Starting phenix.real_space_refine on Sat Dec 28 08:09:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6e_13227/12_2024/7p6e_13227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6e_13227/12_2024/7p6e_13227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p6e_13227/12_2024/7p6e_13227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6e_13227/12_2024/7p6e_13227.map" model { file = "/net/cci-nas-00/data/ceres_data/7p6e_13227/12_2024/7p6e_13227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6e_13227/12_2024/7p6e_13227.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 20 5.16 5 C 5050 2.51 5 N 1500 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8090 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F, I, J, Q, R Time building chain proxies: 3.02, per 1000 atoms: 0.37 Number of scatterers: 8090 At special positions: 0 Unit cell: (182.85, 120.75, 40.25, 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 20 16.00 O 1520 8.00 N 1500 7.00 C 5050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 275 through 279 removed outlier: 6.773A pdb=" N GLN A 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN C 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN C 276 " --> pdb=" O ILE Q 277 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASN Q 279 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 278 " --> pdb=" O ASN Q 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 285 through 287 removed outlier: 8.761A pdb=" N SER E 285 " --> pdb=" O ASN I 286 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N SER A 285 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 287 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL Q 287 " --> pdb=" O ASN C 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 306 through 310 removed outlier: 6.662A pdb=" N GLN E 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR I 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL E 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 314 through 315 removed outlier: 6.094A pdb=" N ASP A 314 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP C 314 " --> pdb=" O LEU Q 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 318 through 322 removed outlier: 6.611A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 318 " --> pdb=" O THR Q 319 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LYS Q 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER C 320 " --> pdb=" O LYS Q 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 336 through 341 removed outlier: 6.410A pdb=" N VAL C 337 " --> pdb=" O GLU Q 338 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LYS Q 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL C 339 " --> pdb=" O LYS Q 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 377 Processing sheet with id=AA8, first strand: chain 'J' and resid 275 through 279 removed outlier: 6.714A pdb=" N VAL F 275 " --> pdb=" O GLN J 276 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE J 278 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE F 277 " --> pdb=" O ILE J 278 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN B 276 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ASN D 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 278 " --> pdb=" O ASN D 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 285 through 287 removed outlier: 8.703A pdb=" N SER F 285 " --> pdb=" O ASN J 286 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N SER B 285 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL D 287 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL R 287 " --> pdb=" O ASN D 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 306 through 310 removed outlier: 6.698A pdb=" N GLN F 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR J 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL F 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 314 through 315 removed outlier: 6.120A pdb=" N ASP B 314 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP D 314 " --> pdb=" O LEU R 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 318 through 322 removed outlier: 6.448A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 318 " --> pdb=" O THR R 319 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LYS R 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER D 320 " --> pdb=" O LYS R 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 336 through 341 removed outlier: 6.301A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 337 " --> pdb=" O GLU R 338 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LYS R 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL D 339 " --> pdb=" O LYS R 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.140A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL D 350 " --> pdb=" O GLN R 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 376 through 377 removed outlier: 6.738A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 376 " --> pdb=" O THR R 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 351 removed outlier: 6.173A pdb=" N VAL C 350 " --> pdb=" O GLN Q 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AB9, first strand: chain 'F' and resid 350 through 351 Processing sheet with id=AC1, first strand: chain 'F' and resid 376 through 377 85 hydrogen bonds defined for protein. 252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2575 1.33 - 1.45: 675 1.45 - 1.56: 4920 1.56 - 1.68: 0 1.68 - 1.79: 20 Bond restraints: 8190 Sorted by residual: bond pdb=" CA ASN J 359 " pdb=" CB ASN J 359 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.76e-02 3.23e+03 4.89e+00 bond pdb=" CA ASN D 359 " pdb=" CB ASN D 359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.76e-02 3.23e+03 4.78e+00 bond pdb=" CA ASN E 359 " pdb=" CB ASN E 359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.76e-02 3.23e+03 4.65e+00 bond pdb=" CA ASN A 359 " pdb=" CB ASN A 359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.76e-02 3.23e+03 4.65e+00 bond pdb=" CA ASN Q 359 " pdb=" CB ASN Q 359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.76e-02 3.23e+03 4.64e+00 ... (remaining 8185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 9729 1.39 - 2.77: 975 2.77 - 4.16: 156 4.16 - 5.55: 60 5.55 - 6.93: 20 Bond angle restraints: 10940 Sorted by residual: angle pdb=" N ASP B 295 " pdb=" CA ASP B 295 " pdb=" C ASP B 295 " ideal model delta sigma weight residual 108.13 115.06 -6.93 1.72e+00 3.38e-01 1.63e+01 angle pdb=" N ASP E 295 " pdb=" CA ASP E 295 " pdb=" C ASP E 295 " ideal model delta sigma weight residual 108.13 115.04 -6.91 1.72e+00 3.38e-01 1.62e+01 angle pdb=" N ASP I 295 " pdb=" CA ASP I 295 " pdb=" C ASP I 295 " ideal model delta sigma weight residual 108.13 115.02 -6.89 1.72e+00 3.38e-01 1.60e+01 angle pdb=" N ASP R 295 " pdb=" CA ASP R 295 " pdb=" C ASP R 295 " ideal model delta sigma weight residual 108.13 115.02 -6.89 1.72e+00 3.38e-01 1.60e+01 angle pdb=" N ASP A 295 " pdb=" CA ASP A 295 " pdb=" C ASP A 295 " ideal model delta sigma weight residual 108.13 115.02 -6.89 1.72e+00 3.38e-01 1.60e+01 ... (remaining 10935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.54: 4200 7.54 - 15.09: 720 15.09 - 22.63: 100 22.63 - 30.17: 40 30.17 - 37.71: 40 Dihedral angle restraints: 5100 sinusoidal: 2160 harmonic: 2940 Sorted by residual: dihedral pdb=" CA PRO R 301 " pdb=" C PRO R 301 " pdb=" N GLY R 302 " pdb=" CA GLY R 302 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PRO C 301 " pdb=" C PRO C 301 " pdb=" N GLY C 302 " pdb=" CA GLY C 302 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PRO A 301 " pdb=" C PRO A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 990 0.073 - 0.146: 240 0.146 - 0.220: 10 0.220 - 0.293: 0 0.293 - 0.366: 10 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CB ILE R 360 " pdb=" CA ILE R 360 " pdb=" CG1 ILE R 360 " pdb=" CG2 ILE R 360 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB ILE J 360 " pdb=" CA ILE J 360 " pdb=" CG1 ILE J 360 " pdb=" CG2 ILE J 360 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE I 360 " pdb=" CA ILE I 360 " pdb=" CG1 ILE I 360 " pdb=" CG2 ILE I 360 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1247 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 300 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO E 301 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 301 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 301 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Q 300 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO Q 301 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO Q 301 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO Q 301 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 300 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO R 301 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " -0.032 5.00e-02 4.00e+02 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2457 2.87 - 3.37: 6930 3.37 - 3.88: 13405 3.88 - 4.39: 13511 4.39 - 4.90: 28040 Nonbonded interactions: 64343 Sorted by model distance: nonbonded pdb=" OD2 ASP D 295 " pdb=" NZ LYS D 311 " model vdw 2.358 3.120 nonbonded pdb=" OD2 ASP J 295 " pdb=" NZ LYS J 311 " model vdw 2.358 3.120 nonbonded pdb=" OD2 ASP E 295 " pdb=" NZ LYS E 311 " model vdw 2.359 3.120 nonbonded pdb=" OD2 ASP A 295 " pdb=" NZ LYS A 311 " model vdw 2.359 3.120 nonbonded pdb=" OD2 ASP Q 295 " pdb=" NZ LYS Q 311 " model vdw 2.359 3.120 ... (remaining 64338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.910 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.009 0.066 8190 Z= 0.582 Angle : 0.957 6.934 10940 Z= 0.533 Chirality : 0.065 0.366 1250 Planarity : 0.008 0.057 1390 Dihedral : 8.257 37.712 3200 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.80 (0.18), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.14), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS J 299 PHE 0.015 0.006 PHE J 378 TYR 0.010 0.006 TYR I 310 ARG 0.001 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.970 Fit side-chains REVERT: A 281 LYS cc_start: 0.8489 (tmtt) cc_final: 0.8174 (ttmt) REVERT: A 295 ASP cc_start: 0.8838 (p0) cc_final: 0.8510 (p0) REVERT: B 281 LYS cc_start: 0.8663 (tmtt) cc_final: 0.8352 (ttmt) REVERT: C 321 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7223 (tmtt) REVERT: D 321 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7188 (tmtt) REVERT: E 281 LYS cc_start: 0.8845 (tmtt) cc_final: 0.8429 (ttmt) REVERT: E 372 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7146 (mp0) REVERT: F 281 LYS cc_start: 0.8767 (tmtt) cc_final: 0.8370 (ttmt) REVERT: F 372 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7167 (mp0) REVERT: I 281 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8559 (tptp) REVERT: I 321 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7410 (pptt) REVERT: I 348 ASP cc_start: 0.8625 (t0) cc_final: 0.7856 (p0) REVERT: I 372 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7246 (mp0) REVERT: J 281 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8663 (ttpt) REVERT: J 321 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7357 (pptt) REVERT: J 348 ASP cc_start: 0.8631 (t0) cc_final: 0.7846 (p0) REVERT: J 372 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6843 (mp0) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1970 time to fit residues: 76.6388 Evaluate side-chains 127 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 336 GLN J 374 HIS Q 286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8190 Z= 0.343 Angle : 0.666 8.049 10940 Z= 0.335 Chirality : 0.051 0.143 1250 Planarity : 0.005 0.041 1390 Dihedral : 5.136 13.079 1060 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.79 % Allowed : 9.79 % Favored : 88.42 % 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: -4.57 (0.19), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.15), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 362 PHE 0.013 0.003 PHE A 346 TYR 0.026 0.003 TYR I 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8780 (tmtt) cc_final: 0.8368 (ttmt) REVERT: B 281 LYS cc_start: 0.8795 (tmtt) cc_final: 0.8393 (ttmt) REVERT: B 283 ASP cc_start: 0.7878 (t0) cc_final: 0.7580 (t0) REVERT: C 362 HIS cc_start: 0.7943 (t-170) cc_final: 0.7433 (t-90) REVERT: D 338 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7434 (tm-30) REVERT: D 362 HIS cc_start: 0.7944 (t-170) cc_final: 0.7471 (t-90) REVERT: E 372 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7058 (mp0) REVERT: F 362 HIS cc_start: 0.7794 (t-90) cc_final: 0.7533 (t-90) REVERT: F 372 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7117 (mp0) REVERT: I 281 LYS cc_start: 0.8866 (tmtt) cc_final: 0.8641 (tptp) REVERT: I 348 ASP cc_start: 0.8577 (t0) cc_final: 0.8037 (p0) REVERT: J 281 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8645 (tptp) REVERT: J 348 ASP cc_start: 0.8587 (t0) cc_final: 0.8046 (p0) REVERT: J 372 GLU cc_start: 0.7797 (mt-10) cc_final: 0.6876 (mp0) REVERT: Q 356 SER cc_start: 0.8525 (m) cc_final: 0.8239 (p) outliers start: 17 outliers final: 14 residues processed: 186 average time/residue: 0.1934 time to fit residues: 49.3511 Evaluate side-chains 127 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN D 286 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 8190 Z= 0.319 Angle : 0.655 7.936 10940 Z= 0.321 Chirality : 0.051 0.145 1250 Planarity : 0.004 0.037 1390 Dihedral : 4.966 13.059 1060 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.58 % Allowed : 12.74 % Favored : 83.68 % 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: -4.32 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.15), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.014 0.003 PHE J 378 TYR 0.018 0.003 TYR I 310 ARG 0.002 0.000 ARG Q 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8830 (tmtt) cc_final: 0.8407 (ttmt) REVERT: A 338 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7511 (tm-30) REVERT: B 281 LYS cc_start: 0.8847 (tmtt) cc_final: 0.8430 (ttmt) REVERT: B 283 ASP cc_start: 0.7936 (t0) cc_final: 0.7657 (t0) REVERT: B 338 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7474 (tm-30) REVERT: C 283 ASP cc_start: 0.8088 (t0) cc_final: 0.7666 (t0) REVERT: D 283 ASP cc_start: 0.7832 (t0) cc_final: 0.7512 (t0) REVERT: D 338 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7403 (tm-30) REVERT: D 349 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.7357 (mtp85) REVERT: E 372 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7083 (mp0) REVERT: F 338 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7636 (tm-30) REVERT: F 372 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7073 (mp0) REVERT: I 281 LYS cc_start: 0.8882 (tmtt) cc_final: 0.8680 (tptp) REVERT: I 310 TYR cc_start: 0.8861 (t80) cc_final: 0.8535 (t80) REVERT: I 348 ASP cc_start: 0.8574 (t0) cc_final: 0.8072 (p0) REVERT: I 379 ARG cc_start: 0.7493 (ttt-90) cc_final: 0.6786 (tmm160) REVERT: J 281 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8638 (tptp) REVERT: J 348 ASP cc_start: 0.8576 (t0) cc_final: 0.8055 (p0) REVERT: J 379 ARG cc_start: 0.7551 (ttt-90) cc_final: 0.6753 (tmm160) outliers start: 34 outliers final: 23 residues processed: 167 average time/residue: 0.1810 time to fit residues: 42.2491 Evaluate side-chains 151 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 54 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8190 Z= 0.286 Angle : 0.617 7.279 10940 Z= 0.304 Chirality : 0.051 0.143 1250 Planarity : 0.003 0.032 1390 Dihedral : 4.785 13.253 1060 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.37 % Allowed : 14.42 % Favored : 82.21 % 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: -4.23 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.018 0.003 PHE J 378 TYR 0.013 0.002 TYR I 310 ARG 0.002 0.000 ARG R 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8847 (tmtt) cc_final: 0.8406 (ttmt) REVERT: A 338 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 281 LYS cc_start: 0.8875 (tmtt) cc_final: 0.8451 (ttmt) REVERT: B 283 ASP cc_start: 0.8009 (t0) cc_final: 0.7767 (t0) REVERT: B 338 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7268 (tm-30) REVERT: C 307 GLN cc_start: 0.8899 (tt0) cc_final: 0.8686 (tt0) REVERT: D 283 ASP cc_start: 0.7919 (t0) cc_final: 0.7679 (t0) REVERT: D 338 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7419 (tm-30) REVERT: E 281 LYS cc_start: 0.8611 (tptp) cc_final: 0.8360 (tptp) REVERT: E 338 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7434 (tm-30) REVERT: E 372 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7097 (mp0) REVERT: F 338 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7453 (tm-30) REVERT: F 372 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7074 (mp0) REVERT: I 281 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8679 (tptp) REVERT: I 348 ASP cc_start: 0.8408 (t0) cc_final: 0.8025 (p0) REVERT: I 379 ARG cc_start: 0.7642 (ttt-90) cc_final: 0.6789 (tmm160) REVERT: J 348 ASP cc_start: 0.8407 (t0) cc_final: 0.8029 (p0) REVERT: J 379 ARG cc_start: 0.7692 (ttt-90) cc_final: 0.6765 (tmm160) REVERT: R 349 ARG cc_start: 0.4642 (mmp-170) cc_final: 0.4389 (mmm160) outliers start: 32 outliers final: 26 residues processed: 172 average time/residue: 0.1849 time to fit residues: 44.4682 Evaluate side-chains 153 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8190 Z= 0.472 Angle : 0.706 6.534 10940 Z= 0.363 Chirality : 0.052 0.146 1250 Planarity : 0.004 0.035 1390 Dihedral : 5.172 14.280 1060 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.47 % Allowed : 16.63 % Favored : 79.89 % 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: -4.26 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 374 PHE 0.023 0.004 PHE A 346 TYR 0.013 0.003 TYR E 310 ARG 0.003 0.001 ARG Q 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8844 (tmtt) cc_final: 0.8428 (ttmt) REVERT: B 281 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8439 (ttmt) REVERT: B 338 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7274 (tm-30) REVERT: D 338 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7406 (tm-30) REVERT: E 338 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7469 (tm-30) REVERT: F 338 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7490 (tm-30) REVERT: I 310 TYR cc_start: 0.8960 (t80) cc_final: 0.8636 (t80) REVERT: I 348 ASP cc_start: 0.8728 (t0) cc_final: 0.7959 (p0) REVERT: I 379 ARG cc_start: 0.7825 (ttt-90) cc_final: 0.6841 (tmm160) REVERT: J 310 TYR cc_start: 0.8948 (t80) cc_final: 0.8623 (t80) REVERT: J 348 ASP cc_start: 0.8722 (t0) cc_final: 0.7962 (p0) REVERT: J 362 HIS cc_start: 0.7675 (t70) cc_final: 0.7422 (t-90) REVERT: J 379 ARG cc_start: 0.7776 (ttt-90) cc_final: 0.6829 (tmm160) REVERT: R 349 ARG cc_start: 0.5040 (mmp-170) cc_final: 0.4775 (mmm160) outliers start: 33 outliers final: 29 residues processed: 162 average time/residue: 0.1782 time to fit residues: 40.3783 Evaluate side-chains 153 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8190 Z= 0.432 Angle : 0.702 6.262 10940 Z= 0.362 Chirality : 0.052 0.143 1250 Planarity : 0.004 0.036 1390 Dihedral : 5.140 14.400 1060 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.26 % Allowed : 18.21 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 374 PHE 0.021 0.004 PHE A 346 TYR 0.025 0.004 TYR Q 310 ARG 0.003 0.001 ARG Q 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8849 (tmtt) cc_final: 0.8384 (ttmt) REVERT: A 283 ASP cc_start: 0.8123 (t0) cc_final: 0.7917 (t0) REVERT: B 281 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8413 (ttmt) REVERT: B 283 ASP cc_start: 0.8285 (t0) cc_final: 0.8051 (t0) REVERT: B 338 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 338 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7368 (tm-30) REVERT: E 338 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7420 (tm-30) REVERT: F 338 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7354 (tm-30) REVERT: I 379 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.6903 (tmm160) REVERT: J 362 HIS cc_start: 0.7676 (t70) cc_final: 0.7456 (t-90) REVERT: J 379 ARG cc_start: 0.7772 (ttt-90) cc_final: 0.6944 (tmm160) REVERT: R 349 ARG cc_start: 0.5244 (mmp-170) cc_final: 0.5023 (mmm160) outliers start: 31 outliers final: 31 residues processed: 162 average time/residue: 0.2097 time to fit residues: 45.9720 Evaluate side-chains 159 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8190 Z= 0.321 Angle : 0.652 5.517 10940 Z= 0.331 Chirality : 0.051 0.140 1250 Planarity : 0.003 0.029 1390 Dihedral : 4.920 14.261 1060 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.37 % Allowed : 18.63 % Favored : 78.00 % 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: -4.18 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 299 PHE 0.021 0.003 PHE J 378 TYR 0.016 0.003 TYR E 310 ARG 0.002 0.001 ARG Q 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8839 (tmtt) cc_final: 0.8366 (ttmt) REVERT: B 281 LYS cc_start: 0.8859 (tmtt) cc_final: 0.8402 (ttmt) REVERT: B 283 ASP cc_start: 0.8315 (t0) cc_final: 0.8016 (t0) REVERT: B 338 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7142 (tm-30) REVERT: D 338 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7302 (tm-30) REVERT: E 338 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7349 (tm-30) REVERT: E 372 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7022 (mp0) REVERT: F 338 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7295 (tm-30) REVERT: I 348 ASP cc_start: 0.8645 (t70) cc_final: 0.7980 (p0) REVERT: I 379 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.6770 (tmm160) REVERT: J 348 ASP cc_start: 0.8638 (t70) cc_final: 0.7990 (p0) REVERT: J 362 HIS cc_start: 0.7641 (t70) cc_final: 0.7390 (t-90) REVERT: J 379 ARG cc_start: 0.7944 (ttt-90) cc_final: 0.6818 (tmm160) REVERT: Q 349 ARG cc_start: 0.5226 (mmp-170) cc_final: 0.4949 (mmm160) REVERT: R 349 ARG cc_start: 0.5248 (mmp-170) cc_final: 0.4829 (mmm160) outliers start: 32 outliers final: 29 residues processed: 161 average time/residue: 0.1861 time to fit residues: 41.6266 Evaluate side-chains 153 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 287 VAL Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 0.0270 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 92 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8190 Z= 0.298 Angle : 0.647 8.511 10940 Z= 0.325 Chirality : 0.051 0.139 1250 Planarity : 0.003 0.025 1390 Dihedral : 4.818 14.092 1060 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.47 % Allowed : 19.16 % Favored : 77.37 % 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: -4.16 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Q 299 PHE 0.024 0.003 PHE J 378 TYR 0.026 0.004 TYR Q 310 ARG 0.003 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8373 (ttmt) REVERT: B 281 LYS cc_start: 0.8851 (tmtt) cc_final: 0.8375 (ttmt) REVERT: B 283 ASP cc_start: 0.8369 (t0) cc_final: 0.7966 (t0) REVERT: B 338 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7115 (tm-30) REVERT: D 338 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7333 (tm-30) REVERT: E 338 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7338 (tm-30) REVERT: E 372 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7018 (mp0) REVERT: F 338 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7259 (tm-30) REVERT: F 372 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7003 (mp0) REVERT: I 348 ASP cc_start: 0.8449 (t70) cc_final: 0.7932 (p0) REVERT: I 379 ARG cc_start: 0.7804 (ttt-90) cc_final: 0.6797 (tmm160) REVERT: J 348 ASP cc_start: 0.8447 (t70) cc_final: 0.7933 (p0) REVERT: J 362 HIS cc_start: 0.7654 (t70) cc_final: 0.7408 (t-90) REVERT: J 379 ARG cc_start: 0.7839 (ttt-90) cc_final: 0.6763 (tmm160) REVERT: Q 349 ARG cc_start: 0.5421 (mmp-170) cc_final: 0.4997 (mmm160) outliers start: 33 outliers final: 30 residues processed: 165 average time/residue: 0.1744 time to fit residues: 40.4213 Evaluate side-chains 162 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 287 VAL Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8190 Z= 0.345 Angle : 0.664 8.357 10940 Z= 0.336 Chirality : 0.052 0.140 1250 Planarity : 0.003 0.027 1390 Dihedral : 4.892 14.452 1060 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.58 % Allowed : 18.63 % Favored : 77.79 % 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: -4.20 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 299 PHE 0.022 0.003 PHE J 378 TYR 0.018 0.003 TYR B 310 ARG 0.003 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8828 (tmtt) cc_final: 0.8330 (ttmt) REVERT: A 349 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7712 (mtp85) REVERT: B 281 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8393 (ttmt) REVERT: B 283 ASP cc_start: 0.8362 (t0) cc_final: 0.7909 (t0) REVERT: D 338 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7299 (tm-30) REVERT: E 338 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7331 (tm-30) REVERT: E 372 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7025 (mp0) REVERT: F 338 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7248 (tm-30) REVERT: I 348 ASP cc_start: 0.8642 (t70) cc_final: 0.8004 (p0) REVERT: I 379 ARG cc_start: 0.7832 (ttt-90) cc_final: 0.6850 (tmm160) REVERT: J 348 ASP cc_start: 0.8638 (t70) cc_final: 0.8000 (p0) REVERT: J 362 HIS cc_start: 0.7673 (t70) cc_final: 0.7418 (t-90) REVERT: J 379 ARG cc_start: 0.7843 (ttt-90) cc_final: 0.6838 (tmm160) REVERT: Q 349 ARG cc_start: 0.5317 (mmp-170) cc_final: 0.4884 (mmm160) REVERT: R 349 ARG cc_start: 0.5356 (mmp-170) cc_final: 0.5065 (mmm160) outliers start: 34 outliers final: 33 residues processed: 160 average time/residue: 0.1941 time to fit residues: 43.0336 Evaluate side-chains 165 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 287 VAL Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8190 Z= 0.322 Angle : 0.656 8.628 10940 Z= 0.331 Chirality : 0.052 0.139 1250 Planarity : 0.003 0.025 1390 Dihedral : 4.838 14.369 1060 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.47 % Allowed : 19.16 % Favored : 77.37 % 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: -4.18 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Q 299 PHE 0.025 0.004 PHE J 378 TYR 0.027 0.005 TYR Q 310 ARG 0.003 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8817 (tmtt) cc_final: 0.8351 (ttmt) REVERT: A 349 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7698 (mtp85) REVERT: B 281 LYS cc_start: 0.8860 (tmtt) cc_final: 0.8405 (ttmt) REVERT: C 328 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8404 (mm) REVERT: D 338 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7252 (tm-30) REVERT: E 310 TYR cc_start: 0.9074 (t80) cc_final: 0.8861 (t80) REVERT: E 338 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7339 (tm-30) REVERT: E 372 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7026 (mp0) REVERT: F 338 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7232 (tm-30) REVERT: F 372 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7015 (mp0) REVERT: I 348 ASP cc_start: 0.8478 (t70) cc_final: 0.7927 (p0) REVERT: I 379 ARG cc_start: 0.7764 (ttt-90) cc_final: 0.6801 (tmm160) REVERT: J 348 ASP cc_start: 0.8479 (t70) cc_final: 0.7932 (p0) REVERT: J 362 HIS cc_start: 0.7670 (t70) cc_final: 0.7409 (t-90) REVERT: J 379 ARG cc_start: 0.7870 (ttt-90) cc_final: 0.6872 (tmm160) REVERT: Q 349 ARG cc_start: 0.5344 (mmp-170) cc_final: 0.4932 (mmm160) REVERT: R 379 ARG cc_start: 0.7842 (ttt-90) cc_final: 0.7350 (tpm170) outliers start: 33 outliers final: 31 residues processed: 158 average time/residue: 0.2037 time to fit residues: 44.0537 Evaluate side-chains 163 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 287 VAL Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.210310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5129 r_free = 0.5129 target = 0.180127 restraints weight = 14459.414| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 2.07 r_work: 0.4419 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4305 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8190 Z= 0.243 Angle : 0.630 8.846 10940 Z= 0.313 Chirality : 0.051 0.137 1250 Planarity : 0.003 0.022 1390 Dihedral : 4.652 14.209 1060 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.63 % Allowed : 19.79 % Favored : 77.58 % 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: -4.14 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 299 PHE 0.028 0.003 PHE J 378 TYR 0.027 0.003 TYR A 310 ARG 0.004 0.001 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.92 seconds wall clock time: 36 minutes 21.69 seconds (2181.69 seconds total)