Starting phenix.real_space_refine on Sat Sep 28 07:01:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/09_2024/6oeg_20020_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/09_2024/6oeg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/09_2024/6oeg_20020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/09_2024/6oeg_20020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/09_2024/6oeg_20020_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/09_2024/6oeg_20020_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18564 Number of models: 1 Model: "" Number of chains: 1 Chain: "a" 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, N, Q, P, S, R, U, T, W, V, Y, X, Z Time building chain proxies: 7.37, per 1000 atoms: 0.40 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: 4.42 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.17 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: 5.33 Time building geometry restraints manager: 5.14 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: 0.00 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: 10.530 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 37.170 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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= 0.504 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.004 TRP U 466 HIS 0.002 0.001 HIS P 389 PHE 0.022 0.004 PHE X 420 TYR 0.018 0.003 TYR R 467 ARG 0.005 0.001 ARG N 399 *********************** 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 fitting. rotamer outliers: 112 poor density : 841 time to evaluate : 2.698 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: 0.8631 (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: 0.8511 (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: 0.4864 (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: 0.6711 (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: 0.7444 (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: 0.8405 (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: 0.3134 time to fit residues: 391.6220 Evaluate side-chains 684 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 635 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 189 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 57 optimal weight: 0.3980 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 R 505 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18942 Z= 0.194 Angle : 0.659 8.054 25536 Z= 0.351 Chirality : 0.047 0.145 2744 Planarity : 0.006 0.045 3304 Dihedral : 7.897 50.647 2614 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.87 % Allowed : 13.05 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.14), residues: 2240 helix: -1.45 (0.18), residues: 574 sheet: -2.56 (0.18), residues: 462 loop : -3.35 (0.14), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP W 466 HIS 0.002 0.001 HIS R 389 PHE 0.027 0.002 PHE R 420 TYR 0.012 0.001 TYR a 467 ARG 0.006 0.001 ARG a 369 *********************** 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 793 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 715 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 373 GLN cc_start: 0.8570 (tp40) cc_final: 0.8314 (tp40) REVERT: N 379 GLN cc_start: 0.8924 (tt0) cc_final: 0.8352 (tm-30) REVERT: N 404 TYR cc_start: 0.8205 (m-10) cc_final: 0.5283 (t80) REVERT: N 405 GLN cc_start: 0.8679 (pt0) cc_final: 0.8150 (pt0) REVERT: N 415 MET cc_start: 0.8142 (ttm) cc_final: 0.7694 (ttm) REVERT: N 449 SER cc_start: 0.9184 (t) cc_final: 0.8746 (p) REVERT: N 450 MET cc_start: 0.7561 (ttp) cc_final: 0.6140 (ptp) REVERT: O 379 GLN cc_start: 0.9059 (tt0) cc_final: 0.8442 (tm-30) REVERT: O 386 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8542 (tm-30) REVERT: O 404 TYR cc_start: 0.8130 (m-10) cc_final: 0.5775 (t80) REVERT: O 405 GLN cc_start: 0.8640 (pt0) cc_final: 0.8342 (pt0) REVERT: O 415 MET cc_start: 0.7762 (ttm) cc_final: 0.7403 (ttm) REVERT: O 418 GLU cc_start: 0.5904 (mp0) cc_final: 0.5514 (mp0) REVERT: O 450 MET cc_start: 0.7724 (ttp) cc_final: 0.6847 (ptp) REVERT: O 461 ASN cc_start: 0.8611 (t0) cc_final: 0.8408 (t0) REVERT: P 367 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7676 (pttm) REVERT: P 372 LYS cc_start: 0.8762 (pptt) cc_final: 0.8350 (mtpt) REVERT: P 379 GLN cc_start: 0.8783 (tt0) cc_final: 0.7845 (tm-30) REVERT: P 384 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8001 (pp20) REVERT: P 386 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: P 404 TYR cc_start: 0.8088 (m-10) cc_final: 0.5475 (t80) REVERT: P 415 MET cc_start: 0.7674 (ttm) cc_final: 0.7294 (ttm) REVERT: P 422 ASP cc_start: 0.9093 (p0) cc_final: 0.8697 (p0) REVERT: P 464 LEU cc_start: 0.9348 (mp) cc_final: 0.9029 (mm) REVERT: Q 404 TYR cc_start: 0.8717 (m-10) cc_final: 0.5719 (t80) REVERT: Q 405 GLN cc_start: 0.8212 (pt0) cc_final: 0.7951 (pt0) REVERT: Q 415 MET cc_start: 0.7631 (ttm) cc_final: 0.7341 (ttm) REVERT: Q 421 ASP cc_start: 0.8509 (p0) cc_final: 0.8170 (p0) REVERT: Q 422 ASP cc_start: 0.9024 (p0) cc_final: 0.8784 (p0) REVERT: Q 427 TYR cc_start: 0.8837 (m-80) cc_final: 0.8498 (m-80) REVERT: Q 448 LEU cc_start: 0.8783 (mt) cc_final: 0.8537 (mt) REVERT: Q 459 MET cc_start: 0.7775 (mtp) cc_final: 0.7376 (mtp) REVERT: R 386 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7515 (pp30) REVERT: R 389 HIS cc_start: 0.7041 (t-90) cc_final: 0.6661 (t70) REVERT: R 415 MET cc_start: 0.7869 (ttm) cc_final: 0.7568 (ttm) REVERT: R 421 ASP cc_start: 0.8033 (p0) cc_final: 0.7764 (p0) REVERT: S 364 ASN cc_start: 0.8030 (t0) cc_final: 0.7568 (t0) REVERT: S 383 LEU cc_start: 0.7450 (tm) cc_final: 0.7182 (mt) REVERT: S 404 TYR cc_start: 0.7937 (m-10) cc_final: 0.5945 (t80) REVERT: S 422 ASP cc_start: 0.9014 (p0) cc_final: 0.8485 (p0) REVERT: S 450 MET cc_start: 0.7198 (ttp) cc_final: 0.6957 (ptp) REVERT: S 452 ASP cc_start: 0.7913 (p0) cc_final: 0.7653 (p0) REVERT: T 364 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8108 (t0) REVERT: T 379 GLN cc_start: 0.8432 (tt0) cc_final: 0.7420 (tm-30) REVERT: T 404 TYR cc_start: 0.7832 (m-10) cc_final: 0.5506 (t80) REVERT: T 405 GLN cc_start: 0.8576 (pt0) cc_final: 0.8070 (pt0) REVERT: T 456 ASP cc_start: 0.8745 (t0) cc_final: 0.8401 (t0) REVERT: T 468 ARG cc_start: 0.8677 (ptt90) cc_final: 0.8464 (ptt90) REVERT: U 367 LYS cc_start: 0.8774 (ptmt) cc_final: 0.8449 (pttm) REVERT: U 379 GLN cc_start: 0.9026 (tt0) cc_final: 0.8257 (tm-30) REVERT: U 386 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8742 (tm-30) REVERT: U 404 TYR cc_start: 0.8167 (m-10) cc_final: 0.5512 (t80) REVERT: U 415 MET cc_start: 0.8206 (ttm) cc_final: 0.7920 (ttm) REVERT: U 449 SER cc_start: 0.9427 (t) cc_final: 0.9197 (t) REVERT: U 450 MET cc_start: 0.7452 (ttp) cc_final: 0.6468 (ptp) REVERT: U 456 ASP cc_start: 0.8886 (t0) cc_final: 0.8611 (t0) REVERT: V 384 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7178 (tm-30) REVERT: V 417 SER cc_start: 0.9163 (t) cc_final: 0.8792 (t) REVERT: V 450 MET cc_start: 0.6959 (ttp) cc_final: 0.5612 (ptp) REVERT: V 452 ASP cc_start: 0.8062 (p0) cc_final: 0.7544 (m-30) REVERT: W 379 GLN cc_start: 0.9069 (tt0) cc_final: 0.8304 (tm-30) REVERT: W 386 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8642 (tm-30) REVERT: W 402 ASN cc_start: 0.8573 (t0) cc_final: 0.8140 (t0) REVERT: W 450 MET cc_start: 0.7459 (ttp) cc_final: 0.6667 (ptp) REVERT: X 355 MET cc_start: 0.8218 (mmp) cc_final: 0.7047 (tpt) REVERT: X 384 GLU cc_start: 0.7887 (tm-30) cc_final: 0.6969 (tm-30) REVERT: X 386 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8909 (tm-30) REVERT: X 404 TYR cc_start: 0.8094 (m-10) cc_final: 0.6239 (t80) REVERT: X 414 ILE cc_start: 0.9124 (tp) cc_final: 0.8911 (tp) REVERT: X 418 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6547 (mm-30) REVERT: X 421 ASP cc_start: 0.8496 (p0) cc_final: 0.8150 (p0) REVERT: X 427 TYR cc_start: 0.8713 (m-80) cc_final: 0.8455 (m-80) REVERT: X 450 MET cc_start: 0.7662 (ttp) cc_final: 0.5883 (ptp) REVERT: X 459 MET cc_start: 0.8484 (mtp) cc_final: 0.8071 (ttm) REVERT: Y 367 LYS cc_start: 0.8505 (ptmt) cc_final: 0.8275 (pttm) REVERT: Y 372 LYS cc_start: 0.9133 (pptt) cc_final: 0.8877 (mmmt) REVERT: Y 379 GLN cc_start: 0.8938 (tt0) cc_final: 0.8504 (tm-30) REVERT: Y 384 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7534 (tm-30) REVERT: Y 404 TYR cc_start: 0.7945 (m-10) cc_final: 0.5464 (t80) REVERT: Y 415 MET cc_start: 0.7928 (ttm) cc_final: 0.7679 (ttm) REVERT: Y 418 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6265 (mm-30) REVERT: Y 421 ASP cc_start: 0.8604 (p0) cc_final: 0.8347 (p0) REVERT: Y 422 ASP cc_start: 0.8929 (p0) cc_final: 0.8700 (p0) REVERT: Y 456 ASP cc_start: 0.8727 (t0) cc_final: 0.8495 (t0) REVERT: Z 367 LYS cc_start: 0.8693 (ptmt) cc_final: 0.8120 (pttm) REVERT: Z 372 LYS cc_start: 0.9063 (pptt) cc_final: 0.8770 (pttm) REVERT: Z 379 GLN cc_start: 0.8789 (tt0) cc_final: 0.8481 (tm-30) REVERT: Z 404 TYR cc_start: 0.8253 (m-10) cc_final: 0.5865 (t80) REVERT: Z 450 MET cc_start: 0.7762 (ttp) cc_final: 0.6956 (ptp) REVERT: Z 456 ASP cc_start: 0.8628 (t0) cc_final: 0.8335 (t0) REVERT: a 355 MET cc_start: 0.8486 (mmp) cc_final: 0.8123 (tpt) REVERT: a 371 GLU cc_start: 0.8636 (tp30) cc_final: 0.8385 (tp30) REVERT: a 417 SER cc_start: 0.8702 (t) cc_final: 0.8251 (t) REVERT: a 421 ASP cc_start: 0.8631 (p0) cc_final: 0.8386 (p0) REVERT: a 449 SER cc_start: 0.9249 (t) cc_final: 0.8598 (m) REVERT: a 450 MET cc_start: 0.6989 (ttp) cc_final: 0.6396 (ptp) outliers start: 78 outliers final: 47 residues processed: 742 average time/residue: 0.2917 time to fit residues: 326.1122 Evaluate side-chains 687 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 638 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 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 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 358 SER Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain V residue 439 ILE 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 449 SER 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 Z residue 484 LEU 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 113 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 181 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 500 ASN O 432 ASN ** R 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 432 ASN T 364 ASN V 443 GLN V 470 ASN X 373 GLN Y 461 ASN Z 413 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3573 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= 0.178 Angle : 0.661 8.606 25536 Z= 0.337 Chirality : 0.047 0.174 2744 Planarity : 0.005 0.039 3304 Dihedral : 5.578 45.584 2496 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.72 % Allowed : 16.17 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.15), residues: 2240 helix: -0.33 (0.20), residues: 574 sheet: -1.63 (0.19), residues: 434 loop : -3.27 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 466 HIS 0.003 0.001 HIS T 413 PHE 0.029 0.001 PHE R 420 TYR 0.019 0.001 TYR X 506 ARG 0.006 0.001 ARG S 468 *********************** 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 755 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 680 time to evaluate : 2.189 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 379 GLN cc_start: 0.9024 (tt0) cc_final: 0.8408 (tm-30) REVERT: N 404 TYR cc_start: 0.8170 (m-10) cc_final: 0.5099 (t80) REVERT: N 405 GLN cc_start: 0.8595 (pt0) cc_final: 0.8050 (pt0) REVERT: N 415 MET cc_start: 0.8162 (ttm) cc_final: 0.7618 (ttm) REVERT: N 449 SER cc_start: 0.9091 (t) cc_final: 0.8578 (p) REVERT: N 450 MET cc_start: 0.7530 (ttp) cc_final: 0.6078 (ptp) REVERT: O 379 GLN cc_start: 0.8961 (tt0) cc_final: 0.8414 (tm-30) REVERT: O 386 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8622 (tm-30) REVERT: O 404 TYR cc_start: 0.8013 (m-10) cc_final: 0.5478 (t80) REVERT: O 418 GLU cc_start: 0.6311 (mp0) cc_final: 0.5989 (mp0) REVERT: O 450 MET cc_start: 0.7617 (ttp) cc_final: 0.6614 (ptp) REVERT: O 509 LEU cc_start: 0.6798 (mm) cc_final: 0.6491 (mm) REVERT: P 367 LYS cc_start: 0.8047 (ptmt) cc_final: 0.7689 (pttm) REVERT: P 379 GLN cc_start: 0.8665 (tt0) cc_final: 0.7851 (tm-30) REVERT: P 384 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7975 (pp20) REVERT: P 404 TYR cc_start: 0.8093 (m-10) cc_final: 0.5399 (t80) REVERT: P 415 MET cc_start: 0.7752 (ttm) cc_final: 0.7395 (ttm) REVERT: P 422 ASP cc_start: 0.9169 (p0) cc_final: 0.8680 (p0) REVERT: P 452 ASP cc_start: 0.8081 (p0) cc_final: 0.7871 (p0) REVERT: P 464 LEU cc_start: 0.9328 (mp) cc_final: 0.8903 (mm) REVERT: Q 404 TYR cc_start: 0.8783 (m-10) cc_final: 0.5705 (t80) REVERT: Q 415 MET cc_start: 0.7800 (ttm) cc_final: 0.7314 (ttm) REVERT: Q 421 ASP cc_start: 0.8584 (p0) cc_final: 0.8063 (p0) REVERT: Q 422 ASP cc_start: 0.9081 (p0) cc_final: 0.8875 (p0) REVERT: Q 427 TYR cc_start: 0.8888 (m-80) cc_final: 0.8490 (m-80) REVERT: Q 459 MET cc_start: 0.7988 (mtp) cc_final: 0.7628 (mtp) REVERT: R 386 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7641 (pp30) REVERT: R 389 HIS cc_start: 0.7533 (t-90) cc_final: 0.7189 (t70) REVERT: R 415 MET cc_start: 0.8077 (ttm) cc_final: 0.7783 (ttm) REVERT: R 418 GLU cc_start: 0.5712 (mp0) cc_final: 0.5320 (mp0) REVERT: S 364 ASN cc_start: 0.7980 (t0) cc_final: 0.7580 (t0) REVERT: S 383 LEU cc_start: 0.7461 (tm) cc_final: 0.7222 (mt) REVERT: S 384 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8378 (pp20) REVERT: S 404 TYR cc_start: 0.8020 (m-10) cc_final: 0.5931 (t80) REVERT: S 436 GLN cc_start: 0.9289 (tp40) cc_final: 0.6303 (pm20) REVERT: S 450 MET cc_start: 0.7238 (ttp) cc_final: 0.7038 (ptp) REVERT: S 452 ASP cc_start: 0.8140 (p0) cc_final: 0.7939 (p0) REVERT: T 364 ASN cc_start: 0.8241 (t0) cc_final: 0.8024 (t0) REVERT: T 379 GLN cc_start: 0.8498 (tt0) cc_final: 0.7356 (pp30) REVERT: T 384 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8167 (tm-30) REVERT: T 404 TYR cc_start: 0.8010 (m-10) cc_final: 0.5808 (t80) REVERT: T 405 GLN cc_start: 0.8378 (pt0) cc_final: 0.8043 (pt0) REVERT: T 426 THR cc_start: 0.9344 (m) cc_final: 0.9098 (m) REVERT: T 456 ASP cc_start: 0.8684 (t0) cc_final: 0.8383 (t0) REVERT: T 468 ARG cc_start: 0.8414 (ptt90) cc_final: 0.8170 (ptt90) REVERT: U 367 LYS cc_start: 0.8772 (ptmt) cc_final: 0.8491 (pttm) REVERT: U 379 GLN cc_start: 0.9071 (tt0) cc_final: 0.8153 (tm-30) REVERT: U 384 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8041 (pp20) REVERT: U 404 TYR cc_start: 0.7946 (m-10) cc_final: 0.5256 (t80) REVERT: U 415 MET cc_start: 0.8131 (ttm) cc_final: 0.7913 (ttm) REVERT: U 449 SER cc_start: 0.9252 (t) cc_final: 0.9030 (t) REVERT: U 450 MET cc_start: 0.7673 (ttp) cc_final: 0.6682 (ptp) REVERT: U 456 ASP cc_start: 0.8838 (t0) cc_final: 0.8637 (t0) REVERT: V 384 GLU cc_start: 0.7577 (tm-30) cc_final: 0.6981 (tm-30) REVERT: V 386 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8900 (tm-30) REVERT: V 450 MET cc_start: 0.7144 (ttp) cc_final: 0.5861 (ptp) REVERT: V 464 LEU cc_start: 0.9503 (mp) cc_final: 0.9043 (mp) REVERT: W 377 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8479 (pp) REVERT: W 379 GLN cc_start: 0.9083 (tt0) cc_final: 0.8216 (tm-30) REVERT: W 386 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8510 (tm-30) REVERT: W 410 ARG cc_start: 0.8466 (ptp-110) cc_final: 0.8141 (ptp90) REVERT: W 485 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9000 (p) REVERT: X 355 MET cc_start: 0.8129 (mmp) cc_final: 0.7025 (tpt) REVERT: X 361 GLN cc_start: 0.8771 (tt0) cc_final: 0.7875 (tm-30) REVERT: X 384 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7189 (tm-30) REVERT: X 386 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8903 (tm-30) REVERT: X 404 TYR cc_start: 0.6093 (m-10) cc_final: 0.5323 (t80) REVERT: X 418 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6321 (mp0) REVERT: X 421 ASP cc_start: 0.8482 (p0) cc_final: 0.8026 (p0) REVERT: X 427 TYR cc_start: 0.8753 (m-80) cc_final: 0.8490 (m-80) REVERT: X 450 MET cc_start: 0.7756 (ttp) cc_final: 0.5972 (ptp) REVERT: Y 372 LYS cc_start: 0.9120 (pptt) cc_final: 0.8811 (pttm) REVERT: Y 379 GLN cc_start: 0.8958 (tt0) cc_final: 0.8418 (tm-30) REVERT: Y 404 TYR cc_start: 0.7829 (m-10) cc_final: 0.5148 (t80) REVERT: Y 418 GLU cc_start: 0.6456 (mm-30) cc_final: 0.5874 (mm-30) REVERT: Y 421 ASP cc_start: 0.8594 (p0) cc_final: 0.8371 (p0) REVERT: Y 422 ASP cc_start: 0.8946 (p0) cc_final: 0.8644 (p0) REVERT: Z 367 LYS cc_start: 0.8811 (ptmt) cc_final: 0.8443 (pttm) REVERT: Z 372 LYS cc_start: 0.9053 (pptt) cc_final: 0.8720 (pttm) REVERT: Z 379 GLN cc_start: 0.8828 (tt0) cc_final: 0.8446 (tm-30) REVERT: Z 404 TYR cc_start: 0.8214 (m-10) cc_final: 0.5716 (t80) REVERT: Z 450 MET cc_start: 0.7749 (ttp) cc_final: 0.6891 (ptp) REVERT: a 355 MET cc_start: 0.8302 (mmp) cc_final: 0.7994 (tpt) REVERT: a 383 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8633 (tt) REVERT: a 386 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8961 (tm-30) REVERT: a 418 GLU cc_start: 0.6404 (mp0) cc_final: 0.5944 (mp0) REVERT: a 426 THR cc_start: 0.9178 (m) cc_final: 0.8888 (m) REVERT: a 450 MET cc_start: 0.6904 (ttp) cc_final: 0.6469 (ptp) REVERT: a 456 ASP cc_start: 0.8913 (t0) cc_final: 0.8688 (t0) outliers start: 75 outliers final: 49 residues processed: 713 average time/residue: 0.3051 time to fit residues: 327.2949 Evaluate side-chains 688 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 636 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 485 VAL 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 439 ILE 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 424 THR 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 355 MET 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 370 GLU Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE 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 464 LEU Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 441 VAL 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 497 LEU Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 383 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 201 optimal weight: 0.0770 chunk 153 optimal weight: 0.0570 chunk 105 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN O 361 GLN P 405 GLN S 470 ASN V 470 ASN ** W 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN Y 373 GLN Y 413 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18942 Z= 0.184 Angle : 0.654 9.627 25536 Z= 0.334 Chirality : 0.046 0.152 2744 Planarity : 0.005 0.036 3304 Dihedral : 5.179 19.609 2492 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.07 % Allowed : 17.91 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.16), residues: 2240 helix: 0.36 (0.21), residues: 574 sheet: -1.54 (0.19), residues: 462 loop : -3.12 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 466 HIS 0.005 0.001 HIS T 389 PHE 0.029 0.001 PHE R 420 TYR 0.014 0.001 TYR Y 506 ARG 0.007 0.001 ARG V 369 *********************** 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 744 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 662 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9044 (tt0) cc_final: 0.8386 (tm-30) REVERT: N 404 TYR cc_start: 0.8078 (m-10) cc_final: 0.5003 (t80) REVERT: N 405 GLN cc_start: 0.8533 (pt0) cc_final: 0.8028 (pt0) REVERT: N 415 MET cc_start: 0.8223 (ttm) cc_final: 0.7588 (ttm) REVERT: N 449 SER cc_start: 0.9068 (t) cc_final: 0.8674 (p) REVERT: N 450 MET cc_start: 0.7566 (ttp) cc_final: 0.6153 (ptp) REVERT: O 379 GLN cc_start: 0.8898 (tt0) cc_final: 0.8480 (tm-30) REVERT: O 386 GLN cc_start: 0.9301 (tm-30) cc_final: 0.8608 (tm-30) REVERT: O 404 TYR cc_start: 0.8060 (m-10) cc_final: 0.5479 (t80) REVERT: O 450 MET cc_start: 0.7676 (ttp) cc_final: 0.6555 (ptp) REVERT: P 358 SER cc_start: 0.8292 (m) cc_final: 0.7870 (t) REVERT: P 367 LYS cc_start: 0.8307 (ptmt) cc_final: 0.7870 (pttm) REVERT: P 370 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7870 (tm-30) REVERT: P 372 LYS cc_start: 0.8833 (pptt) cc_final: 0.8360 (mtpt) REVERT: P 379 GLN cc_start: 0.8718 (tt0) cc_final: 0.7865 (tm-30) REVERT: P 384 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7881 (tm-30) REVERT: P 404 TYR cc_start: 0.8010 (m-10) cc_final: 0.5325 (t80) REVERT: P 415 MET cc_start: 0.7717 (ttm) cc_final: 0.7504 (ttm) REVERT: P 418 GLU cc_start: 0.4819 (mp0) cc_final: 0.4185 (mp0) REVERT: P 422 ASP cc_start: 0.9181 (p0) cc_final: 0.8688 (p0) REVERT: P 464 LEU cc_start: 0.9288 (mp) cc_final: 0.8904 (mt) REVERT: P 485 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9056 (p) REVERT: Q 404 TYR cc_start: 0.8849 (m-10) cc_final: 0.5507 (t80) REVERT: Q 421 ASP cc_start: 0.8550 (p0) cc_final: 0.8131 (p0) REVERT: Q 422 ASP cc_start: 0.9143 (p0) cc_final: 0.8906 (p0) REVERT: Q 427 TYR cc_start: 0.8921 (m-80) cc_final: 0.8512 (m-80) REVERT: Q 459 MET cc_start: 0.8026 (mtp) cc_final: 0.7694 (mtp) REVERT: R 386 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8275 (pp30) REVERT: R 389 HIS cc_start: 0.7791 (t-90) cc_final: 0.7529 (t70) REVERT: R 415 MET cc_start: 0.8126 (ttm) cc_final: 0.7833 (ttm) REVERT: S 364 ASN cc_start: 0.7907 (t0) cc_final: 0.7550 (t0) REVERT: S 384 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8307 (tm-30) REVERT: S 386 GLN cc_start: 0.8759 (tp40) cc_final: 0.8534 (tm-30) REVERT: S 404 TYR cc_start: 0.8089 (m-10) cc_final: 0.5889 (t80) REVERT: S 436 GLN cc_start: 0.9380 (tp40) cc_final: 0.6452 (pm20) REVERT: S 450 MET cc_start: 0.7313 (ttp) cc_final: 0.7008 (ptp) REVERT: S 452 ASP cc_start: 0.8183 (p0) cc_final: 0.7971 (p0) REVERT: T 364 ASN cc_start: 0.8280 (t0) cc_final: 0.8064 (t0) REVERT: T 379 GLN cc_start: 0.8302 (tt0) cc_final: 0.7392 (pp30) REVERT: T 404 TYR cc_start: 0.8035 (m-10) cc_final: 0.5649 (t80) REVERT: T 405 GLN cc_start: 0.8741 (pt0) cc_final: 0.8140 (pt0) REVERT: U 365 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8278 (ptpt) REVERT: U 367 LYS cc_start: 0.8803 (ptmt) cc_final: 0.8507 (pttm) REVERT: U 379 GLN cc_start: 0.9101 (tt0) cc_final: 0.8156 (tm-30) REVERT: U 404 TYR cc_start: 0.7988 (m-10) cc_final: 0.5117 (t80) REVERT: U 415 MET cc_start: 0.8166 (ttm) cc_final: 0.7930 (ttm) REVERT: U 425 PHE cc_start: 0.7726 (m-10) cc_final: 0.7515 (m-10) REVERT: U 449 SER cc_start: 0.9246 (t) cc_final: 0.8764 (p) REVERT: U 450 MET cc_start: 0.7849 (ttp) cc_final: 0.6886 (ptp) REVERT: V 356 MET cc_start: 0.7779 (mmp) cc_final: 0.7547 (ptt) REVERT: V 384 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7088 (tm-30) REVERT: V 386 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8922 (tm-30) REVERT: V 418 GLU cc_start: 0.5819 (mp0) cc_final: 0.5580 (mp0) REVERT: V 450 MET cc_start: 0.7118 (ttp) cc_final: 0.5816 (ptp) REVERT: V 452 ASP cc_start: 0.8099 (p0) cc_final: 0.7588 (m-30) REVERT: V 464 LEU cc_start: 0.9467 (mp) cc_final: 0.8997 (mp) REVERT: W 377 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8489 (pp) REVERT: W 379 GLN cc_start: 0.8956 (tt0) cc_final: 0.8143 (tm-30) REVERT: W 386 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8525 (tm-30) REVERT: W 415 MET cc_start: 0.8286 (ttm) cc_final: 0.8043 (ttm) REVERT: X 361 GLN cc_start: 0.8799 (tt0) cc_final: 0.7918 (tm-30) REVERT: X 384 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7010 (tm-30) REVERT: X 386 GLN cc_start: 0.9256 (tm-30) cc_final: 0.8892 (tm-30) REVERT: X 404 TYR cc_start: 0.6357 (m-10) cc_final: 0.4665 (t80) REVERT: X 418 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6439 (mp0) REVERT: X 421 ASP cc_start: 0.8442 (p0) cc_final: 0.7998 (p0) REVERT: X 427 TYR cc_start: 0.8768 (m-80) cc_final: 0.8504 (m-80) REVERT: X 450 MET cc_start: 0.7834 (ttp) cc_final: 0.6046 (ptp) REVERT: X 503 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.7167 (mp) REVERT: Y 372 LYS cc_start: 0.9149 (pptt) cc_final: 0.8822 (pttm) REVERT: Y 379 GLN cc_start: 0.8933 (tt0) cc_final: 0.8396 (tm-30) REVERT: Y 384 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7636 (tm-30) REVERT: Y 386 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: Y 404 TYR cc_start: 0.7893 (m-10) cc_final: 0.5311 (t80) REVERT: Y 421 ASP cc_start: 0.8507 (p0) cc_final: 0.8279 (p0) REVERT: Y 422 ASP cc_start: 0.8952 (p0) cc_final: 0.8618 (p0) REVERT: Y 441 VAL cc_start: 0.9529 (t) cc_final: 0.9129 (p) REVERT: Y 485 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.9071 (p) REVERT: Z 367 LYS cc_start: 0.8916 (ptmt) cc_final: 0.8341 (pttm) REVERT: Z 372 LYS cc_start: 0.9065 (pptt) cc_final: 0.8773 (pttm) REVERT: Z 379 GLN cc_start: 0.8910 (tt0) cc_final: 0.8460 (pp30) REVERT: Z 404 TYR cc_start: 0.8278 (m-10) cc_final: 0.5693 (t80) REVERT: Z 450 MET cc_start: 0.7787 (ttp) cc_final: 0.6803 (ptp) REVERT: a 355 MET cc_start: 0.8244 (mmp) cc_final: 0.7914 (tpt) REVERT: a 371 GLU cc_start: 0.8700 (tp30) cc_final: 0.8459 (tp30) REVERT: a 375 ILE cc_start: 0.8831 (mm) cc_final: 0.8547 (mm) REVERT: a 383 LEU cc_start: 0.9026 (tm) cc_final: 0.8720 (tt) REVERT: a 426 THR cc_start: 0.9316 (m) cc_final: 0.9040 (m) REVERT: a 450 MET cc_start: 0.7012 (ttp) cc_final: 0.6446 (ptp) REVERT: a 456 ASP cc_start: 0.8843 (t0) cc_final: 0.8391 (t0) REVERT: a 503 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7341 (mp) outliers start: 82 outliers final: 62 residues processed: 703 average time/residue: 0.2930 time to fit residues: 310.5276 Evaluate side-chains 702 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 634 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 485 VAL 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 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 485 VAL 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 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 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 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 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 V residue 497 LEU 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 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain X residue 364 ASN 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 484 LEU 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 367 LYS 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 484 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 361 GLN R 389 HIS T 413 HIS T 461 ASN W 413 HIS X 373 GLN X 413 HIS Y 373 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18942 Z= 0.194 Angle : 0.666 8.632 25536 Z= 0.339 Chirality : 0.046 0.156 2744 Planarity : 0.004 0.032 3304 Dihedral : 5.062 20.594 2492 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.96 % Allowed : 18.01 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.16), residues: 2240 helix: 0.74 (0.21), residues: 574 sheet: -1.22 (0.20), residues: 462 loop : -3.03 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 466 HIS 0.004 0.001 HIS T 389 PHE 0.030 0.001 PHE R 420 TYR 0.020 0.001 TYR T 506 ARG 0.009 0.001 ARG V 369 *********************** 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 771 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 671 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9073 (tt0) cc_final: 0.8393 (tm-30) REVERT: N 404 TYR cc_start: 0.8027 (m-10) cc_final: 0.4825 (t80) REVERT: N 405 GLN cc_start: 0.8502 (pt0) cc_final: 0.8103 (pt0) REVERT: N 415 MET cc_start: 0.8311 (ttm) cc_final: 0.7711 (ttm) REVERT: N 418 GLU cc_start: 0.7139 (mp0) cc_final: 0.6676 (mp0) REVERT: N 421 ASP cc_start: 0.8836 (p0) cc_final: 0.8583 (p0) REVERT: N 450 MET cc_start: 0.7619 (ttp) cc_final: 0.6181 (ptp) REVERT: N 503 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.7275 (mp) REVERT: O 379 GLN cc_start: 0.8922 (tt0) cc_final: 0.8448 (tm-30) REVERT: O 386 GLN cc_start: 0.9318 (tm-30) cc_final: 0.8553 (tm-30) REVERT: O 404 TYR cc_start: 0.8085 (m-10) cc_final: 0.5453 (t80) REVERT: O 450 MET cc_start: 0.7733 (ttp) cc_final: 0.6455 (ptp) REVERT: P 358 SER cc_start: 0.8331 (m) cc_final: 0.7897 (t) REVERT: P 367 LYS cc_start: 0.8374 (ptmt) cc_final: 0.7933 (pttm) REVERT: P 379 GLN cc_start: 0.8726 (tt0) cc_final: 0.7867 (tm-30) REVERT: P 384 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7922 (pp20) REVERT: P 404 TYR cc_start: 0.8059 (m-10) cc_final: 0.5277 (t80) REVERT: P 418 GLU cc_start: 0.4924 (mp0) cc_final: 0.4316 (mp0) REVERT: P 422 ASP cc_start: 0.9208 (p0) cc_final: 0.8673 (p0) REVERT: P 464 LEU cc_start: 0.9311 (mp) cc_final: 0.8906 (mt) REVERT: P 485 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.9091 (t) REVERT: P 503 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.7364 (mp) REVERT: Q 404 TYR cc_start: 0.8879 (m-10) cc_final: 0.5407 (t80) REVERT: Q 421 ASP cc_start: 0.8519 (p0) cc_final: 0.8135 (p0) REVERT: Q 422 ASP cc_start: 0.9139 (p0) cc_final: 0.8890 (p0) REVERT: Q 427 TYR cc_start: 0.8928 (m-80) cc_final: 0.8511 (m-80) REVERT: Q 459 MET cc_start: 0.8098 (mtp) cc_final: 0.7743 (mtp) REVERT: R 384 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8209 (tm-30) REVERT: R 386 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8313 (pp30) REVERT: R 389 HIS cc_start: 0.7877 (t70) cc_final: 0.7606 (t70) REVERT: R 418 GLU cc_start: 0.5682 (mp0) cc_final: 0.5465 (mp0) REVERT: R 497 LEU cc_start: 0.7722 (mp) cc_final: 0.7441 (mt) REVERT: S 364 ASN cc_start: 0.7995 (t0) cc_final: 0.7685 (t0) REVERT: S 372 LYS cc_start: 0.8568 (pptt) cc_final: 0.8130 (mtpt) REVERT: S 404 TYR cc_start: 0.8164 (m-10) cc_final: 0.5863 (t80) REVERT: S 436 GLN cc_start: 0.9398 (tp40) cc_final: 0.6449 (pm20) REVERT: S 452 ASP cc_start: 0.8122 (p0) cc_final: 0.7896 (p0) REVERT: T 367 LYS cc_start: 0.8637 (ptmt) cc_final: 0.8085 (pttm) REVERT: T 379 GLN cc_start: 0.8404 (tt0) cc_final: 0.7604 (pp30) REVERT: T 404 TYR cc_start: 0.8050 (m-10) cc_final: 0.5728 (t80) REVERT: T 405 GLN cc_start: 0.8740 (pt0) cc_final: 0.8182 (pt0) REVERT: T 468 ARG cc_start: 0.8357 (ptt-90) cc_final: 0.8010 (ptt90) REVERT: U 365 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8308 (ptpt) REVERT: U 379 GLN cc_start: 0.9115 (tt0) cc_final: 0.8159 (tm-30) REVERT: U 384 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8251 (pp20) REVERT: U 404 TYR cc_start: 0.8038 (m-10) cc_final: 0.5024 (t80) REVERT: U 415 MET cc_start: 0.8193 (ttm) cc_final: 0.7960 (ttm) REVERT: U 418 GLU cc_start: 0.6371 (mp0) cc_final: 0.5923 (mp0) REVERT: U 421 ASP cc_start: 0.8713 (p0) cc_final: 0.8467 (p0) REVERT: U 425 PHE cc_start: 0.7734 (m-10) cc_final: 0.7482 (m-10) REVERT: U 449 SER cc_start: 0.9119 (t) cc_final: 0.8675 (p) REVERT: U 450 MET cc_start: 0.7551 (ttp) cc_final: 0.6890 (ptp) REVERT: V 356 MET cc_start: 0.7666 (mmp) cc_final: 0.7293 (ptt) REVERT: V 384 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7142 (tm-30) REVERT: V 386 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8967 (tm-30) REVERT: V 418 GLU cc_start: 0.5790 (mp0) cc_final: 0.5563 (mp0) REVERT: V 450 MET cc_start: 0.7204 (ttp) cc_final: 0.5813 (ptp) REVERT: V 464 LEU cc_start: 0.9437 (mp) cc_final: 0.8947 (mp) REVERT: W 377 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8480 (pp) REVERT: W 379 GLN cc_start: 0.8997 (tt0) cc_final: 0.8154 (tm-30) REVERT: W 386 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8594 (tm-30) REVERT: W 425 PHE cc_start: 0.9034 (m-80) cc_final: 0.8788 (m-80) REVERT: X 355 MET cc_start: 0.7662 (mmm) cc_final: 0.7378 (mmp) REVERT: X 361 GLN cc_start: 0.8899 (tt0) cc_final: 0.7997 (tm-30) REVERT: X 384 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7671 (tm-30) REVERT: X 386 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8877 (tm-30) REVERT: X 403 TYR cc_start: 0.9064 (m-10) cc_final: 0.8769 (m-10) REVERT: X 421 ASP cc_start: 0.8483 (p0) cc_final: 0.8183 (p0) REVERT: X 427 TYR cc_start: 0.8814 (m-80) cc_final: 0.8576 (m-80) REVERT: X 450 MET cc_start: 0.8048 (ttp) cc_final: 0.6209 (ptp) REVERT: Y 372 LYS cc_start: 0.9103 (pptt) cc_final: 0.8815 (pttm) REVERT: Y 379 GLN cc_start: 0.8773 (tt0) cc_final: 0.8208 (tm-30) REVERT: Y 384 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7343 (tm-30) REVERT: Y 386 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: Y 404 TYR cc_start: 0.7796 (m-10) cc_final: 0.5466 (t80) REVERT: Y 421 ASP cc_start: 0.8508 (p0) cc_final: 0.8305 (p0) REVERT: Y 422 ASP cc_start: 0.8950 (p0) cc_final: 0.8599 (p0) REVERT: Y 485 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.9032 (p) REVERT: Z 358 SER cc_start: 0.7623 (OUTLIER) cc_final: 0.7256 (p) REVERT: Z 365 LYS cc_start: 0.8340 (ptpp) cc_final: 0.7986 (ptpp) REVERT: Z 367 LYS cc_start: 0.8969 (ptmt) cc_final: 0.8285 (pttm) REVERT: Z 372 LYS cc_start: 0.9091 (pptt) cc_final: 0.8813 (pttm) REVERT: Z 379 GLN cc_start: 0.8879 (tt0) cc_final: 0.8481 (pp30) REVERT: Z 404 TYR cc_start: 0.8221 (m-10) cc_final: 0.5680 (t80) REVERT: Z 450 MET cc_start: 0.7841 (ttp) cc_final: 0.6593 (ptp) REVERT: a 355 MET cc_start: 0.8237 (mmp) cc_final: 0.7917 (tpt) REVERT: a 371 GLU cc_start: 0.8713 (tp30) cc_final: 0.8340 (tp30) REVERT: a 375 ILE cc_start: 0.8868 (mm) cc_final: 0.8480 (mm) REVERT: a 383 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8624 (tt) REVERT: a 450 MET cc_start: 0.7152 (ttp) cc_final: 0.6509 (ptp) REVERT: a 456 ASP cc_start: 0.8781 (t0) cc_final: 0.8376 (t0) REVERT: a 459 MET cc_start: 0.7668 (ptm) cc_final: 0.7154 (ptm) REVERT: a 503 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7348 (mp) outliers start: 100 outliers final: 65 residues processed: 718 average time/residue: 0.2972 time to fit residues: 321.0001 Evaluate side-chains 712 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 638 time to evaluate : 2.320 ------------------------------------------------------------------------------- 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 N residue 503 ILE 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 449 SER 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 485 VAL 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 383 LEU 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 362 ILE 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 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 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 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 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 Y residue 364 ASN Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 386 GLN Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Z residue 358 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 0.0060 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN O 361 GLN Q 405 GLN T 461 ASN X 373 GLN Y 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18942 Z= 0.203 Angle : 0.687 10.153 25536 Z= 0.349 Chirality : 0.047 0.172 2744 Planarity : 0.005 0.048 3304 Dihedral : 4.974 20.186 2492 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.06 % Allowed : 19.94 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.16), residues: 2240 helix: 0.94 (0.21), residues: 574 sheet: -0.92 (0.20), residues: 462 loop : -2.97 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 466 HIS 0.004 0.001 HIS Z 413 PHE 0.026 0.001 PHE R 420 TYR 0.013 0.001 TYR a 506 ARG 0.011 0.001 ARG Y 410 *********************** 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 767 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 665 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9113 (tt0) cc_final: 0.8383 (tm-30) REVERT: N 404 TYR cc_start: 0.8053 (m-10) cc_final: 0.4793 (t80) REVERT: N 405 GLN cc_start: 0.8483 (pt0) cc_final: 0.8066 (pt0) REVERT: N 415 MET cc_start: 0.8220 (ttm) cc_final: 0.7623 (ttm) REVERT: N 418 GLU cc_start: 0.6051 (mp0) cc_final: 0.5679 (mp0) REVERT: N 421 ASP cc_start: 0.8841 (p0) cc_final: 0.8548 (p0) REVERT: N 450 MET cc_start: 0.7599 (ttp) cc_final: 0.6230 (ptp) REVERT: O 356 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7443 (tmm) REVERT: O 379 GLN cc_start: 0.8951 (tt0) cc_final: 0.8452 (tm-30) REVERT: O 386 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8981 (tm-30) REVERT: O 404 TYR cc_start: 0.8112 (m-10) cc_final: 0.5435 (t80) REVERT: O 450 MET cc_start: 0.7749 (ttp) cc_final: 0.6427 (ptp) REVERT: P 358 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7967 (t) REVERT: P 367 LYS cc_start: 0.8471 (ptmt) cc_final: 0.7997 (pttm) REVERT: P 379 GLN cc_start: 0.8734 (tt0) cc_final: 0.7872 (tm-30) REVERT: P 384 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7923 (pp20) REVERT: P 404 TYR cc_start: 0.8085 (m-10) cc_final: 0.5965 (t80) REVERT: P 418 GLU cc_start: 0.4934 (mp0) cc_final: 0.4368 (mp0) REVERT: P 422 ASP cc_start: 0.9215 (p0) cc_final: 0.8658 (p0) REVERT: P 464 LEU cc_start: 0.9291 (mp) cc_final: 0.8903 (mt) REVERT: P 485 VAL cc_start: 0.9303 (OUTLIER) cc_final: 0.9084 (p) REVERT: P 503 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7370 (mp) REVERT: Q 384 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8502 (tm-30) REVERT: Q 403 TYR cc_start: 0.9188 (m-10) cc_final: 0.8440 (m-10) REVERT: Q 421 ASP cc_start: 0.8533 (p0) cc_final: 0.8095 (p0) REVERT: Q 422 ASP cc_start: 0.9151 (p0) cc_final: 0.8799 (p0) REVERT: Q 427 TYR cc_start: 0.8936 (m-80) cc_final: 0.8489 (m-80) REVERT: Q 459 MET cc_start: 0.8124 (mtp) cc_final: 0.7733 (mtp) REVERT: R 370 GLU cc_start: 0.8338 (tp30) cc_final: 0.8090 (mm-30) REVERT: R 384 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8101 (tm-30) REVERT: R 385 THR cc_start: 0.9273 (m) cc_final: 0.8926 (t) REVERT: R 386 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8427 (pp30) REVERT: R 390 ASN cc_start: 0.8769 (t0) cc_final: 0.8509 (t0) REVERT: R 404 TYR cc_start: 0.8534 (m-80) cc_final: 0.8222 (m-80) REVERT: R 418 GLU cc_start: 0.5647 (mp0) cc_final: 0.5401 (mp0) REVERT: R 497 LEU cc_start: 0.7784 (mp) cc_final: 0.7546 (mt) REVERT: S 364 ASN cc_start: 0.8060 (t0) cc_final: 0.7768 (t0) REVERT: S 372 LYS cc_start: 0.8396 (pptt) cc_final: 0.7887 (mtpt) REVERT: S 436 GLN cc_start: 0.9427 (tp40) cc_final: 0.6330 (pm20) REVERT: S 452 ASP cc_start: 0.8043 (p0) cc_final: 0.7813 (p0) REVERT: S 503 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8213 (tp) REVERT: T 367 LYS cc_start: 0.8667 (ptmt) cc_final: 0.8018 (pttm) REVERT: T 379 GLN cc_start: 0.8478 (tt0) cc_final: 0.7633 (pp30) REVERT: T 384 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8187 (tm-30) REVERT: T 404 TYR cc_start: 0.8104 (m-10) cc_final: 0.5709 (t80) REVERT: T 405 GLN cc_start: 0.8679 (pt0) cc_final: 0.8176 (pt0) REVERT: U 365 LYS cc_start: 0.8582 (ptpp) cc_final: 0.8298 (ptpt) REVERT: U 379 GLN cc_start: 0.9120 (tt0) cc_final: 0.8164 (tm-30) REVERT: U 384 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8223 (pp20) REVERT: U 404 TYR cc_start: 0.8075 (m-10) cc_final: 0.5027 (t80) REVERT: U 415 MET cc_start: 0.8164 (ttm) cc_final: 0.7915 (ttm) REVERT: U 418 GLU cc_start: 0.6425 (mp0) cc_final: 0.6053 (mp0) REVERT: U 421 ASP cc_start: 0.8719 (p0) cc_final: 0.8500 (p0) REVERT: U 425 PHE cc_start: 0.7700 (m-10) cc_final: 0.7421 (m-10) REVERT: U 449 SER cc_start: 0.9156 (t) cc_final: 0.8923 (p) REVERT: U 450 MET cc_start: 0.7614 (ttp) cc_final: 0.7092 (ptp) REVERT: U 503 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.7269 (mp) REVERT: V 356 MET cc_start: 0.7690 (mmp) cc_final: 0.7317 (ptt) REVERT: V 361 GLN cc_start: 0.8117 (pp30) cc_final: 0.7838 (tm-30) REVERT: V 384 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7202 (tm-30) REVERT: V 386 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8868 (tm-30) REVERT: V 418 GLU cc_start: 0.5832 (mp0) cc_final: 0.5624 (mp0) REVERT: V 450 MET cc_start: 0.7218 (ttp) cc_final: 0.5806 (ptp) REVERT: V 464 LEU cc_start: 0.9426 (mp) cc_final: 0.9018 (mp) REVERT: W 377 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8478 (pp) REVERT: W 379 GLN cc_start: 0.9026 (tt0) cc_final: 0.8141 (tm-30) REVERT: W 425 PHE cc_start: 0.9047 (m-80) cc_final: 0.8826 (m-80) REVERT: X 361 GLN cc_start: 0.8952 (tt0) cc_final: 0.8028 (tm-30) REVERT: X 384 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7626 (tm-30) REVERT: X 386 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8819 (tm-30) REVERT: X 403 TYR cc_start: 0.8966 (m-80) cc_final: 0.8522 (m-10) REVERT: X 421 ASP cc_start: 0.8487 (p0) cc_final: 0.8126 (p0) REVERT: X 427 TYR cc_start: 0.8912 (m-80) cc_final: 0.8656 (m-80) REVERT: X 450 MET cc_start: 0.8070 (ttp) cc_final: 0.6230 (ptp) REVERT: Y 371 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8479 (tp30) REVERT: Y 379 GLN cc_start: 0.8801 (tt0) cc_final: 0.8218 (tm-30) REVERT: Y 386 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: Y 404 TYR cc_start: 0.7323 (m-10) cc_final: 0.5729 (t80) REVERT: Y 415 MET cc_start: 0.8161 (ttp) cc_final: 0.7888 (ttm) REVERT: Y 485 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.8981 (p) REVERT: Y 503 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7219 (mp) REVERT: Z 358 SER cc_start: 0.7613 (OUTLIER) cc_final: 0.7166 (p) REVERT: Z 365 LYS cc_start: 0.8330 (ptpp) cc_final: 0.8031 (ptpp) REVERT: Z 372 LYS cc_start: 0.9099 (pptt) cc_final: 0.8839 (pttm) REVERT: Z 379 GLN cc_start: 0.8908 (tt0) cc_final: 0.8482 (pp30) REVERT: Z 404 TYR cc_start: 0.8154 (m-10) cc_final: 0.5330 (t80) REVERT: Z 412 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7966 (mmmt) REVERT: Z 450 MET cc_start: 0.7885 (ttp) cc_final: 0.6566 (ptp) REVERT: a 355 MET cc_start: 0.8237 (mmp) cc_final: 0.7903 (tpt) REVERT: a 371 GLU cc_start: 0.8589 (tp30) cc_final: 0.8291 (tp30) REVERT: a 383 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8627 (tt) REVERT: a 386 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8922 (tm-30) REVERT: a 450 MET cc_start: 0.7052 (ttp) cc_final: 0.6431 (ptp) REVERT: a 456 ASP cc_start: 0.8725 (t0) cc_final: 0.8345 (t0) REVERT: a 459 MET cc_start: 0.8075 (ptm) cc_final: 0.7610 (ptm) REVERT: a 503 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7381 (mp) outliers start: 102 outliers final: 71 residues processed: 710 average time/residue: 0.2953 time to fit residues: 316.7784 Evaluate side-chains 729 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 645 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 370 GLU Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain O residue 356 MET Chi-restraints excluded: chain O residue 415 MET 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 484 LEU Chi-restraints excluded: chain P residue 485 VAL 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 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 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 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 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 439 ILE 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 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 364 ASN 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 449 SER Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Y residue 370 GLU 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 485 VAL Chi-restraints excluded: chain Y residue 497 LEU Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 411 SER Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 449 SER 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 208 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 470 ASN V 443 GLN X 373 GLN Y 373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4808 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= 0.218 Angle : 0.698 11.036 25536 Z= 0.354 Chirality : 0.047 0.152 2744 Planarity : 0.005 0.056 3304 Dihedral : 5.005 19.912 2492 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.01 % Allowed : 20.73 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.16), residues: 2240 helix: 1.07 (0.21), residues: 574 sheet: -1.07 (0.20), residues: 490 loop : -2.86 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 466 HIS 0.004 0.001 HIS T 389 PHE 0.027 0.001 PHE R 420 TYR 0.013 0.001 TYR Y 387 ARG 0.013 0.001 ARG Y 410 *********************** 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 757 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 656 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9115 (tt0) cc_final: 0.8442 (tm-30) REVERT: N 404 TYR cc_start: 0.7518 (m-10) cc_final: 0.4712 (t80) REVERT: N 405 GLN cc_start: 0.8496 (pt0) cc_final: 0.8151 (pt0) REVERT: N 415 MET cc_start: 0.8235 (ttm) cc_final: 0.7716 (ttm) REVERT: N 418 GLU cc_start: 0.5864 (mp0) cc_final: 0.5351 (mp0) REVERT: N 421 ASP cc_start: 0.8862 (p0) cc_final: 0.8586 (p0) REVERT: N 443 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7581 (mp10) REVERT: N 450 MET cc_start: 0.7993 (ttp) cc_final: 0.6898 (ptp) REVERT: N 503 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.7355 (mp) REVERT: O 356 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7458 (tmm) REVERT: O 379 GLN cc_start: 0.8976 (tt0) cc_final: 0.8509 (tm-30) REVERT: O 386 GLN cc_start: 0.9322 (tm-30) cc_final: 0.9020 (tm-30) REVERT: O 404 TYR cc_start: 0.8162 (m-10) cc_final: 0.5837 (t80) REVERT: O 450 MET cc_start: 0.7821 (ttp) cc_final: 0.6430 (ptp) REVERT: P 358 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.8025 (t) REVERT: P 367 LYS cc_start: 0.8632 (ptmt) cc_final: 0.8174 (pttm) REVERT: P 379 GLN cc_start: 0.8735 (tt0) cc_final: 0.7889 (tm-30) REVERT: P 384 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7935 (pp20) REVERT: P 404 TYR cc_start: 0.7499 (m-10) cc_final: 0.5972 (t80) REVERT: P 418 GLU cc_start: 0.5063 (mp0) cc_final: 0.4418 (mp0) REVERT: P 421 ASP cc_start: 0.8623 (p0) cc_final: 0.8412 (p0) REVERT: P 422 ASP cc_start: 0.9196 (p0) cc_final: 0.8548 (p0) REVERT: P 464 LEU cc_start: 0.9193 (mp) cc_final: 0.8809 (mt) REVERT: P 485 VAL cc_start: 0.9283 (OUTLIER) cc_final: 0.9058 (p) REVERT: P 503 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7340 (mp) REVERT: Q 370 GLU cc_start: 0.8140 (pp20) cc_final: 0.7813 (tm-30) REVERT: Q 403 TYR cc_start: 0.9136 (m-10) cc_final: 0.8403 (m-10) REVERT: Q 421 ASP cc_start: 0.8472 (p0) cc_final: 0.7942 (p0) REVERT: Q 422 ASP cc_start: 0.9102 (p0) cc_final: 0.8837 (p0) REVERT: Q 427 TYR cc_start: 0.8915 (m-80) cc_final: 0.8498 (m-80) REVERT: Q 459 MET cc_start: 0.8136 (mtp) cc_final: 0.7776 (mtp) REVERT: R 370 GLU cc_start: 0.8406 (tp30) cc_final: 0.8203 (mm-30) REVERT: R 384 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8105 (tm-30) REVERT: R 385 THR cc_start: 0.9321 (m) cc_final: 0.9032 (t) REVERT: R 386 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8465 (pp30) REVERT: R 390 ASN cc_start: 0.8654 (t0) cc_final: 0.8416 (t0) REVERT: R 418 GLU cc_start: 0.5679 (mp0) cc_final: 0.5365 (mp0) REVERT: R 497 LEU cc_start: 0.7911 (mp) cc_final: 0.7686 (mt) REVERT: S 364 ASN cc_start: 0.8115 (t0) cc_final: 0.7821 (t0) REVERT: S 372 LYS cc_start: 0.8432 (pptt) cc_final: 0.7921 (mtpt) REVERT: S 418 GLU cc_start: 0.6370 (mp0) cc_final: 0.6029 (mp0) REVERT: S 436 GLN cc_start: 0.9435 (tp40) cc_final: 0.6316 (pm20) REVERT: S 452 ASP cc_start: 0.7938 (p0) cc_final: 0.7696 (p0) REVERT: T 379 GLN cc_start: 0.8539 (tt0) cc_final: 0.7649 (pp30) REVERT: T 384 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8182 (tm-30) REVERT: T 404 TYR cc_start: 0.8174 (m-10) cc_final: 0.5652 (t80) REVERT: T 405 GLN cc_start: 0.8803 (pt0) cc_final: 0.8299 (pt0) REVERT: U 365 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8244 (ptpp) REVERT: U 379 GLN cc_start: 0.9130 (tt0) cc_final: 0.8172 (tm-30) REVERT: U 384 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8036 (pp20) REVERT: U 404 TYR cc_start: 0.8122 (m-10) cc_final: 0.4991 (t80) REVERT: U 415 MET cc_start: 0.8166 (ttm) cc_final: 0.7932 (ttm) REVERT: U 418 GLU cc_start: 0.5808 (mp0) cc_final: 0.5112 (mp0) REVERT: U 421 ASP cc_start: 0.8739 (p0) cc_final: 0.8485 (p0) REVERT: U 425 PHE cc_start: 0.7786 (m-10) cc_final: 0.7444 (m-10) REVERT: U 450 MET cc_start: 0.7631 (ttp) cc_final: 0.7095 (ptp) REVERT: U 503 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7291 (mp) REVERT: V 355 MET cc_start: 0.7764 (mmp) cc_final: 0.6883 (tpt) REVERT: V 377 LEU cc_start: 0.8652 (tp) cc_final: 0.8108 (pp) REVERT: V 384 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7219 (tm-30) REVERT: V 386 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8845 (tm-30) REVERT: V 418 GLU cc_start: 0.5674 (mp0) cc_final: 0.5432 (mp0) REVERT: V 450 MET cc_start: 0.7297 (ttp) cc_final: 0.5840 (ptp) REVERT: V 464 LEU cc_start: 0.9389 (mp) cc_final: 0.9002 (mp) REVERT: W 377 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8477 (pp) REVERT: W 379 GLN cc_start: 0.9047 (tt0) cc_final: 0.8173 (tm-30) REVERT: X 361 GLN cc_start: 0.9015 (tt0) cc_final: 0.8063 (tm-30) REVERT: X 384 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7696 (tm-30) REVERT: X 386 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8847 (tm-30) REVERT: X 403 TYR cc_start: 0.8991 (m-80) cc_final: 0.8585 (m-10) REVERT: X 421 ASP cc_start: 0.8469 (p0) cc_final: 0.8113 (p0) REVERT: X 427 TYR cc_start: 0.8919 (m-80) cc_final: 0.8613 (m-80) REVERT: X 450 MET cc_start: 0.8141 (ttp) cc_final: 0.6266 (ptp) REVERT: Y 379 GLN cc_start: 0.8789 (tt0) cc_final: 0.8068 (tm-30) REVERT: Y 384 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7720 (tm-30) REVERT: Y 386 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: Y 404 TYR cc_start: 0.7437 (m-10) cc_final: 0.5781 (t80) REVERT: Y 415 MET cc_start: 0.8257 (ttp) cc_final: 0.7897 (ttm) REVERT: Y 485 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8947 (p) REVERT: Y 503 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7249 (mp) REVERT: Z 358 SER cc_start: 0.7559 (m) cc_final: 0.7220 (p) REVERT: Z 365 LYS cc_start: 0.8446 (ptpp) cc_final: 0.8121 (ptpp) REVERT: Z 372 LYS cc_start: 0.9116 (pptt) cc_final: 0.8817 (pttm) REVERT: Z 379 GLN cc_start: 0.8929 (tt0) cc_final: 0.8476 (pp30) REVERT: Z 404 TYR cc_start: 0.8182 (m-10) cc_final: 0.5920 (t80) REVERT: Z 450 MET cc_start: 0.7876 (ttp) cc_final: 0.6456 (ptp) REVERT: a 355 MET cc_start: 0.8247 (mmp) cc_final: 0.7916 (tpt) REVERT: a 371 GLU cc_start: 0.8589 (tp30) cc_final: 0.8091 (tp30) REVERT: a 383 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8741 (tt) REVERT: a 450 MET cc_start: 0.7102 (ttp) cc_final: 0.6390 (ptp) REVERT: a 456 ASP cc_start: 0.8715 (t0) cc_final: 0.8366 (t0) REVERT: a 459 MET cc_start: 0.8150 (ptm) cc_final: 0.7648 (ptm) REVERT: a 503 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7466 (mp) outliers start: 101 outliers final: 77 residues processed: 709 average time/residue: 0.2901 time to fit residues: 313.1052 Evaluate side-chains 731 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 642 time to evaluate : 2.181 ------------------------------------------------------------------------------- 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 383 LEU 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 356 MET Chi-restraints excluded: chain O residue 415 MET 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 484 LEU Chi-restraints excluded: chain P residue 485 VAL 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 417 SER 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 439 ILE Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain S residue 460 THR 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 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 439 ILE 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 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 355 MET Chi-restraints excluded: chain W residue 358 SER 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 415 MET Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 441 VAL Chi-restraints excluded: chain X residue 484 LEU Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 367 LYS 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 485 VAL Chi-restraints excluded: chain Y residue 497 LEU Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 364 ASN Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 411 SER 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 370 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 0.0170 chunk 137 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 169 optimal weight: 0.0020 overall best weight: 0.5026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 413 HIS R 389 HIS ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN Y 373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18942 Z= 0.197 Angle : 0.714 11.291 25536 Z= 0.360 Chirality : 0.047 0.168 2744 Planarity : 0.005 0.062 3304 Dihedral : 4.825 19.334 2492 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.77 % Allowed : 22.32 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2240 helix: 1.16 (0.21), residues: 574 sheet: -0.91 (0.20), residues: 490 loop : -2.82 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 466 HIS 0.004 0.001 HIS T 389 PHE 0.023 0.001 PHE R 420 TYR 0.015 0.001 TYR Z 403 ARG 0.014 0.001 ARG Y 410 *********************** 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 756 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 680 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9123 (tt0) cc_final: 0.8378 (tm-30) REVERT: N 404 TYR cc_start: 0.7507 (m-10) cc_final: 0.5391 (t80) REVERT: N 405 GLN cc_start: 0.8567 (pt0) cc_final: 0.8256 (pt0) REVERT: N 415 MET cc_start: 0.8250 (ttm) cc_final: 0.7723 (ttm) REVERT: N 421 ASP cc_start: 0.8752 (p0) cc_final: 0.8499 (p0) REVERT: N 443 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7593 (mp10) REVERT: N 450 MET cc_start: 0.7803 (ttp) cc_final: 0.6460 (ptp) REVERT: N 503 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7353 (mp) REVERT: O 356 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7464 (tmm) REVERT: O 366 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7911 (tm-30) REVERT: O 379 GLN cc_start: 0.8990 (tt0) cc_final: 0.8502 (tm-30) REVERT: O 386 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8970 (tm-30) REVERT: O 404 TYR cc_start: 0.7096 (m-10) cc_final: 0.5768 (t80) REVERT: O 450 MET cc_start: 0.7770 (ttp) cc_final: 0.6405 (ptp) REVERT: P 358 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.8056 (t) REVERT: P 367 LYS cc_start: 0.8613 (ptmt) cc_final: 0.8185 (pttm) REVERT: P 379 GLN cc_start: 0.8736 (tt0) cc_final: 0.7900 (tm-30) REVERT: P 384 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7708 (tm-30) REVERT: P 403 TYR cc_start: 0.9115 (m-80) cc_final: 0.8909 (m-10) REVERT: P 404 TYR cc_start: 0.7297 (m-10) cc_final: 0.5786 (t80) REVERT: P 415 MET cc_start: 0.8085 (ttp) cc_final: 0.7517 (ttm) REVERT: P 418 GLU cc_start: 0.4996 (mp0) cc_final: 0.4351 (mp0) REVERT: P 421 ASP cc_start: 0.8597 (p0) cc_final: 0.8373 (p0) REVERT: P 422 ASP cc_start: 0.9208 (p0) cc_final: 0.8622 (p0) REVERT: P 464 LEU cc_start: 0.9119 (mp) cc_final: 0.8654 (mt) REVERT: Q 403 TYR cc_start: 0.9076 (m-10) cc_final: 0.8510 (m-10) REVERT: Q 422 ASP cc_start: 0.9026 (p0) cc_final: 0.8823 (p0) REVERT: Q 427 TYR cc_start: 0.9015 (m-80) cc_final: 0.8594 (m-80) REVERT: Q 450 MET cc_start: 0.8728 (ppp) cc_final: 0.7684 (ptp) REVERT: Q 459 MET cc_start: 0.8046 (mtp) cc_final: 0.7673 (mtp) REVERT: R 375 ILE cc_start: 0.8944 (mm) cc_final: 0.8670 (pt) REVERT: R 384 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8098 (tm-30) REVERT: R 385 THR cc_start: 0.9304 (m) cc_final: 0.9033 (t) REVERT: R 386 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8511 (pp30) REVERT: R 390 ASN cc_start: 0.8564 (t0) cc_final: 0.8356 (t0) REVERT: R 418 GLU cc_start: 0.5638 (mp0) cc_final: 0.5353 (mp0) REVERT: R 497 LEU cc_start: 0.7274 (mp) cc_final: 0.7036 (mt) REVERT: S 367 LYS cc_start: 0.8161 (ptmt) cc_final: 0.7675 (pttm) REVERT: S 372 LYS cc_start: 0.8617 (pptt) cc_final: 0.8058 (mtpt) REVERT: S 373 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7206 (tp40) REVERT: S 418 GLU cc_start: 0.6283 (mp0) cc_final: 0.5879 (mp0) REVERT: S 436 GLN cc_start: 0.9427 (tp40) cc_final: 0.6380 (pm20) REVERT: T 367 LYS cc_start: 0.8651 (ptmt) cc_final: 0.8032 (pttm) REVERT: T 379 GLN cc_start: 0.8649 (tt0) cc_final: 0.7829 (pp30) REVERT: T 384 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8052 (tm-30) REVERT: T 404 TYR cc_start: 0.8147 (m-10) cc_final: 0.5675 (t80) REVERT: T 405 GLN cc_start: 0.8721 (pt0) cc_final: 0.8255 (pt0) REVERT: U 365 LYS cc_start: 0.8583 (ptpp) cc_final: 0.8269 (ptpt) REVERT: U 379 GLN cc_start: 0.9125 (tt0) cc_final: 0.8182 (tm-30) REVERT: U 384 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7893 (tm-30) REVERT: U 404 TYR cc_start: 0.8177 (m-10) cc_final: 0.5767 (t80) REVERT: U 415 MET cc_start: 0.8181 (ttm) cc_final: 0.7930 (ttm) REVERT: U 425 PHE cc_start: 0.7745 (m-10) cc_final: 0.7406 (m-10) REVERT: U 450 MET cc_start: 0.7645 (ttp) cc_final: 0.7218 (ptp) REVERT: U 503 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7400 (mp) REVERT: V 355 MET cc_start: 0.7750 (mmp) cc_final: 0.6862 (tpt) REVERT: V 377 LEU cc_start: 0.8662 (tp) cc_final: 0.8119 (pp) REVERT: V 384 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7222 (tm-30) REVERT: V 386 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8846 (tm-30) REVERT: V 418 GLU cc_start: 0.5728 (mp0) cc_final: 0.5486 (mp0) REVERT: V 450 MET cc_start: 0.7243 (ttp) cc_final: 0.5839 (ptp) REVERT: V 464 LEU cc_start: 0.9286 (mp) cc_final: 0.8879 (mp) REVERT: W 373 GLN cc_start: 0.8365 (tp-100) cc_final: 0.8140 (tp40) REVERT: W 377 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8500 (pp) REVERT: W 379 GLN cc_start: 0.9054 (tt0) cc_final: 0.8149 (tm-30) REVERT: W 425 PHE cc_start: 0.9016 (m-80) cc_final: 0.8810 (m-80) REVERT: X 361 GLN cc_start: 0.9005 (tt0) cc_final: 0.8050 (tm-30) REVERT: X 384 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7658 (tm-30) REVERT: X 386 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8825 (tm-30) REVERT: X 403 TYR cc_start: 0.8907 (m-80) cc_final: 0.8494 (m-10) REVERT: X 421 ASP cc_start: 0.8458 (p0) cc_final: 0.8092 (p0) REVERT: X 427 TYR cc_start: 0.8902 (m-80) cc_final: 0.8609 (m-80) REVERT: X 450 MET cc_start: 0.8093 (ttp) cc_final: 0.6274 (ptp) REVERT: Y 379 GLN cc_start: 0.8724 (tt0) cc_final: 0.8002 (tm-30) REVERT: Y 384 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7639 (tm-30) REVERT: Y 386 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: Y 404 TYR cc_start: 0.7442 (m-10) cc_final: 0.5714 (t80) REVERT: Y 415 MET cc_start: 0.8305 (ttp) cc_final: 0.7917 (ttm) REVERT: Y 485 VAL cc_start: 0.9266 (OUTLIER) cc_final: 0.8997 (p) REVERT: Y 503 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7235 (mp) REVERT: Z 358 SER cc_start: 0.8102 (m) cc_final: 0.7632 (p) REVERT: Z 365 LYS cc_start: 0.8421 (ptpp) cc_final: 0.7940 (ptpp) REVERT: Z 372 LYS cc_start: 0.9122 (pptt) cc_final: 0.8829 (pttm) REVERT: Z 379 GLN cc_start: 0.8934 (tt0) cc_final: 0.8467 (pp30) REVERT: Z 404 TYR cc_start: 0.7341 (m-10) cc_final: 0.6097 (t80) REVERT: Z 450 MET cc_start: 0.7778 (ttp) cc_final: 0.6335 (ptp) REVERT: a 355 MET cc_start: 0.8380 (mmp) cc_final: 0.8072 (tpt) REVERT: a 371 GLU cc_start: 0.8617 (tp30) cc_final: 0.8139 (tp30) REVERT: a 383 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8656 (tt) REVERT: a 386 GLN cc_start: 0.9221 (tm-30) cc_final: 0.9008 (tm-30) REVERT: a 450 MET cc_start: 0.7036 (ttp) cc_final: 0.6362 (ptp) REVERT: a 456 ASP cc_start: 0.8669 (t0) cc_final: 0.8347 (t0) REVERT: a 459 MET cc_start: 0.8367 (ptm) cc_final: 0.7927 (ptm) REVERT: a 464 LEU cc_start: 0.9431 (mp) cc_final: 0.9112 (mp) outliers start: 76 outliers final: 54 residues processed: 712 average time/residue: 0.2828 time to fit residues: 305.4214 Evaluate side-chains 716 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 653 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 484 LEU Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 356 MET Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 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 484 LEU 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 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 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 439 ILE 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 370 GLU 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 484 LEU Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 355 MET Chi-restraints excluded: chain W residue 358 SER Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 449 SER Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 484 LEU Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 386 GLN 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 370 GLU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 411 SER 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 448 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.7980 chunk 206 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 190 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN R 364 ASN ** R 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 443 GLN X 373 GLN Y 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5173 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= 0.216 Angle : 0.735 12.428 25536 Z= 0.372 Chirality : 0.048 0.170 2744 Planarity : 0.005 0.061 3304 Dihedral : 4.879 19.327 2492 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.72 % Allowed : 23.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2240 helix: 1.19 (0.21), residues: 574 sheet: -0.78 (0.21), residues: 490 loop : -2.79 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 466 HIS 0.003 0.001 HIS T 389 PHE 0.023 0.001 PHE R 420 TYR 0.029 0.001 TYR N 404 ARG 0.015 0.001 ARG Z 410 *********************** 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 740 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 665 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9140 (tt0) cc_final: 0.8393 (tm-30) REVERT: N 404 TYR cc_start: 0.8037 (m-10) cc_final: 0.5511 (t80) REVERT: N 415 MET cc_start: 0.8259 (ttm) cc_final: 0.7762 (ttm) REVERT: N 421 ASP cc_start: 0.8739 (p0) cc_final: 0.7984 (p0) REVERT: N 450 MET cc_start: 0.7832 (ttp) cc_final: 0.6441 (ptp) REVERT: N 503 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7182 (mp) REVERT: O 356 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7367 (tmm) REVERT: O 379 GLN cc_start: 0.8987 (tt0) cc_final: 0.8501 (tm-30) REVERT: O 386 GLN cc_start: 0.9319 (tm-30) cc_final: 0.9017 (tm-30) REVERT: O 404 TYR cc_start: 0.6889 (m-10) cc_final: 0.5692 (t80) REVERT: O 450 MET cc_start: 0.7837 (ttp) cc_final: 0.6139 (ptp) REVERT: O 503 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.7549 (mp) REVERT: P 379 GLN cc_start: 0.8717 (tt0) cc_final: 0.7920 (tm-30) REVERT: P 384 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7960 (pp20) REVERT: P 403 TYR cc_start: 0.9155 (m-80) cc_final: 0.8918 (m-10) REVERT: P 404 TYR cc_start: 0.6537 (m-10) cc_final: 0.5481 (t80) REVERT: P 418 GLU cc_start: 0.4994 (mp0) cc_final: 0.4374 (mp0) REVERT: P 464 LEU cc_start: 0.9133 (mp) cc_final: 0.8676 (mt) REVERT: P 485 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.8963 (p) REVERT: P 503 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7365 (mp) REVERT: Q 403 TYR cc_start: 0.8996 (m-10) cc_final: 0.8706 (m-10) REVERT: Q 422 ASP cc_start: 0.9008 (p0) cc_final: 0.8796 (p0) REVERT: Q 427 TYR cc_start: 0.8991 (m-80) cc_final: 0.8576 (m-80) REVERT: Q 459 MET cc_start: 0.8081 (mtp) cc_final: 0.7633 (mtp) REVERT: R 356 MET cc_start: 0.6451 (tpp) cc_final: 0.6069 (tpp) REVERT: R 370 GLU cc_start: 0.8927 (tp30) cc_final: 0.8719 (mm-30) REVERT: R 384 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8161 (tm-30) REVERT: R 385 THR cc_start: 0.9218 (m) cc_final: 0.8889 (t) REVERT: R 386 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8532 (pp30) REVERT: R 418 GLU cc_start: 0.5626 (mp0) cc_final: 0.5324 (mp0) REVERT: R 460 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8773 (p) REVERT: R 497 LEU cc_start: 0.7379 (mp) cc_final: 0.7115 (mt) REVERT: S 367 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7699 (pttm) REVERT: S 372 LYS cc_start: 0.8651 (pptt) cc_final: 0.8094 (mtpt) REVERT: S 384 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8508 (tm-30) REVERT: S 418 GLU cc_start: 0.4713 (mp0) cc_final: 0.4383 (mp0) REVERT: S 436 GLN cc_start: 0.9439 (tp40) cc_final: 0.6382 (pm20) REVERT: T 367 LYS cc_start: 0.8702 (ptmt) cc_final: 0.8038 (pttm) REVERT: T 372 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8419 (pttp) REVERT: T 379 GLN cc_start: 0.8633 (tt0) cc_final: 0.7731 (pp30) REVERT: T 384 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8126 (tm-30) REVERT: T 405 GLN cc_start: 0.8746 (pt0) cc_final: 0.8484 (pt0) REVERT: T 503 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7552 (mp) REVERT: U 365 LYS cc_start: 0.8710 (ptpp) cc_final: 0.8324 (ptpt) REVERT: U 379 GLN cc_start: 0.9167 (tt0) cc_final: 0.8180 (tm-30) REVERT: U 384 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7941 (tm-30) REVERT: U 404 TYR cc_start: 0.7255 (m-10) cc_final: 0.6027 (t80) REVERT: U 415 MET cc_start: 0.8210 (ttm) cc_final: 0.7967 (ttm) REVERT: U 425 PHE cc_start: 0.7714 (m-10) cc_final: 0.7334 (m-10) REVERT: U 450 MET cc_start: 0.7487 (ttp) cc_final: 0.6992 (ptp) REVERT: U 503 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7329 (mp) REVERT: V 355 MET cc_start: 0.7752 (mmp) cc_final: 0.6873 (tpt) REVERT: V 384 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7260 (tm-30) REVERT: V 386 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8848 (tm-30) REVERT: V 418 GLU cc_start: 0.5700 (mp0) cc_final: 0.5459 (mp0) REVERT: V 450 MET cc_start: 0.7262 (ttp) cc_final: 0.5845 (ptp) REVERT: V 464 LEU cc_start: 0.9256 (mp) cc_final: 0.8853 (mp) REVERT: W 372 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8612 (pttm) REVERT: W 377 LEU cc_start: 0.9005 (tt) cc_final: 0.8472 (pp) REVERT: W 379 GLN cc_start: 0.9053 (tt0) cc_final: 0.8180 (tm-30) REVERT: W 404 TYR cc_start: 0.7033 (m-80) cc_final: 0.6689 (m-80) REVERT: X 361 GLN cc_start: 0.9026 (tt0) cc_final: 0.8072 (tm-30) REVERT: X 384 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7746 (tm-30) REVERT: X 386 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8831 (tm-30) REVERT: X 403 TYR cc_start: 0.8909 (m-80) cc_final: 0.8656 (m-10) REVERT: X 421 ASP cc_start: 0.8476 (p0) cc_final: 0.7979 (p0) REVERT: X 427 TYR cc_start: 0.8884 (m-80) cc_final: 0.8643 (m-80) REVERT: X 450 MET cc_start: 0.8140 (ttp) cc_final: 0.6240 (ptp) REVERT: Y 379 GLN cc_start: 0.8739 (tt0) cc_final: 0.8062 (tm-30) REVERT: Y 384 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7650 (tm-30) REVERT: Y 386 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: Y 404 TYR cc_start: 0.7458 (m-10) cc_final: 0.5953 (t80) REVERT: Y 485 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8956 (p) REVERT: Y 503 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7262 (mp) REVERT: Z 358 SER cc_start: 0.8153 (m) cc_final: 0.7878 (t) REVERT: Z 365 LYS cc_start: 0.8503 (ptpp) cc_final: 0.8197 (ptpt) REVERT: Z 372 LYS cc_start: 0.9125 (pptt) cc_final: 0.8840 (pttm) REVERT: Z 379 GLN cc_start: 0.8940 (tt0) cc_final: 0.8484 (pp30) REVERT: Z 404 TYR cc_start: 0.7192 (m-10) cc_final: 0.5826 (t80) REVERT: Z 450 MET cc_start: 0.7811 (ttp) cc_final: 0.6393 (ptp) REVERT: a 355 MET cc_start: 0.8226 (mmp) cc_final: 0.7863 (tpt) REVERT: a 371 GLU cc_start: 0.8621 (tp30) cc_final: 0.8066 (tp30) REVERT: a 383 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8629 (tt) REVERT: a 386 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8946 (tm-30) REVERT: a 450 MET cc_start: 0.7092 (ttp) cc_final: 0.6346 (ptp) REVERT: a 456 ASP cc_start: 0.8677 (t0) cc_final: 0.8340 (t0) REVERT: a 459 MET cc_start: 0.8310 (ptm) cc_final: 0.8055 (ptm) REVERT: a 464 LEU cc_start: 0.9405 (mp) cc_final: 0.9085 (mp) REVERT: a 503 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7532 (mp) outliers start: 75 outliers final: 54 residues processed: 701 average time/residue: 0.2857 time to fit residues: 304.3982 Evaluate side-chains 721 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 653 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 356 MET Chi-restraints excluded: chain O residue 372 LYS 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 484 LEU Chi-restraints excluded: chain P residue 485 VAL 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 370 GLU Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 388 VAL 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 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 439 ILE 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 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 484 LEU Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 355 MET Chi-restraints excluded: chain W residue 358 SER Chi-restraints excluded: chain W residue 372 LYS Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Y residue 370 GLU 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 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 370 GLU Chi-restraints excluded: chain Z residue 383 LEU 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 370 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 223 optimal weight: 0.9980 chunk 205 optimal weight: 0.3980 chunk 177 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN ** R 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN Y 373 GLN Y 405 GLN Z 461 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18942 Z= 0.211 Angle : 0.759 13.200 25536 Z= 0.382 Chirality : 0.048 0.226 2744 Planarity : 0.005 0.066 3304 Dihedral : 4.809 18.649 2492 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.67 % Allowed : 24.26 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2240 helix: 1.21 (0.21), residues: 574 sheet: -0.68 (0.21), residues: 490 loop : -2.78 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 466 HIS 0.003 0.001 HIS T 389 PHE 0.023 0.001 PHE R 420 TYR 0.028 0.001 TYR N 404 ARG 0.016 0.001 ARG Z 410 ********************** 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 747 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 673 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9151 (tt0) cc_final: 0.8352 (tm-30) REVERT: N 404 TYR cc_start: 0.8033 (m-10) cc_final: 0.5300 (t80) REVERT: N 405 GLN cc_start: 0.8258 (pt0) cc_final: 0.7742 (pt0) REVERT: N 415 MET cc_start: 0.8264 (ttm) cc_final: 0.7906 (ttm) REVERT: N 421 ASP cc_start: 0.8696 (p0) cc_final: 0.7929 (p0) REVERT: N 450 MET cc_start: 0.7805 (ttp) cc_final: 0.6404 (ptp) REVERT: N 503 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7258 (mp) REVERT: O 379 GLN cc_start: 0.9044 (tt0) cc_final: 0.8584 (pp30) REVERT: O 386 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8986 (tm-30) REVERT: O 404 TYR cc_start: 0.6901 (m-10) cc_final: 0.6046 (t80) REVERT: O 450 MET cc_start: 0.7799 (ttp) cc_final: 0.6117 (ptp) REVERT: O 503 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7491 (mp) REVERT: P 379 GLN cc_start: 0.8769 (tt0) cc_final: 0.7931 (tm-30) REVERT: P 384 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7964 (pp20) REVERT: P 404 TYR cc_start: 0.6512 (m-10) cc_final: 0.5530 (t80) REVERT: P 415 MET cc_start: 0.8268 (mtp) cc_final: 0.7927 (mmm) REVERT: P 418 GLU cc_start: 0.5021 (mp0) cc_final: 0.4440 (mp0) REVERT: P 464 LEU cc_start: 0.9078 (mp) cc_final: 0.8643 (mt) REVERT: P 503 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7355 (mp) REVERT: Q 403 TYR cc_start: 0.9076 (m-10) cc_final: 0.8573 (m-10) REVERT: Q 421 ASP cc_start: 0.8279 (p0) cc_final: 0.7971 (p0) REVERT: Q 422 ASP cc_start: 0.9018 (p0) cc_final: 0.8815 (p0) REVERT: Q 427 TYR cc_start: 0.9001 (m-80) cc_final: 0.8580 (m-80) REVERT: Q 459 MET cc_start: 0.8069 (mtp) cc_final: 0.7632 (mtp) REVERT: R 356 MET cc_start: 0.6459 (tpp) cc_final: 0.6098 (tpp) REVERT: R 384 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8161 (tm-30) REVERT: R 385 THR cc_start: 0.9221 (m) cc_final: 0.8919 (t) REVERT: R 386 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8535 (pp30) REVERT: R 481 ASP cc_start: 0.7573 (p0) cc_final: 0.6826 (m-30) REVERT: R 497 LEU cc_start: 0.7409 (mp) cc_final: 0.7159 (mt) REVERT: S 367 LYS cc_start: 0.8489 (ptmt) cc_final: 0.7903 (pttm) REVERT: S 372 LYS cc_start: 0.8665 (pptt) cc_final: 0.8101 (mtpt) REVERT: S 373 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7232 (tp40) REVERT: S 384 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8545 (tm-30) REVERT: S 410 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7334 (ptp-110) REVERT: S 418 GLU cc_start: 0.5869 (mp0) cc_final: 0.5405 (mp0) REVERT: S 436 GLN cc_start: 0.9436 (tp40) cc_final: 0.6366 (pm20) REVERT: T 367 LYS cc_start: 0.8687 (ptmt) cc_final: 0.8029 (pttm) REVERT: T 379 GLN cc_start: 0.8637 (tt0) cc_final: 0.7902 (pp30) REVERT: T 384 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8180 (tm-30) REVERT: T 405 GLN cc_start: 0.8720 (pt0) cc_final: 0.8481 (pt0) REVERT: T 503 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7562 (mp) REVERT: U 365 LYS cc_start: 0.8664 (ptpp) cc_final: 0.8263 (ptpt) REVERT: U 379 GLN cc_start: 0.9165 (tt0) cc_final: 0.8359 (tm-30) REVERT: U 384 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7984 (pp20) REVERT: U 404 TYR cc_start: 0.7060 (m-10) cc_final: 0.5985 (t80) REVERT: U 425 PHE cc_start: 0.7761 (m-10) cc_final: 0.7339 (m-10) REVERT: U 450 MET cc_start: 0.7463 (ttp) cc_final: 0.6971 (ptp) REVERT: U 503 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7391 (mp) REVERT: V 355 MET cc_start: 0.8002 (mmp) cc_final: 0.7138 (tpt) REVERT: V 377 LEU cc_start: 0.8695 (tp) cc_final: 0.8134 (pp) REVERT: V 384 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7271 (tm-30) REVERT: V 386 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8852 (tm-30) REVERT: V 418 GLU cc_start: 0.5781 (mp0) cc_final: 0.5555 (mp0) REVERT: V 450 MET cc_start: 0.7329 (ttp) cc_final: 0.5992 (ptp) REVERT: V 464 LEU cc_start: 0.9186 (mp) cc_final: 0.8777 (mp) REVERT: W 377 LEU cc_start: 0.9012 (tt) cc_final: 0.8495 (pp) REVERT: W 379 GLN cc_start: 0.9048 (tt0) cc_final: 0.8205 (tm-30) REVERT: X 361 GLN cc_start: 0.9031 (tt0) cc_final: 0.8072 (tm-30) REVERT: X 384 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7675 (tm-30) REVERT: X 386 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8809 (tm-30) REVERT: X 403 TYR cc_start: 0.8902 (m-80) cc_final: 0.8510 (m-10) REVERT: X 421 ASP cc_start: 0.8464 (p0) cc_final: 0.7881 (p0) REVERT: X 450 MET cc_start: 0.8030 (ttp) cc_final: 0.6256 (ptp) REVERT: X 452 ASP cc_start: 0.8540 (p0) cc_final: 0.8054 (m-30) REVERT: Y 371 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8368 (tp30) REVERT: Y 372 LYS cc_start: 0.9072 (pttm) cc_final: 0.8758 (ptpt) REVERT: Y 379 GLN cc_start: 0.8757 (tt0) cc_final: 0.8030 (tm-30) REVERT: Y 404 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.5872 (t80) REVERT: Y 485 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8958 (p) REVERT: Y 503 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7257 (mp) REVERT: Z 358 SER cc_start: 0.8152 (m) cc_final: 0.6699 (t) REVERT: Z 371 GLU cc_start: 0.8998 (tp30) cc_final: 0.8672 (mm-30) REVERT: Z 372 LYS cc_start: 0.9120 (pptt) cc_final: 0.8867 (pttm) REVERT: Z 379 GLN cc_start: 0.8931 (tt0) cc_final: 0.8470 (pp30) REVERT: Z 404 TYR cc_start: 0.7198 (m-10) cc_final: 0.5853 (t80) REVERT: Z 450 MET cc_start: 0.7784 (ttp) cc_final: 0.6331 (ptp) REVERT: a 355 MET cc_start: 0.8379 (mmp) cc_final: 0.8039 (tpt) REVERT: a 371 GLU cc_start: 0.8619 (tp30) cc_final: 0.8051 (tp30) REVERT: a 383 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8588 (tt) REVERT: a 450 MET cc_start: 0.7083 (ttp) cc_final: 0.6338 (ptp) REVERT: a 456 ASP cc_start: 0.8692 (t0) cc_final: 0.8338 (t0) REVERT: a 464 LEU cc_start: 0.9355 (mp) cc_final: 0.9016 (mp) REVERT: a 503 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7524 (mp) outliers start: 74 outliers final: 51 residues processed: 706 average time/residue: 0.2977 time to fit residues: 319.8917 Evaluate side-chains 716 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 654 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 370 GLU 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 484 LEU Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain S residue 370 GLU Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 410 ARG 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 439 ILE 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 370 GLU 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 484 LEU Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 355 MET Chi-restraints excluded: chain W residue 358 SER Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 449 SER Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 404 TYR 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 383 LEU Chi-restraints excluded: chain Z residue 411 SER Chi-restraints excluded: chain Z residue 484 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 3.9990 chunk 189 optimal weight: 0.4980 chunk 54 optimal weight: 0.0050 chunk 163 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 182 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN Y 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098535 restraints weight = 44560.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100247 restraints weight = 20933.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101274 restraints weight = 12506.675| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18942 Z= 0.214 Angle : 0.770 13.225 25536 Z= 0.387 Chirality : 0.048 0.259 2744 Planarity : 0.005 0.063 3304 Dihedral : 4.773 20.624 2492 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.27 % Allowed : 24.75 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2240 helix: 1.21 (0.21), residues: 574 sheet: -0.60 (0.21), residues: 490 loop : -2.75 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 466 HIS 0.004 0.001 HIS O 413 PHE 0.025 0.001 PHE X 420 TYR 0.022 0.001 TYR N 404 ARG 0.015 0.001 ARG Z 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5613.59 seconds wall clock time: 101 minutes 20.13 seconds (6080.13 seconds total)