT: U 379 GLN cc_start: 0.9025 (tt0) cc_final: 0.8254 (tm-30) REVERT: U 404 TYR cc_start: 0.7963 (m-10) cc_final: 0.5169 (t80) REVERT: U 421 ASP cc_start: 0.8629 (p0) cc_final: 0.8417 (p0) REVERT: U 425 PHE cc_start: 0.7704 (m-10) cc_final: 0.7497 (m-10) REVERT: U 450 MET cc_start: 0.7087 (ttp) cc_final: 0.6581 (ptp) REVERT: V 384 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7022 (tm-30) REVERT: V 386 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8995 (tm-30) REVERT: V 417 SER cc_start: 0.8775 (t) cc_final: 0.8460 (t) REVERT: V 418 GLU cc_start: 0.6438 (mm-30) cc_final: 0.6113 (mm-30) REVERT: V 422 ASP cc_start: 0.8886 (p0) cc_final: 0.8673 (p0) REVERT: V 450 MET cc_start: 0.6971 (ttp) cc_final: 0.5801 (ptp) REVERT: V 452 ASP cc_start: 0.8065 (p0) cc_final: 0.7506 (m-30) REVERT: V 464 LEU cc_start: 0.9388 (mp) cc_final: 0.8993 (mp) REVERT: W 377 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8593 (pp) REVERT: W 379 GLN cc_start: 0.8890 (tt0) cc_final: 0.8175 (tm-30) REVERT: W 384 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7862 (tm-30) REVERT: W 386 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8708 (tm-30) REVERT: X 355 MET cc_start: 0.8291 (mmp) cc_final: 0.8066 (mmm) REVERT: X 361 GLN cc_start: 0.8754 (tt0) cc_final: 0.7896 (tm-30) REVERT: X 384 GLU cc_start: 0.7839 (tm-30) cc_final: 0.6896 (tm-30) REVERT: X 386 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8910 (tm-30) REVERT: X 404 TYR cc_start: 0.7033 (m-10) cc_final: 0.4954 (t80) REVERT: X 421 ASP cc_start: 0.8378 (p0) cc_final: 0.8042 (p0) REVERT: X 427 TYR cc_start: 0.8690 (m-80) cc_final: 0.8403 (m-80) REVERT: X 450 MET cc_start: 0.7862 (ttp) cc_final: 0.6071 (ptp) REVERT: X 503 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7336 (mp) REVERT: Y 371 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8300 (mm-30) REVERT: Y 379 GLN cc_start: 0.8792 (tt0) cc_final: 0.8452 (tm-30) REVERT: Y 384 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7898 (tm-30) REVERT: Y 386 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8596 (tt0) REVERT: Y 404 TYR cc_start: 0.7795 (m-10) cc_final: 0.5300 (t80) REVERT: Y 418 GLU cc_start: 0.6470 (mm-30) cc_final: 0.6107 (mm-30) REVERT: Y 422 ASP cc_start: 0.8744 (p0) cc_final: 0.8415 (p0) REVERT: Y 441 VAL cc_start: 0.9556 (t) cc_final: 0.9182 (p) REVERT: Y 485 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9192 (p) REVERT: Z 367 LYS cc_start: 0.8975 (ptmt) cc_final: 0.8445 (pttm) REVERT: Z 372 LYS cc_start: 0.9051 (pptt) cc_final: 0.8766 (pttm) REVERT: Z 379 GLN cc_start: 0.8826 (tt0) cc_final: 0.8502 (pp30) REVERT: Z 404 TYR cc_start: 0.8105 (m-10) cc_final: 0.5712 (t80) REVERT: Z 422 ASP cc_start: 0.9014 (p0) cc_final: 0.8703 (p0) REVERT: Z 450 MET cc_start: 0.7482 (ttp) cc_final: 0.6595 (ptp) REVERT: a 355 MET cc_start: 0.8163 (mmp) cc_final: 0.7785 (tpt) REVERT: a 383 LEU cc_start: 0.9117 (tm) cc_final: 0.8763 (tt) REVERT: a 426 THR cc_start: 0.9312 (m) cc_final: 0.9087 (m) REVERT: a 456 ASP cc_start: 0.8654 (t0) cc_final: 0.8359 (t0) REVERT: a 503 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7340 (mp) outliers start: 86 outliers final: 60 residues processed: 695 average time/residue: 0.1307 time to fit residues: 139.9238 Evaluate side-chains 694 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 629 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 383 LEU Chi-restraints excluded: chain R residue 417 SER Chi-restraints excluded: chain R residue 441 VAL Chi-restraints excluded: chain R residue 443 GLN Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain T residue 424 THR Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 364 ASN Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 383 LEU Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 364 ASN Chi-restraints excluded: chain X residue 370 GLU Chi-restraints excluded: chain X residue 424 THR Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 441 VAL Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain X residue 503 ILE Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 386 GLN Chi-restraints excluded: chain Y residue 415 MET Chi-restraints excluded: chain Y residue 448 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 497 LEU Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 449 SER Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 40 optimal weight: 1.9990 chunk 204 optimal weight: 0.1980 chunk 92 optimal weight: 0.0050 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 361 GLN R 389 HIS T 413 HIS T 461 ASN V 361 GLN W 413 HIS X 413 HIS Y 373 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098479 restraints weight = 44379.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100108 restraints weight = 20685.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101078 restraints weight = 12326.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101663 restraints weight = 8843.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101995 restraints weight = 7242.224| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18942 Z= 0.121 Angle : 0.662 8.736 25536 Z= 0.337 Chirality : 0.046 0.158 2744 Planarity : 0.004 0.033 3304 Dihedral : 4.965 21.003 2492 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.37 % Allowed : 19.25 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.16), residues: 2240 helix: 0.77 (0.21), residues: 574 sheet: -1.15 (0.19), residues: 462 loop : -3.04 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 369 TYR 0.011 0.001 TYR a 467 PHE 0.026 0.001 PHE R 420 TRP 0.010 0.002 TRP a 466 HIS 0.005 0.001 HIS T 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (18942) covalent geometry : angle 0.66219 / 0.34 (25536) hydrogen bonds : bond 0.02611 / 1.74 ( 784) hydrogen bonds : angle 4.60164 / 3.05 ( 2142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 674 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.8949 (tt0) cc_final: 0.8449 (tm-30) REVERT: N 404 TYR cc_start: 0.8019 (m-10) cc_final: 0.5057 (t80) REVERT: N 405 GLN cc_start: 0.8426 (pt0) cc_final: 0.8039 (pt0) REVERT: N 415 MET cc_start: 0.8099 (ttm) cc_final: 0.7520 (ttm) REVERT: N 418 GLU cc_start: 0.7146 (mp0) cc_final: 0.6888 (mp0) REVERT: N 450 MET cc_start: 0.7318 (ttp) cc_final: 0.6114 (ptp) REVERT: N 503 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7192 (mp) REVERT: O 379 GLN cc_start: 0.8819 (tt0) cc_final: 0.8486 (tm-30) REVERT: O 386 GLN cc_start: 0.9279 (tm-30) cc_final: 0.8571 (tm-30) REVERT: O 404 TYR cc_start: 0.7930 (m-10) cc_final: 0.5436 (t80) REVERT: O 422 ASP cc_start: 0.8585 (p0) cc_final: 0.8353 (p0) REVERT: O 450 MET cc_start: 0.7481 (ttp) cc_final: 0.6386 (ptp) REVERT: P 358 SER cc_start: 0.8460 (m) cc_final: 0.7945 (t) REVERT: P 367 LYS cc_start: 0.8331 (ptmt) cc_final: 0.7932 (pttm) REVERT: P 379 GLN cc_start: 0.8694 (tt0) cc_final: 0.7913 (tm-30) REVERT: P 384 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7944 (pp20) REVERT: P 387 TYR cc_start: 0.9164 (t80) cc_final: 0.8633 (t80) REVERT: P 404 TYR cc_start: 0.8037 (m-10) cc_final: 0.5386 (t80) REVERT: P 418 GLU cc_start: 0.4951 (mp0) cc_final: 0.4399 (mp0) REVERT: P 422 ASP cc_start: 0.8990 (p0) cc_final: 0.8588 (p0) REVERT: P 503 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7283 (mp) REVERT: Q 384 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8331 (tm-30) REVERT: Q 403 TYR cc_start: 0.9093 (m-10) cc_final: 0.8245 (m-10) REVERT: Q 404 TYR cc_start: 0.8768 (m-10) cc_final: 0.5466 (t80) REVERT: Q 421 ASP cc_start: 0.8401 (p0) cc_final: 0.7995 (p0) REVERT: Q 422 ASP cc_start: 0.8989 (p0) cc_final: 0.8699 (p0) REVERT: Q 427 TYR cc_start: 0.8846 (m-80) cc_final: 0.8423 (m-80) REVERT: Q 459 MET cc_start: 0.7818 (mtp) cc_final: 0.7504 (mtp) REVERT: R 363 ILE cc_start: 0.6359 (mm) cc_final: 0.5805 (tp) REVERT: R 386 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8409 (pp30) REVERT: R 404 TYR cc_start: 0.8403 (m-80) cc_final: 0.8183 (m-80) REVERT: R 415 MET cc_start: 0.7993 (ttm) cc_final: 0.7763 (ttm) REVERT: R 497 LEU cc_start: 0.7725 (mp) cc_final: 0.7415 (mt) REVERT: S 364 ASN cc_start: 0.8032 (t0) cc_final: 0.7733 (t0) REVERT: S 372 LYS cc_start: 0.8634 (pptt) cc_final: 0.8170 (mtpt) REVERT: S 373 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7460 (tm-30) REVERT: S 404 TYR cc_start: 0.8043 (m-10) cc_final: 0.5911 (t80) REVERT: S 422 ASP cc_start: 0.8734 (p0) cc_final: 0.8525 (p0) REVERT: S 436 GLN cc_start: 0.9338 (tp40) cc_final: 0.6465 (pm20) REVERT: T 367 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8118 (pttm) REVERT: T 379 GLN cc_start: 0.8238 (tt0) cc_final: 0.7674 (pp30) REVERT: T 404 TYR cc_start: 0.7849 (m-10) cc_final: 0.5799 (t80) REVERT: T 405 GLN cc_start: 0.8600 (pt0) cc_final: 0.8082 (pt0) REVERT: U 365 LYS cc_start: 0.8381 (ptpp) cc_final: 0.8070 (ptpt) REVERT: U 379 GLN cc_start: 0.9018 (tt0) cc_final: 0.8239 (tm-30) REVERT: U 404 TYR cc_start: 0.7935 (m-10) cc_final: 0.5147 (t80) REVERT: U 425 PHE cc_start: 0.7664 (m-10) cc_final: 0.7351 (m-10) REVERT: U 450 MET cc_start: 0.7556 (ttp) cc_final: 0.6736 (ptp) REVERT: V 377 LEU cc_start: 0.8769 (tp) cc_final: 0.8217 (pp) REVERT: V 384 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7021 (tm-30) REVERT: V 386 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8953 (tm-30) REVERT: V 417 SER cc_start: 0.8571 (t) cc_final: 0.8356 (t) REVERT: V 450 MET cc_start: 0.6944 (ttp) cc_final: 0.5726 (ptp) REVERT: W 377 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8612 (pp) REVERT: W 379 GLN cc_start: 0.8899 (tt0) cc_final: 0.8188 (tm-30) REVERT: W 384 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7880 (tm-30) REVERT: X 361 GLN cc_start: 0.8781 (tt0) cc_final: 0.7936 (tm-30) REVERT: X 386 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8905 (tm-30) REVERT: X 404 TYR cc_start: 0.7113 (m-10) cc_final: 0.5153 (t80) REVERT: X 417 SER cc_start: 0.8414 (t) cc_final: 0.8185 (t) REVERT: X 421 ASP cc_start: 0.8339 (p0) cc_final: 0.8033 (p0) REVERT: X 427 TYR cc_start: 0.8685 (m-80) cc_final: 0.8474 (m-80) REVERT: X 450 MET cc_start: 0.7818 (ttp) cc_final: 0.6071 (ptp) REVERT: Y 371 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8253 (mm-30) REVERT: Y 379 GLN cc_start: 0.8790 (tt0) cc_final: 0.8409 (tm-30) REVERT: Y 384 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7344 (tm-30) REVERT: Y 404 TYR cc_start: 0.7605 (m-10) cc_final: 0.5533 (t80) REVERT: Y 418 GLU cc_start: 0.6449 (mm-30) cc_final: 0.6045 (mm-30) REVERT: Y 441 VAL cc_start: 0.9476 (t) cc_final: 0.9094 (p) REVERT: Z 358 SER cc_start: 0.7812 (m) cc_final: 0.7289 (p) REVERT: Z 365 LYS cc_start: 0.8178 (ptpp) cc_final: 0.7899 (ptpp) REVERT: Z 372 LYS cc_start: 0.9058 (pptt) cc_final: 0.8769 (pttm) REVERT: Z 373 GLN cc_start: 0.8472 (tp-100) cc_final: 0.8258 (tp40) REVERT: Z 379 GLN cc_start: 0.8780 (tt0) cc_final: 0.8483 (pp30) REVERT: Z 404 TYR cc_start: 0.8084 (m-10) cc_final: 0.5670 (t80) REVERT: Z 422 ASP cc_start: 0.8989 (p0) cc_final: 0.8649 (p0) REVERT: Z 450 MET cc_start: 0.7531 (ttp) cc_final: 0.6538 (ptp) REVERT: a 355 MET cc_start: 0.8116 (mmp) cc_final: 0.7776 (tpt) REVERT: a 371 GLU cc_start: 0.8530 (tp30) cc_final: 0.8149 (tp30) REVERT: a 375 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8566 (mm) REVERT: a 383 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8668 (tt) REVERT: a 503 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7422 (mp) outliers start: 88 outliers final: 58 residues processed: 717 average time/residue: 0.1333 time to fit residues: 146.0834 Evaluate side-chains 701 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 637 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 415 MET Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 417 SER Chi-restraints excluded: chain R residue 441 VAL Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain S residue 370 GLU Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 439 ILE Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain V residue 361 GLN Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 370 GLU Chi-restraints excluded: chain X residue 411 SER Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain Y residue 448 LEU Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 497 LEU Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 375 ILE Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 67 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 0.0670 chunk 194 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 373 GLN O 361 GLN R 389 HIS T 461 ASN ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN Y 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.092617 restraints weight = 44728.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.094291 restraints weight = 20669.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095293 restraints weight = 12314.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.095860 restraints weight = 8895.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.096215 restraints weight = 7347.423| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18942 Z= 0.225 Angle : 0.741 10.388 25536 Z= 0.382 Chirality : 0.048 0.184 2744 Planarity : 0.005 0.053 3304 Dihedral : 5.494 22.150 2492 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 5.41 % Allowed : 19.64 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.16), residues: 2240 helix: 0.85 (0.21), residues: 574 sheet: -1.27 (0.20), residues: 490 loop : -2.95 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 410 TYR 0.024 0.002 TYR Z 403 PHE 0.024 0.002 PHE R 420 TRP 0.010 0.002 TRP R 466 HIS 0.004 0.001 HIS T 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (18942) covalent geometry : angle 0.74130 / 0.38 (25536) hydrogen bonds : bond 0.03023 / 2.02 ( 784) hydrogen bonds : angle 4.67747 / 3.08 ( 2142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 653 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9070 (tt0) cc_final: 0.8501 (tm-30) REVERT: N 405 GLN cc_start: 0.8551 (pt0) cc_final: 0.8156 (pt0) REVERT: N 415 MET cc_start: 0.8015 (ttm) cc_final: 0.7468 (ttm) REVERT: N 418 GLU cc_start: 0.5939 (mp0) cc_final: 0.5451 (mp0) REVERT: N 450 MET cc_start: 0.8015 (ttp) cc_final: 0.6563 (ptp) REVERT: O 379 GLN cc_start: 0.8987 (tt0) cc_final: 0.8650 (pp30) REVERT: O 404 TYR cc_start: 0.8119 (m-10) cc_final: 0.5333 (t80) REVERT: O 422 ASP cc_start: 0.8917 (p0) cc_final: 0.8661 (p0) REVERT: O 450 MET cc_start: 0.7693 (ttp) cc_final: 0.6447 (ptp) REVERT: P 358 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8137 (t) REVERT: P 367 LYS cc_start: 0.8714 (ptmt) cc_final: 0.8237 (pttm) REVERT: P 379 GLN cc_start: 0.8699 (tt0) cc_final: 0.7933 (tm-30) REVERT: P 384 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8001 (pp20) REVERT: P 418 GLU cc_start: 0.5405 (mp0) cc_final: 0.4728 (mp0) REVERT: P 421 ASP cc_start: 0.8624 (p0) cc_final: 0.8355 (p0) REVERT: P 422 ASP cc_start: 0.9112 (p0) cc_final: 0.8497 (p0) REVERT: P 464 LEU cc_start: 0.9333 (mt) cc_final: 0.9020 (mp) REVERT: P 503 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.7422 (mp) REVERT: Q 421 ASP cc_start: 0.8465 (p0) cc_final: 0.8109 (p0) REVERT: Q 422 ASP cc_start: 0.9077 (p0) cc_final: 0.8717 (p0) REVERT: Q 427 TYR cc_start: 0.8837 (m-80) cc_final: 0.8410 (m-80) REVERT: Q 459 MET cc_start: 0.8205 (mtp) cc_final: 0.7847 (mtp) REVERT: R 356 MET cc_start: 0.6198 (tpp) cc_final: 0.5818 (tpp) REVERT: R 363 ILE cc_start: 0.6656 (mm) cc_final: 0.6261 (mm) REVERT: R 384 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8081 (tm-30) REVERT: R 385 THR cc_start: 0.9391 (m) cc_final: 0.8968 (t) REVERT: R 386 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8606 (pp30) REVERT: R 404 TYR cc_start: 0.7945 (m-80) cc_final: 0.7720 (m-80) REVERT: R 460 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8657 (p) REVERT: R 497 LEU cc_start: 0.7913 (mp) cc_final: 0.7585 (mp) REVERT: S 364 ASN cc_start: 0.8178 (t0) cc_final: 0.7882 (t0) REVERT: S 372 LYS cc_start: 0.8559 (pptt) cc_final: 0.8028 (mtpt) REVERT: S 422 ASP cc_start: 0.8894 (p0) cc_final: 0.8667 (p0) REVERT: S 503 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8275 (tp) REVERT: T 379 GLN cc_start: 0.8518 (tt0) cc_final: 0.7806 (pp30) REVERT: T 405 GLN cc_start: 0.8773 (pt0) cc_final: 0.8567 (pt0) REVERT: U 365 LYS cc_start: 0.8480 (ptpp) cc_final: 0.8138 (ptpt) REVERT: U 379 GLN cc_start: 0.9100 (tt0) cc_final: 0.8277 (tm-30) REVERT: U 384 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8063 (pp20) REVERT: U 404 TYR cc_start: 0.8129 (m-10) cc_final: 0.5068 (t80) REVERT: U 450 MET cc_start: 0.7577 (ttp) cc_final: 0.6901 (ptp) REVERT: U 503 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7223 (mp) REVERT: V 384 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7165 (tm-30) REVERT: V 386 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8876 (tm-30) REVERT: V 450 MET cc_start: 0.7388 (ttp) cc_final: 0.6142 (ptp) REVERT: W 379 GLN cc_start: 0.9002 (tt0) cc_final: 0.8217 (tm-30) REVERT: W 384 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7987 (tm-30) REVERT: X 355 MET cc_start: 0.7983 (mmm) cc_final: 0.7604 (mmp) REVERT: X 361 GLN cc_start: 0.8996 (tt0) cc_final: 0.7996 (tm-30) REVERT: X 384 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7350 (tm-30) REVERT: X 386 GLN cc_start: 0.9328 (tm-30) cc_final: 0.8955 (tm-30) REVERT: X 404 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: X 421 ASP cc_start: 0.8443 (p0) cc_final: 0.7779 (p0) REVERT: X 427 TYR cc_start: 0.8734 (m-80) cc_final: 0.8352 (m-80) REVERT: X 450 MET cc_start: 0.8172 (ttp) cc_final: 0.6299 (ptp) REVERT: Y 379 GLN cc_start: 0.8768 (tt0) cc_final: 0.8213 (tm-30) REVERT: Y 404 TYR cc_start: 0.7804 (m-10) cc_final: 0.5900 (t80) REVERT: Y 415 MET cc_start: 0.8060 (ttp) cc_final: 0.7801 (ttm) REVERT: Y 503 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.7328 (mp) REVERT: Z 358 SER cc_start: 0.7878 (m) cc_final: 0.7382 (p) REVERT: Z 365 LYS cc_start: 0.8416 (ptpp) cc_final: 0.8140 (ptpp) REVERT: Z 372 LYS cc_start: 0.9114 (pptt) cc_final: 0.8841 (pttm) REVERT: Z 379 GLN cc_start: 0.8908 (tt0) cc_final: 0.8537 (pp30) REVERT: Z 404 TYR cc_start: 0.8176 (m-10) cc_final: 0.5332 (t80) REVERT: Z 450 MET cc_start: 0.7807 (ttp) cc_final: 0.6683 (ptp) REVERT: a 355 MET cc_start: 0.8239 (mmp) cc_final: 0.7887 (tpt) REVERT: a 371 GLU cc_start: 0.8494 (tp30) cc_final: 0.8225 (tp30) REVERT: a 383 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8723 (tt) REVERT: a 404 TYR cc_start: 0.7819 (m-80) cc_final: 0.7562 (m-80) REVERT: a 459 MET cc_start: 0.8544 (ptm) cc_final: 0.8185 (ptp) REVERT: a 503 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7347 (mp) outliers start: 109 outliers final: 82 residues processed: 705 average time/residue: 0.1291 time to fit residues: 140.6044 Evaluate side-chains 718 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 627 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 360 GLU Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 449 SER Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 383 LEU Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 439 ILE Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain S residue 503 ILE Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 388 VAL Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 364 ASN Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 449 SER Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 383 LEU Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 415 MET Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 364 ASN Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 364 ASN Chi-restraints excluded: chain X residue 370 GLU Chi-restraints excluded: chain X residue 404 TYR Chi-restraints excluded: chain X residue 411 SER Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 424 THR Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 383 LEU Chi-restraints excluded: chain Y residue 448 LEU Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 364 ASN Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 50 optimal weight: 0.9980 chunk 169 optimal weight: 0.0040 chunk 110 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 152 optimal weight: 0.2980 chunk 109 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 373 GLN O 361 GLN Q 413 HIS R 389 HIS T 461 ASN V 361 GLN V 364 ASN V 443 GLN Y 373 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096272 restraints weight = 44949.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097895 restraints weight = 21369.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098869 restraints weight = 12890.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099439 restraints weight = 9322.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099778 restraints weight = 7676.491| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18942 Z= 0.134 Angle : 0.713 10.887 25536 Z= 0.360 Chirality : 0.047 0.152 2744 Planarity : 0.005 0.054 3304 Dihedral : 5.018 20.178 2492 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 4.51 % Allowed : 21.92 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.16), residues: 2240 helix: 1.11 (0.21), residues: 574 sheet: -1.06 (0.20), residues: 490 loop : -2.88 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Y 410 TYR 0.013 0.001 TYR Y 404 PHE 0.021 0.001 PHE R 420 TRP 0.010 0.002 TRP a 466 HIS 0.005 0.001 HIS T 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (18942) covalent geometry : angle 0.71254 / 0.36 (25536) hydrogen bonds : bond 0.02626 / 1.75 ( 784) hydrogen bonds : angle 4.48389 / 2.97 ( 2142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 673 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9022 (tt0) cc_final: 0.8464 (tm-30) REVERT: N 404 TYR cc_start: 0.7452 (m-10) cc_final: 0.5391 (t80) REVERT: N 405 GLN cc_start: 0.8566 (pt0) cc_final: 0.8205 (pt0) REVERT: N 414 ILE cc_start: 0.9518 (tp) cc_final: 0.9194 (tt) REVERT: N 415 MET cc_start: 0.7999 (ttm) cc_final: 0.7627 (ttm) REVERT: N 418 GLU cc_start: 0.5900 (mp0) cc_final: 0.5304 (mp0) REVERT: N 450 MET cc_start: 0.7708 (ttp) cc_final: 0.6723 (ptp) REVERT: N 503 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.7414 (mp) REVERT: O 366 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8090 (tm-30) REVERT: O 379 GLN cc_start: 0.8953 (tt0) cc_final: 0.8649 (pp30) REVERT: O 404 TYR cc_start: 0.7948 (m-10) cc_final: 0.5826 (t80) REVERT: O 422 ASP cc_start: 0.8813 (p0) cc_final: 0.8525 (p0) REVERT: O 450 MET cc_start: 0.7600 (ttp) cc_final: 0.6135 (ptp) REVERT: O 503 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.7312 (mp) REVERT: P 358 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8206 (t) REVERT: P 367 LYS cc_start: 0.8648 (ptmt) cc_final: 0.8227 (pttm) REVERT: P 379 GLN cc_start: 0.8649 (tt0) cc_final: 0.7951 (tm-30) REVERT: P 384 GLU cc_start: 0.8234 (tm-30) cc_final: 0.8007 (pp20) REVERT: P 418 GLU cc_start: 0.5123 (mp0) cc_final: 0.4450 (mp0) REVERT: P 503 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7281 (mp) REVERT: Q 386 GLN cc_start: 0.8531 (tt0) cc_final: 0.8312 (tm-30) REVERT: Q 403 TYR cc_start: 0.9085 (m-10) cc_final: 0.8604 (m-10) REVERT: Q 422 ASP cc_start: 0.8862 (p0) cc_final: 0.8616 (p0) REVERT: Q 427 TYR cc_start: 0.8834 (m-80) cc_final: 0.8389 (m-80) REVERT: Q 459 MET cc_start: 0.7897 (mtp) cc_final: 0.7538 (mtp) REVERT: R 356 MET cc_start: 0.6921 (tpp) cc_final: 0.6635 (tpp) REVERT: R 384 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7826 (tm-30) REVERT: R 385 THR cc_start: 0.9436 (m) cc_final: 0.9158 (t) REVERT: R 386 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8565 (pp30) REVERT: R 497 LEU cc_start: 0.7889 (mp) cc_final: 0.7534 (mt) REVERT: S 364 ASN cc_start: 0.8166 (t0) cc_final: 0.7891 (t0) REVERT: S 372 LYS cc_start: 0.8715 (pptt) cc_final: 0.8152 (mtpt) REVERT: S 373 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7723 (tm-30) REVERT: S 384 GLU cc_start: 0.8536 (pp20) cc_final: 0.8283 (pp20) REVERT: S 422 ASP cc_start: 0.8650 (p0) cc_final: 0.8430 (p0) REVERT: S 436 GLN cc_start: 0.9354 (tp40) cc_final: 0.6458 (pm20) REVERT: T 379 GLN cc_start: 0.8468 (tt0) cc_final: 0.7975 (pp30) REVERT: T 384 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8045 (tm-30) REVERT: T 405 GLN cc_start: 0.8631 (pt0) cc_final: 0.8372 (pt0) REVERT: T 503 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7520 (mp) REVERT: U 365 LYS cc_start: 0.8394 (ptpp) cc_final: 0.8075 (ptpt) REVERT: U 379 GLN cc_start: 0.9053 (tt0) cc_final: 0.8273 (tm-30) REVERT: U 384 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8141 (pp20) REVERT: U 404 TYR cc_start: 0.8018 (m-10) cc_final: 0.5860 (t80) REVERT: U 414 ILE cc_start: 0.9485 (tp) cc_final: 0.9211 (tt) REVERT: U 425 PHE cc_start: 0.7751 (m-10) cc_final: 0.7439 (m-10) REVERT: U 450 MET cc_start: 0.7392 (ttp) cc_final: 0.6824 (ptp) REVERT: U 503 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7188 (mp) REVERT: V 356 MET cc_start: 0.7720 (mmp) cc_final: 0.7109 (ptt) REVERT: V 384 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7079 (tm-30) REVERT: V 386 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8906 (tm-30) REVERT: V 450 MET cc_start: 0.7192 (ttp) cc_final: 0.6096 (ptp) REVERT: W 377 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8601 (pp) REVERT: W 379 GLN cc_start: 0.8961 (tt0) cc_final: 0.8213 (tm-30) REVERT: W 384 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7866 (tm-30) REVERT: X 355 MET cc_start: 0.7973 (mmm) cc_final: 0.7562 (mmp) REVERT: X 361 GLN cc_start: 0.8950 (tt0) cc_final: 0.8006 (tm-30) REVERT: X 386 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8883 (tm-30) REVERT: X 403 TYR cc_start: 0.8971 (m-80) cc_final: 0.8601 (m-10) REVERT: X 404 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.4681 (t80) REVERT: X 427 TYR cc_start: 0.8672 (m-80) cc_final: 0.8376 (m-80) REVERT: X 450 MET cc_start: 0.8004 (ttp) cc_final: 0.6272 (ptp) REVERT: Y 379 GLN cc_start: 0.8668 (tt0) cc_final: 0.8137 (tm-30) REVERT: Y 384 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7676 (tm-30) REVERT: Y 404 TYR cc_start: 0.7616 (m-10) cc_final: 0.5868 (t80) REVERT: Y 415 MET cc_start: 0.8111 (ttp) cc_final: 0.7825 (ttm) REVERT: Y 485 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9096 (p) REVERT: Y 503 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7202 (mp) REVERT: Z 358 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7437 (p) REVERT: Z 365 LYS cc_start: 0.8322 (ptpp) cc_final: 0.8074 (ptpp) REVERT: Z 372 LYS cc_start: 0.9078 (pptt) cc_final: 0.8840 (pttm) REVERT: Z 373 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8312 (tp40) REVERT: Z 379 GLN cc_start: 0.8856 (tt0) cc_final: 0.8547 (pp30) REVERT: Z 381 LYS cc_start: 0.8836 (tptt) cc_final: 0.8626 (tppt) REVERT: Z 404 TYR cc_start: 0.8002 (m-10) cc_final: 0.5863 (t80) REVERT: Z 450 MET cc_start: 0.7639 (ttp) cc_final: 0.6386 (ptp) REVERT: a 355 MET cc_start: 0.8145 (mmp) cc_final: 0.7749 (tpt) REVERT: a 371 GLU cc_start: 0.8473 (tp30) cc_final: 0.8078 (tp30) REVERT: a 383 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8786 (tt) REVERT: a 404 TYR cc_start: 0.7650 (m-80) cc_final: 0.7368 (m-80) REVERT: a 459 MET cc_start: 0.8547 (ptm) cc_final: 0.8204 (ptp) REVERT: a 503 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7423 (mp) outliers start: 91 outliers final: 62 residues processed: 712 average time/residue: 0.1298 time to fit residues: 143.3649 Evaluate side-chains 725 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 650 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 484 LEU Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 361 GLN Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 424 THR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 417 SER Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain S residue 360 GLU Chi-restraints excluded: chain S residue 370 GLU Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 439 ILE Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 370 GLU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 364 ASN Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 449 SER Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 370 GLU Chi-restraints excluded: chain X residue 404 TYR Chi-restraints excluded: chain X residue 411 SER Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 434 THR Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 355 MET Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 448 LEU Chi-restraints excluded: chain Y residue 449 SER Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 76 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 405 GLN R 364 ASN R 389 HIS V 361 GLN V 364 ASN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 373 GLN Y 405 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.096360 restraints weight = 44864.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097994 restraints weight = 21181.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098960 restraints weight = 12731.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099533 restraints weight = 9204.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099793 restraints weight = 7565.577| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18942 Z= 0.143 Angle : 0.728 11.446 25536 Z= 0.367 Chirality : 0.048 0.165 2744 Planarity : 0.005 0.058 3304 Dihedral : 4.991 20.452 2492 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.72 % Allowed : 23.21 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2240 helix: 1.25 (0.21), residues: 574 sheet: -0.94 (0.20), residues: 490 loop : -2.85 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Y 410 TYR 0.015 0.001 TYR U 404 PHE 0.021 0.001 PHE R 420 TRP 0.009 0.002 TRP a 466 HIS 0.005 0.001 HIS T 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (18942) covalent geometry : angle 0.72804 / 0.37 (25536) hydrogen bonds : bond 0.02723 / 1.79 ( 784) hydrogen bonds : angle 4.42397 / 2.93 ( 2142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 667 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9039 (tt0) cc_final: 0.8449 (tm-30) REVERT: N 405 GLN cc_start: 0.8522 (pt0) cc_final: 0.8220 (pt0) REVERT: N 415 MET cc_start: 0.8040 (ttm) cc_final: 0.7683 (ttm) REVERT: N 418 GLU cc_start: 0.5696 (mp0) cc_final: 0.5449 (mp0) REVERT: N 450 MET cc_start: 0.7825 (ttp) cc_final: 0.6510 (ptp) REVERT: N 503 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7322 (mp) REVERT: O 379 GLN cc_start: 0.8975 (tt0) cc_final: 0.8627 (pp30) REVERT: O 386 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8969 (tm-30) REVERT: O 404 TYR cc_start: 0.7043 (m-10) cc_final: 0.6066 (t80) REVERT: O 422 ASP cc_start: 0.8923 (p0) cc_final: 0.8567 (p0) REVERT: O 450 MET cc_start: 0.7649 (ttp) cc_final: 0.6089 (ptp) REVERT: O 503 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.7347 (mp) REVERT: P 358 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8185 (t) REVERT: P 379 GLN cc_start: 0.8663 (tt0) cc_final: 0.7945 (tm-30) REVERT: P 384 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8016 (pp20) REVERT: P 418 GLU cc_start: 0.5508 (mp0) cc_final: 0.4624 (mp0) REVERT: P 503 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7286 (mp) REVERT: Q 422 ASP cc_start: 0.8899 (p0) cc_final: 0.8631 (p0) REVERT: Q 427 TYR cc_start: 0.8816 (m-80) cc_final: 0.8409 (m-80) REVERT: Q 459 MET cc_start: 0.7904 (mtp) cc_final: 0.7554 (mtp) REVERT: R 356 MET cc_start: 0.6895 (tpp) cc_final: 0.6595 (tpp) REVERT: R 375 ILE cc_start: 0.8974 (tp) cc_final: 0.8583 (pt) REVERT: R 384 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7965 (tm-30) REVERT: R 385 THR cc_start: 0.9340 (m) cc_final: 0.8987 (t) REVERT: R 386 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8590 (pp30) REVERT: R 460 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8617 (p) REVERT: R 497 LEU cc_start: 0.7403 (mp) cc_final: 0.7138 (mt) REVERT: S 367 LYS cc_start: 0.8217 (ptmt) cc_final: 0.7726 (pttm) REVERT: S 372 LYS cc_start: 0.8741 (pptt) cc_final: 0.8168 (mtpt) REVERT: S 373 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7483 (tm-30) REVERT: S 422 ASP cc_start: 0.8679 (p0) cc_final: 0.8475 (p0) REVERT: S 436 GLN cc_start: 0.9381 (tp40) cc_final: 0.6424 (pm20) REVERT: T 379 GLN cc_start: 0.8468 (tt0) cc_final: 0.7824 (pp30) REVERT: T 384 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8157 (tm-30) REVERT: T 405 GLN cc_start: 0.8671 (pt0) cc_final: 0.8421 (pt0) REVERT: U 365 LYS cc_start: 0.8429 (ptpp) cc_final: 0.8112 (ptpp) REVERT: U 379 GLN cc_start: 0.9082 (tt0) cc_final: 0.8265 (tm-30) REVERT: U 384 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8133 (pp20) REVERT: U 404 TYR cc_start: 0.7688 (m-10) cc_final: 0.5732 (t80) REVERT: U 414 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9214 (tt) REVERT: U 421 ASP cc_start: 0.8493 (p0) cc_final: 0.7676 (p0) REVERT: U 425 PHE cc_start: 0.7778 (m-10) cc_final: 0.7454 (m-10) REVERT: U 450 MET cc_start: 0.7483 (ttp) cc_final: 0.7039 (ptp) REVERT: U 503 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7198 (mp) REVERT: V 356 MET cc_start: 0.7654 (mmp) cc_final: 0.7053 (ptt) REVERT: V 384 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7128 (tm-30) REVERT: V 386 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8897 (tm-30) REVERT: V 450 MET cc_start: 0.7238 (ttp) cc_final: 0.6120 (ptp) REVERT: W 377 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8596 (pp) REVERT: W 379 GLN cc_start: 0.8972 (tt0) cc_final: 0.8215 (tm-30) REVERT: W 384 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7898 (tm-30) REVERT: X 355 MET cc_start: 0.7953 (mmm) cc_final: 0.7555 (mmp) REVERT: X 361 GLN cc_start: 0.8999 (tt0) cc_final: 0.8006 (tm-30) REVERT: X 384 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7528 (tm-30) REVERT: X 386 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8858 (tm-30) REVERT: X 404 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.4694 (t80) REVERT: X 427 TYR cc_start: 0.8635 (m-80) cc_final: 0.8354 (m-80) REVERT: X 450 MET cc_start: 0.8059 (ttp) cc_final: 0.6273 (ptp) REVERT: Y 379 GLN cc_start: 0.8687 (tt0) cc_final: 0.8121 (tm-30) REVERT: Y 384 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7617 (tm-30) REVERT: Y 404 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.5716 (t80) REVERT: Y 422 ASP cc_start: 0.9007 (p0) cc_final: 0.8632 (p0) REVERT: Y 485 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9071 (p) REVERT: Y 503 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7160 (mp) REVERT: Z 358 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.7962 (t) REVERT: Z 372 LYS cc_start: 0.9106 (pptt) cc_final: 0.8846 (pttm) REVERT: Z 379 GLN cc_start: 0.8885 (tt0) cc_final: 0.8533 (pp30) REVERT: Z 404 TYR cc_start: 0.6923 (m-10) cc_final: 0.6048 (t80) REVERT: Z 412 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7734 (mmmt) REVERT: Z 450 MET cc_start: 0.7655 (ttp) cc_final: 0.6350 (ptp) REVERT: a 355 MET cc_start: 0.8152 (mmp) cc_final: 0.7756 (tpt) REVERT: a 371 GLU cc_start: 0.8418 (tp30) cc_final: 0.7905 (tp30) REVERT: a 383 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8663 (tt) REVERT: a 404 TYR cc_start: 0.7698 (m-80) cc_final: 0.7413 (m-80) REVERT: a 503 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7440 (mp) outliers start: 75 outliers final: 56 residues processed: 700 average time/residue: 0.1335 time to fit residues: 144.2956 Evaluate side-chains 720 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 649 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 484 LEU Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 424 THR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 370 GLU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 364 ASN Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 414 ILE Chi-restraints excluded: chain U residue 449 SER Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 361 GLN Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 370 GLU Chi-restraints excluded: chain X residue 404 TYR Chi-restraints excluded: chain X residue 411 SER Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 404 TYR Chi-restraints excluded: chain Y residue 448 LEU Chi-restraints excluded: chain Y residue 449 SER Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 370 GLU Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 157 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 373 GLN O 361 GLN R 389 HIS V 361 GLN V 364 ASN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 443 GLN Y 373 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.104813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091563 restraints weight = 44868.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093234 restraints weight = 20740.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094232 restraints weight = 12346.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.094842 restraints weight = 8897.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095115 restraints weight = 7277.460| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18942 Z= 0.235 Angle : 0.804 12.263 25536 Z= 0.411 Chirality : 0.050 0.208 2744 Planarity : 0.005 0.061 3304 Dihedral : 5.525 21.713 2492 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 4.66 % Allowed : 22.52 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2240 helix: 1.01 (0.20), residues: 574 sheet: -0.54 (0.21), residues: 462 loop : -2.87 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Y 410 TYR 0.022 0.002 TYR S 403 PHE 0.020 0.002 PHE R 420 TRP 0.009 0.001 TRP Q 466 HIS 0.005 0.001 HIS T 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (18942) covalent geometry : angle 0.80357 / 0.41 (25536) hydrogen bonds : bond 0.03149 / 2.09 ( 784) hydrogen bonds : angle 4.57029 / 3.02 ( 2142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 654 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9114 (tt0) cc_final: 0.8457 (tm-30) REVERT: N 405 GLN cc_start: 0.8533 (pt0) cc_final: 0.8176 (pt0) REVERT: N 415 MET cc_start: 0.8131 (ttm) cc_final: 0.7655 (ttm) REVERT: N 418 GLU cc_start: 0.5858 (mp0) cc_final: 0.5604 (mp0) REVERT: N 450 MET cc_start: 0.7922 (ttp) cc_final: 0.6685 (ptp) REVERT: N 503 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.7422 (mp) REVERT: O 379 GLN cc_start: 0.9018 (tt0) cc_final: 0.8645 (pp30) REVERT: O 404 TYR cc_start: 0.6261 (m-10) cc_final: 0.5224 (t80) REVERT: O 422 ASP cc_start: 0.9054 (p0) cc_final: 0.8786 (p0) REVERT: O 450 MET cc_start: 0.7774 (ttp) cc_final: 0.6183 (ptp) REVERT: O 503 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.7430 (mp) REVERT: P 358 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8167 (t) REVERT: P 379 GLN cc_start: 0.8646 (tt0) cc_final: 0.7978 (tm-30) REVERT: P 384 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8059 (pp20) REVERT: P 418 GLU cc_start: 0.5713 (mp0) cc_final: 0.4834 (mp0) REVERT: P 422 ASP cc_start: 0.9165 (p0) cc_final: 0.8786 (p0) REVERT: P 464 LEU cc_start: 0.9227 (mp) cc_final: 0.9006 (mp) REVERT: P 503 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.7394 (mp) REVERT: Q 422 ASP cc_start: 0.9077 (p0) cc_final: 0.8825 (p0) REVERT: Q 427 TYR cc_start: 0.8961 (m-80) cc_final: 0.8552 (m-80) REVERT: Q 459 MET cc_start: 0.8198 (mtp) cc_final: 0.7864 (mtp) REVERT: Q 503 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7510 (mp) REVERT: R 379 GLN cc_start: 0.8786 (tt0) cc_final: 0.7965 (tm-30) REVERT: R 384 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7889 (tm-30) REVERT: R 456 ASP cc_start: 0.8502 (t0) cc_final: 0.8294 (t0) REVERT: R 460 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8853 (p) REVERT: R 497 LEU cc_start: 0.7933 (mp) cc_final: 0.7607 (mt) REVERT: S 372 LYS cc_start: 0.8808 (pptt) cc_final: 0.8252 (mtpt) REVERT: S 373 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7474 (tm-30) REVERT: S 384 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8060 (tm-30) REVERT: T 379 GLN cc_start: 0.8865 (tt0) cc_final: 0.8416 (pp30) REVERT: T 384 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8118 (tm-30) REVERT: T 503 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7574 (mp) REVERT: U 365 LYS cc_start: 0.8751 (ptpp) cc_final: 0.8356 (ptpp) REVERT: U 379 GLN cc_start: 0.9120 (tt0) cc_final: 0.8509 (tm-30) REVERT: U 384 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8000 (pp20) REVERT: U 404 TYR cc_start: 0.7623 (m-10) cc_final: 0.5416 (t80) REVERT: U 421 ASP cc_start: 0.8590 (p0) cc_final: 0.7637 (p0) REVERT: U 450 MET cc_start: 0.7456 (ttp) cc_final: 0.6775 (ptp) REVERT: U 503 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7220 (mp) REVERT: V 355 MET cc_start: 0.8130 (tpp) cc_final: 0.7768 (tpt) REVERT: V 356 MET cc_start: 0.7574 (mmp) cc_final: 0.6998 (ptt) REVERT: V 384 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7227 (tm-30) REVERT: V 386 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8870 (tm-30) REVERT: V 450 MET cc_start: 0.7534 (ttp) cc_final: 0.6182 (ptp) REVERT: W 379 GLN cc_start: 0.9022 (tt0) cc_final: 0.8273 (tm-30) REVERT: X 361 GLN cc_start: 0.9102 (tt0) cc_final: 0.8099 (tm-30) REVERT: X 384 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7747 (tm-30) REVERT: X 386 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8909 (tm-30) REVERT: X 404 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: X 427 TYR cc_start: 0.8697 (m-80) cc_final: 0.8393 (m-80) REVERT: X 450 MET cc_start: 0.8254 (ttp) cc_final: 0.6419 (ptp) REVERT: X 452 ASP cc_start: 0.6624 (m-30) cc_final: 0.6329 (m-30) REVERT: Y 355 MET cc_start: 0.2399 (OUTLIER) cc_final: 0.1867 (tpt) REVERT: Y 371 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8212 (tp30) REVERT: Y 379 GLN cc_start: 0.8783 (tt0) cc_final: 0.8167 (tm-30) REVERT: Y 404 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.5654 (t80) REVERT: Y 485 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.8975 (p) REVERT: Y 503 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7396 (mp) REVERT: Z 372 LYS cc_start: 0.9114 (pptt) cc_final: 0.8883 (pttm) REVERT: Z 379 GLN cc_start: 0.8991 (tt0) cc_final: 0.8484 (pp30) REVERT: Z 404 TYR cc_start: 0.6364 (m-10) cc_final: 0.5709 (t80) REVERT: Z 412 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7934 (mmmt) REVERT: Z 450 MET cc_start: 0.7833 (ttp) cc_final: 0.6576 (ptp) REVERT: a 355 MET cc_start: 0.8164 (mmp) cc_final: 0.7830 (tpt) REVERT: a 371 GLU cc_start: 0.8658 (tp30) cc_final: 0.8074 (tp30) REVERT: a 383 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8560 (tt) REVERT: a 425 PHE cc_start: 0.9031 (m-80) cc_final: 0.8431 (m-80) REVERT: a 503 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7557 (mp) outliers start: 94 outliers final: 71 residues processed: 696 average time/residue: 0.1306 time to fit residues: 139.8021 Evaluate side-chains 714 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 628 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 484 LEU Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 424 THR Chi-restraints excluded: chain P residue 449 SER Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain Q residue 503 ILE Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 370 GLU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 364 ASN Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 449 SER Chi-restraints excluded: chain U residue 484 LEU Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 361 GLN Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 370 GLU Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 370 GLU Chi-restraints excluded: chain X residue 404 TYR Chi-restraints excluded: chain X residue 411 SER Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 434 THR Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 355 MET Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 404 TYR Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 448 LEU Chi-restraints excluded: chain Y residue 449 SER Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 360 GLU Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 187 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 chunk 159 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 373 GLN O 361 GLN R 389 HIS T 373 GLN U 373 GLN V 361 GLN V 364 ASN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 373 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095407 restraints weight = 45129.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.097027 restraints weight = 21333.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097994 restraints weight = 12858.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098556 restraints weight = 9290.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098865 restraints weight = 7664.813| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18942 Z= 0.150 Angle : 0.790 12.568 25536 Z= 0.398 Chirality : 0.049 0.239 2744 Planarity : 0.005 0.065 3304 Dihedral : 5.125 24.355 2492 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.07 % Allowed : 24.11 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.16), residues: 2240 helix: 1.18 (0.21), residues: 574 sheet: -0.47 (0.21), residues: 462 loop : -2.84 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG a 410 TYR 0.015 0.001 TYR Z 506 PHE 0.020 0.001 PHE R 420 TRP 0.011 0.002 TRP S 466 HIS 0.005 0.001 HIS T 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (18942) covalent geometry : angle 0.79027 / 0.40 (25536) hydrogen bonds : bond 0.02813 / 1.85 ( 784) hydrogen bonds : angle 4.43159 / 2.94 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 681 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9060 (tt0) cc_final: 0.8443 (tm-30) REVERT: N 405 GLN cc_start: 0.8382 (pt0) cc_final: 0.8103 (pt0) REVERT: N 415 MET cc_start: 0.8063 (ttm) cc_final: 0.7607 (ttm) REVERT: N 418 GLU cc_start: 0.5821 (mp0) cc_final: 0.5589 (mp0) REVERT: N 425 PHE cc_start: 0.7560 (m-10) cc_final: 0.7149 (m-10) REVERT: N 450 MET cc_start: 0.7664 (ttp) cc_final: 0.6473 (ptp) REVERT: N 503 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.7463 (mp) REVERT: O 373 GLN cc_start: 0.8613 (tp-100) cc_final: 0.8316 (tp40) REVERT: O 379 GLN cc_start: 0.8974 (tt0) cc_final: 0.8638 (pp30) REVERT: O 386 GLN cc_start: 0.9267 (tm-30) cc_final: 0.9025 (tm-30) REVERT: O 404 TYR cc_start: 0.6094 (m-10) cc_final: 0.5488 (t80) REVERT: O 450 MET cc_start: 0.7629 (ttp) cc_final: 0.5856 (ptp) REVERT: O 503 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7396 (mp) REVERT: P 379 GLN cc_start: 0.8646 (tt0) cc_final: 0.8005 (tm-30) REVERT: P 384 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7856 (tm-30) REVERT: P 422 ASP cc_start: 0.8965 (p0) cc_final: 0.8637 (p0) REVERT: P 503 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7228 (mp) REVERT: Q 422 ASP cc_start: 0.8864 (p0) cc_final: 0.8653 (p0) REVERT: Q 427 TYR cc_start: 0.8906 (m-80) cc_final: 0.8523 (m-80) REVERT: Q 459 MET cc_start: 0.7922 (mtp) cc_final: 0.7586 (mtp) REVERT: R 379 GLN cc_start: 0.8750 (tt0) cc_final: 0.8055 (tm-30) REVERT: R 460 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8656 (p) REVERT: R 481 ASP cc_start: 0.7395 (p0) cc_final: 0.6730 (m-30) REVERT: R 497 LEU cc_start: 0.7581 (mp) cc_final: 0.7125 (mt) REVERT: S 367 LYS cc_start: 0.8718 (ptmt) cc_final: 0.8104 (pttm) REVERT: S 372 LYS cc_start: 0.8864 (pptt) cc_final: 0.8334 (mtpt) REVERT: S 373 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7727 (tp40) REVERT: S 384 GLU cc_start: 0.8628 (tm-30) cc_final: 0.7949 (tm-30) REVERT: S 436 GLN cc_start: 0.9369 (tp40) cc_final: 0.6455 (pm20) REVERT: T 379 GLN cc_start: 0.8723 (tt0) cc_final: 0.8383 (pp30) REVERT: T 384 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8148 (tm-30) REVERT: T 460 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8796 (p) REVERT: T 503 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7511 (mp) REVERT: U 365 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8255 (ptpp) REVERT: U 379 GLN cc_start: 0.9081 (tt0) cc_final: 0.8527 (tm-30) REVERT: U 404 TYR cc_start: 0.7433 (m-10) cc_final: 0.5507 (t80) REVERT: U 421 ASP cc_start: 0.8318 (p0) cc_final: 0.7443 (p0) REVERT: U 425 PHE cc_start: 0.7747 (m-10) cc_final: 0.7421 (m-10) REVERT: U 450 MET cc_start: 0.7426 (ttp) cc_final: 0.6783 (ptp) REVERT: U 503 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7335 (mp) REVERT: V 355 MET cc_start: 0.8103 (tpp) cc_final: 0.7746 (tpt) REVERT: V 356 MET cc_start: 0.7493 (mmp) cc_final: 0.7062 (ptt) REVERT: V 384 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7159 (tm-30) REVERT: V 386 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8856 (tm-30) REVERT: V 450 MET cc_start: 0.7302 (ttp) cc_final: 0.6103 (ptp) REVERT: W 379 GLN cc_start: 0.9007 (tt0) cc_final: 0.8251 (tm-30) REVERT: W 421 ASP cc_start: 0.8263 (p0) cc_final: 0.7786 (p0) REVERT: W 425 PHE cc_start: 0.8850 (m-80) cc_final: 0.8562 (m-10) REVERT: X 361 GLN cc_start: 0.9063 (tt0) cc_final: 0.8064 (tm-30) REVERT: X 384 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7432 (tm-30) REVERT: X 386 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8814 (tm-30) REVERT: X 427 TYR cc_start: 0.8649 (m-80) cc_final: 0.8382 (m-80) REVERT: X 450 MET cc_start: 0.8123 (ttp) cc_final: 0.6376 (ptp) REVERT: Y 355 MET cc_start: 0.2248 (OUTLIER) cc_final: 0.1775 (tpt) REVERT: Y 379 GLN cc_start: 0.8728 (tt0) cc_final: 0.8177 (tm-30) REVERT: Y 384 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7659 (tm-30) REVERT: Y 404 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.5863 (t80) REVERT: Y 485 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9064 (p) REVERT: Y 503 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7252 (mp) REVERT: Z 371 GLU cc_start: 0.8726 (tp30) cc_final: 0.8433 (tp30) REVERT: Z 379 GLN cc_start: 0.8959 (tt0) cc_final: 0.8562 (pp30) REVERT: Z 404 TYR cc_start: 0.6173 (m-10) cc_final: 0.5527 (t80) REVERT: Z 412 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7665 (mmmt) REVERT: Z 450 MET cc_start: 0.7694 (ttp) cc_final: 0.5993 (ptp) REVERT: a 355 MET cc_start: 0.8084 (mmp) cc_final: 0.7753 (tpt) REVERT: a 371 GLU cc_start: 0.8418 (tp30) cc_final: 0.7869 (tp30) REVERT: a 383 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8598 (tt) REVERT: a 426 THR cc_start: 0.9346 (m) cc_final: 0.9081 (m) REVERT: a 464 LEU cc_start: 0.9381 (mp) cc_final: 0.9173 (mp) REVERT: a 503 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7500 (mp) outliers start: 82 outliers final: 66 residues processed: 717 average time/residue: 0.1348 time to fit residues: 148.3726 Evaluate side-chains 734 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 655 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 484 LEU Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 361 GLN Chi-restraints excluded: chain O residue 370 GLU Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 469 VAL Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 424 THR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 370 GLU Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 370 GLU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 449 SER Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain V residue 361 GLN Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 370 GLU Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 370 GLU Chi-restraints excluded: chain X residue 411 SER Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 434 THR Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 355 MET Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 404 TYR Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 448 LEU Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 370 GLU Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 97 optimal weight: 3.9990 chunk 207 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 373 GLN O 361 GLN O 400 ASN P 405 GLN R 389 HIS T 373 GLN U 373 GLN ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 ASN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN Y 373 GLN ** Z 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.091180 restraints weight = 45253.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.092749 restraints weight = 21693.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093708 restraints weight = 13241.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094253 restraints weight = 9635.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094556 restraints weight = 8006.042| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 18942 Z= 0.252 Angle : 0.849 13.293 25536 Z= 0.434 Chirality : 0.051 0.219 2744 Planarity : 0.005 0.067 3304 Dihedral : 5.616 24.867 2492 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 4.66 % Allowed : 24.11 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.16), residues: 2240 helix: 0.91 (0.20), residues: 574 sheet: -0.49 (0.21), residues: 462 loop : -2.88 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG R 369 TYR 0.019 0.002 TYR S 403 PHE 0.019 0.002 PHE R 420 TRP 0.010 0.001 TRP X 466 HIS 0.003 0.001 HIS P 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (18942) covalent geometry : angle 0.84870 / 0.43 (25536) hydrogen bonds : bond 0.03246 / 2.15 ( 784) hydrogen bonds : angle 4.59345 / 3.04 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4066.26 seconds wall clock time: 70 minutes 51.58 seconds (4251.58 seconds total)