Starting phenix.real_space_refine on Mon Mar 11 11:05:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/03_2024/7p6e_13227.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/03_2024/7p6e_13227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/03_2024/7p6e_13227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/03_2024/7p6e_13227.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/03_2024/7p6e_13227.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8090 Number of models: 1 Model: "" Number of chains: 10 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Chain: "F" 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 Chain: "I" 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 Chain: "J" 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 Chain: "Q" 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 Chain: "R" 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 Time building chain proxies: 4.81, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.5 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: 0.86 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: 1.97 Time building geometry restraints manager: 3.42 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: 102.09 - 107.95: 570 107.95 - 113.80: 4731 113.80 - 119.65: 1854 119.65 - 125.50: 3695 125.50 - 131.35: 90 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 2.520 nonbonded pdb=" OD2 ASP J 295 " pdb=" NZ LYS J 311 " model vdw 2.358 2.520 nonbonded pdb=" OD2 ASP E 295 " pdb=" NZ LYS E 311 " model vdw 2.359 2.520 nonbonded pdb=" OD2 ASP A 295 " pdb=" NZ LYS A 311 " model vdw 2.359 2.520 nonbonded pdb=" OD2 ASP Q 295 " pdb=" NZ LYS Q 311 " model vdw 2.359 2.520 ... (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 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: 4.650 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: 0.000 Extract box with map and model: 7.870 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.540 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.550 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.052 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: 0.1987 time to fit residues: 77.0325 Evaluate side-chains 127 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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: 0.9980 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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** C 374 HIS D 381 ASN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS ** J 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 336 GLN J 374 HIS Q 286 ASN R 359 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2236 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= 0.237 Angle : 0.612 7.793 10940 Z= 0.299 Chirality : 0.050 0.139 1250 Planarity : 0.005 0.037 1390 Dihedral : 4.928 12.896 1060 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.11 % Allowed : 9.47 % 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: -4.53 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.15), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 362 PHE 0.011 0.003 PHE A 346 TYR 0.027 0.003 TYR I 310 ARG 0.007 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 193 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.151 Fit side-chains REVERT: A 281 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8287 (ttpt) REVERT: B 281 LYS cc_start: 0.8724 (tmtt) cc_final: 0.8351 (ttmt) REVERT: C 362 HIS cc_start: 0.7847 (t-170) cc_final: 0.7400 (t-90) REVERT: D 314 ASP cc_start: 0.7844 (t0) cc_final: 0.7627 (t0) REVERT: D 338 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 362 HIS cc_start: 0.7852 (t-170) cc_final: 0.7421 (t-90) REVERT: E 281 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8447 (tptp) REVERT: E 372 GLU cc_start: 0.8101 (mt-10) cc_final: 0.6991 (mp0) REVERT: F 281 LYS cc_start: 0.8786 (tmtt) cc_final: 0.8394 (tptp) REVERT: F 372 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7012 (mp0) REVERT: I 281 LYS cc_start: 0.8812 (tmtt) cc_final: 0.8575 (tptp) REVERT: I 348 ASP cc_start: 0.8444 (t0) cc_final: 0.8022 (p0) REVERT: I 372 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7154 (mp0) REVERT: J 281 LYS cc_start: 0.8853 (tmtt) cc_final: 0.8593 (tptp) REVERT: J 310 TYR cc_start: 0.8870 (t80) cc_final: 0.8517 (t80) REVERT: J 348 ASP cc_start: 0.8358 (t0) cc_final: 0.7996 (p0) REVERT: J 372 GLU cc_start: 0.7717 (mt-10) cc_final: 0.6854 (mp0) outliers start: 20 outliers final: 16 residues processed: 192 average time/residue: 0.1992 time to fit residues: 51.7892 Evaluate side-chains 131 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F 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: 20.0000 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN B 286 ASN C 286 ASN D 286 ASN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 ASN R 359 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8190 Z= 0.418 Angle : 0.694 7.864 10940 Z= 0.350 Chirality : 0.052 0.146 1250 Planarity : 0.004 0.034 1390 Dihedral : 5.141 13.666 1060 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.11 % Allowed : 12.00 % Favored : 83.89 % 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: -4.40 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.15), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 374 PHE 0.014 0.004 PHE E 346 TYR 0.018 0.003 TYR J 310 ARG 0.003 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 178 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8855 (tmtt) cc_final: 0.8393 (ttmt) REVERT: A 338 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7577 (tm-30) REVERT: B 281 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8443 (ttmt) REVERT: B 338 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7468 (tm-30) REVERT: D 338 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7664 (tm-30) REVERT: E 281 LYS cc_start: 0.8923 (tmtt) cc_final: 0.8457 (tptp) REVERT: E 283 ASP cc_start: 0.8283 (t0) cc_final: 0.8066 (t0) REVERT: E 310 TYR cc_start: 0.9081 (t80) cc_final: 0.8814 (t80) REVERT: E 338 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7638 (tm-30) REVERT: F 281 LYS cc_start: 0.8926 (tmtt) cc_final: 0.8533 (tptp) REVERT: F 338 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7551 (tm-30) REVERT: I 281 LYS cc_start: 0.8992 (tmtt) cc_final: 0.8771 (tptp) REVERT: I 310 TYR cc_start: 0.8907 (t80) cc_final: 0.8690 (t80) REVERT: I 348 ASP cc_start: 0.8654 (t0) cc_final: 0.8019 (p0) REVERT: I 379 ARG cc_start: 0.7568 (ttt-90) cc_final: 0.6804 (tmm160) REVERT: J 281 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8744 (tptp) REVERT: J 310 TYR cc_start: 0.8978 (t80) cc_final: 0.8615 (t80) REVERT: J 348 ASP cc_start: 0.8642 (t0) cc_final: 0.8028 (p0) REVERT: J 379 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.6813 (tmm160) REVERT: Q 324 SER cc_start: 0.6381 (OUTLIER) cc_final: 0.6081 (p) REVERT: Q 349 ARG cc_start: 0.4922 (mmp-170) cc_final: 0.4676 (mmm160) outliers start: 39 outliers final: 31 residues processed: 168 average time/residue: 0.1776 time to fit residues: 41.9351 Evaluate side-chains 160 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 324 SER 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 324 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 324 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 341 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 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.3980 chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8190 Z= 0.197 Angle : 0.576 7.292 10940 Z= 0.278 Chirality : 0.050 0.142 1250 Planarity : 0.003 0.032 1390 Dihedral : 4.571 12.794 1060 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.74 % Allowed : 14.42 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.003 0.001 HIS D 362 PHE 0.018 0.003 PHE J 378 TYR 0.019 0.002 TYR Q 310 ARG 0.002 0.000 ARG Q 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 185 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.180 Fit side-chains REVERT: A 281 LYS cc_start: 0.8823 (tmtt) cc_final: 0.8345 (ttpt) REVERT: A 338 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7213 (tm-30) REVERT: B 281 LYS cc_start: 0.8882 (tmtt) cc_final: 0.8421 (ttpt) REVERT: B 338 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7265 (tm-30) REVERT: C 338 GLU cc_start: 0.7709 (tt0) cc_final: 0.7141 (tm-30) REVERT: D 338 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7546 (tm-30) REVERT: E 281 LYS cc_start: 0.8862 (tmtt) cc_final: 0.8495 (tptp) REVERT: E 338 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7474 (tm-30) REVERT: E 372 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7041 (mp0) REVERT: F 281 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8437 (tptp) REVERT: F 338 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7417 (tm-30) REVERT: F 372 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7028 (mp0) REVERT: I 281 LYS cc_start: 0.8927 (tmtt) cc_final: 0.8688 (tptp) REVERT: I 310 TYR cc_start: 0.8726 (t80) cc_final: 0.8436 (t80) REVERT: I 348 ASP cc_start: 0.8407 (t0) cc_final: 0.8084 (p0) REVERT: I 372 GLU cc_start: 0.7959 (mt-10) cc_final: 0.6915 (mp0) REVERT: I 379 ARG cc_start: 0.7515 (ttt-90) cc_final: 0.6735 (tmm160) REVERT: J 281 LYS cc_start: 0.8927 (tmtt) cc_final: 0.8672 (tptp) REVERT: J 310 TYR cc_start: 0.8873 (t80) cc_final: 0.8571 (t80) REVERT: J 338 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7703 (tm-30) REVERT: J 348 ASP cc_start: 0.8273 (t0) cc_final: 0.8059 (p0) REVERT: J 372 GLU cc_start: 0.7917 (mt-10) cc_final: 0.6915 (mp0) REVERT: J 379 ARG cc_start: 0.7617 (ttt-90) cc_final: 0.6777 (tmm160) REVERT: Q 324 SER cc_start: 0.6188 (OUTLIER) cc_final: 0.5873 (p) REVERT: Q 381 ASN cc_start: 0.7741 (m110) cc_final: 0.6576 (t0) outliers start: 26 outliers final: 17 residues processed: 179 average time/residue: 0.1849 time to fit residues: 46.8158 Evaluate side-chains 154 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 324 SER 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: 10.0000 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 8190 Z= 0.575 Angle : 0.759 6.019 10940 Z= 0.397 Chirality : 0.053 0.152 1250 Planarity : 0.004 0.038 1390 Dihedral : 5.378 15.135 1060 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.85 % Favored : 85.15 % Rotamer: Outliers : 4.42 % Allowed : 15.58 % Favored : 80.00 % 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: -4.35 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 374 PHE 0.017 0.004 PHE F 346 TYR 0.025 0.004 TYR R 310 ARG 0.002 0.000 ARG R 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 176 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 0.964 Fit side-chains REVERT: A 281 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8456 (ttmt) REVERT: A 295 ASP cc_start: 0.8805 (p0) cc_final: 0.8499 (p0) REVERT: A 338 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7460 (tm-30) REVERT: B 281 LYS cc_start: 0.8995 (tmtt) cc_final: 0.8541 (ttmt) REVERT: D 338 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7534 (tm-30) REVERT: E 281 LYS cc_start: 0.9083 (tmtt) cc_final: 0.8661 (tptp) REVERT: E 372 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8074 (mt-10) REVERT: F 281 LYS cc_start: 0.9119 (tmtt) cc_final: 0.8708 (tptp) REVERT: F 372 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7892 (mt-10) REVERT: I 281 LYS cc_start: 0.9050 (tmtt) cc_final: 0.8836 (tptp) REVERT: I 310 TYR cc_start: 0.8996 (t80) cc_final: 0.8607 (t80) REVERT: I 379 ARG cc_start: 0.7813 (ttt-90) cc_final: 0.6978 (tmm160) REVERT: J 338 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7829 (tm-30) REVERT: J 379 ARG cc_start: 0.7752 (ttt-90) cc_final: 0.6835 (tmm160) REVERT: Q 324 SER cc_start: 0.6370 (OUTLIER) cc_final: 0.6051 (p) outliers start: 42 outliers final: 39 residues processed: 166 average time/residue: 0.1782 time to fit residues: 41.3682 Evaluate side-chains 172 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 327 ASN 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 300 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 324 SER 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 324 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 327 ASN 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 Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8190 Z= 0.412 Angle : 0.684 5.767 10940 Z= 0.351 Chirality : 0.052 0.147 1250 Planarity : 0.003 0.036 1390 Dihedral : 5.121 14.207 1060 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.11 % Allowed : 17.16 % Favored : 78.74 % 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: -4.31 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 374 PHE 0.018 0.003 PHE J 378 TYR 0.027 0.003 TYR E 310 ARG 0.003 0.001 ARG R 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 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 LEU cc_start: 0.8223 (tt) cc_final: 0.8009 (tt) REVERT: A 295 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8527 (p0) REVERT: B 281 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8501 (ttmt) REVERT: D 338 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 281 LYS cc_start: 0.9063 (tmtt) cc_final: 0.8635 (tptp) REVERT: E 372 GLU cc_start: 0.8184 (mt-10) cc_final: 0.6886 (mp0) REVERT: F 281 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8721 (tptp) REVERT: F 372 GLU cc_start: 0.8210 (mt-10) cc_final: 0.6879 (mp0) REVERT: I 281 LYS cc_start: 0.9070 (tmtt) cc_final: 0.8868 (tptp) REVERT: I 310 TYR cc_start: 0.8970 (t80) cc_final: 0.8387 (t80) REVERT: I 379 ARG cc_start: 0.7789 (ttt-90) cc_final: 0.6895 (tmm160) REVERT: J 310 TYR cc_start: 0.8961 (t80) cc_final: 0.8725 (t80) REVERT: J 338 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7884 (tm-30) REVERT: J 379 ARG cc_start: 0.7759 (ttt-90) cc_final: 0.6896 (tmm160) REVERT: Q 324 SER cc_start: 0.6161 (OUTLIER) cc_final: 0.5832 (p) outliers start: 39 outliers final: 37 residues processed: 170 average time/residue: 0.1910 time to fit residues: 44.9023 Evaluate side-chains 172 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 327 ASN 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 300 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 324 SER 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 324 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 341 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 Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8190 Z= 0.246 Angle : 0.611 6.517 10940 Z= 0.303 Chirality : 0.051 0.141 1250 Planarity : 0.003 0.025 1390 Dihedral : 4.730 15.076 1060 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.68 % Allowed : 18.32 % 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 0.005 0.001 HIS R 299 PHE 0.024 0.003 PHE J 378 TYR 0.025 0.003 TYR R 310 ARG 0.002 0.000 ARG R 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 184 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 281 LYS cc_start: 0.8971 (tmtt) cc_final: 0.8763 (tptp) REVERT: B 295 ASP cc_start: 0.8747 (p0) cc_final: 0.8252 (p0) REVERT: D 324 SER cc_start: 0.6692 (OUTLIER) cc_final: 0.6373 (p) REVERT: D 338 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7370 (tm-30) REVERT: E 281 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8575 (tptp) REVERT: E 372 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7181 (mp0) REVERT: F 281 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8660 (tptp) REVERT: F 338 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7396 (tm-30) REVERT: F 372 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7098 (mp0) REVERT: I 281 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8846 (tptp) REVERT: I 310 TYR cc_start: 0.8734 (t80) cc_final: 0.8400 (t80) REVERT: I 348 ASP cc_start: 0.8315 (t70) cc_final: 0.7841 (p0) REVERT: I 379 ARG cc_start: 0.7758 (ttt-90) cc_final: 0.6823 (tmm160) REVERT: J 310 TYR cc_start: 0.8859 (t80) cc_final: 0.8646 (t80) REVERT: J 338 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7797 (tm-30) REVERT: J 348 ASP cc_start: 0.8296 (t70) cc_final: 0.7840 (p0) REVERT: J 379 ARG cc_start: 0.7834 (ttt-90) cc_final: 0.6841 (tmm160) REVERT: Q 324 SER cc_start: 0.6082 (OUTLIER) cc_final: 0.5841 (p) REVERT: Q 349 ARG cc_start: 0.5239 (mmp-170) cc_final: 0.4934 (mmm160) REVERT: R 349 ARG cc_start: 0.5179 (mmp-170) cc_final: 0.4866 (mmm160) outliers start: 35 outliers final: 29 residues processed: 177 average time/residue: 0.1916 time to fit residues: 46.6361 Evaluate side-chains 171 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 327 ASN 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 324 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 300 VAL Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 75 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3869 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= 0.331 Angle : 0.649 7.654 10940 Z= 0.328 Chirality : 0.051 0.149 1250 Planarity : 0.003 0.025 1390 Dihedral : 4.814 17.451 1060 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.21 % Allowed : 18.95 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.22 (0.21), 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 0.004 0.001 HIS F 374 PHE 0.023 0.004 PHE J 378 TYR 0.016 0.003 TYR F 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 176 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 281 LYS cc_start: 0.8975 (tmtt) cc_final: 0.8475 (ttpt) REVERT: B 295 ASP cc_start: 0.8834 (p0) cc_final: 0.8291 (p0) REVERT: C 378 PHE cc_start: 0.8284 (m-80) cc_final: 0.8033 (m-80) REVERT: D 338 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7398 (tm-30) REVERT: E 281 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8609 (tptp) REVERT: E 372 GLU cc_start: 0.8187 (mt-10) cc_final: 0.6859 (mp0) REVERT: F 281 LYS cc_start: 0.9106 (tmtt) cc_final: 0.8707 (tptp) REVERT: F 372 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7104 (mp0) REVERT: I 281 LYS cc_start: 0.9076 (tmtt) cc_final: 0.8870 (tptp) REVERT: I 310 TYR cc_start: 0.8768 (t80) cc_final: 0.8518 (t80) REVERT: I 379 ARG cc_start: 0.7768 (ttt-90) cc_final: 0.6847 (tmm160) REVERT: J 310 TYR cc_start: 0.8875 (t80) cc_final: 0.8652 (t80) REVERT: J 338 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7874 (tm-30) REVERT: J 379 ARG cc_start: 0.7852 (ttt-90) cc_final: 0.6870 (tmm160) REVERT: Q 324 SER cc_start: 0.6113 (OUTLIER) cc_final: 0.5862 (p) REVERT: Q 349 ARG cc_start: 0.5315 (mmp-170) cc_final: 0.5034 (mmm160) REVERT: R 349 ARG cc_start: 0.5267 (mmp-170) cc_final: 0.4985 (mmm160) outliers start: 40 outliers final: 36 residues processed: 166 average time/residue: 0.1782 time to fit residues: 41.4477 Evaluate side-chains 167 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 324 SER 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 324 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 327 ASN 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 324 SER Chi-restraints excluded: chain J residue 327 ASN 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 287 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8190 Z= 0.264 Angle : 0.625 8.052 10940 Z= 0.309 Chirality : 0.051 0.139 1250 Planarity : 0.003 0.025 1390 Dihedral : 4.689 16.857 1060 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.11 % Allowed : 19.05 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.004 0.001 HIS R 299 PHE 0.026 0.004 PHE J 378 TYR 0.025 0.003 TYR R 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 184 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8885 (p0) cc_final: 0.8312 (p0) REVERT: B 281 LYS cc_start: 0.8964 (tmtt) cc_final: 0.8758 (tptp) REVERT: C 378 PHE cc_start: 0.8313 (m-80) cc_final: 0.8071 (m-80) REVERT: D 324 SER cc_start: 0.6564 (OUTLIER) cc_final: 0.6269 (p) REVERT: D 338 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7415 (tm-30) REVERT: E 281 LYS cc_start: 0.8987 (tmtt) cc_final: 0.8590 (tptp) REVERT: E 372 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7174 (mp0) REVERT: F 281 LYS cc_start: 0.9072 (tmtt) cc_final: 0.8634 (tptp) REVERT: F 372 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7114 (mp0) REVERT: I 281 LYS cc_start: 0.9059 (tmtt) cc_final: 0.8851 (tptp) REVERT: I 348 ASP cc_start: 0.8319 (t70) cc_final: 0.7822 (p0) REVERT: I 379 ARG cc_start: 0.7786 (ttt-90) cc_final: 0.6836 (tmm160) REVERT: J 310 TYR cc_start: 0.8834 (t80) cc_final: 0.8574 (t80) REVERT: J 338 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7844 (tm-30) REVERT: J 348 ASP cc_start: 0.8369 (t70) cc_final: 0.7872 (p0) REVERT: J 379 ARG cc_start: 0.7831 (ttt-90) cc_final: 0.6829 (tmm160) REVERT: Q 324 SER cc_start: 0.6074 (OUTLIER) cc_final: 0.5851 (p) REVERT: Q 349 ARG cc_start: 0.5305 (mmp-170) cc_final: 0.5029 (mmm160) REVERT: R 349 ARG cc_start: 0.5160 (mmp-170) cc_final: 0.4861 (mmm160) outliers start: 39 outliers final: 33 residues processed: 175 average time/residue: 0.1778 time to fit residues: 43.5463 Evaluate side-chains 173 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 327 ASN 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 324 SER Chi-restraints excluded: chain J residue 327 ASN 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 287 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 0.0670 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 overall best weight: 4.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8190 Z= 0.354 Angle : 0.658 7.714 10940 Z= 0.333 Chirality : 0.051 0.139 1250 Planarity : 0.003 0.029 1390 Dihedral : 4.847 16.973 1060 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.21 % Allowed : 18.95 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 374 PHE 0.025 0.004 PHE J 378 TYR 0.026 0.005 TYR Q 310 ARG 0.004 0.001 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 173 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8898 (p0) cc_final: 0.8292 (p0) REVERT: B 281 LYS cc_start: 0.8988 (tmtt) cc_final: 0.8786 (tptp) REVERT: D 338 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7449 (tm-30) REVERT: E 281 LYS cc_start: 0.9015 (tmtt) cc_final: 0.8627 (tptp) REVERT: F 281 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8669 (tptp) REVERT: F 372 GLU cc_start: 0.8204 (mt-10) cc_final: 0.6842 (mp0) REVERT: I 281 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8907 (tptp) REVERT: I 310 TYR cc_start: 0.8908 (t80) cc_final: 0.8451 (t80) REVERT: I 379 ARG cc_start: 0.7821 (ttt-90) cc_final: 0.6893 (tmm160) REVERT: J 310 TYR cc_start: 0.8867 (t80) cc_final: 0.8635 (t80) REVERT: J 338 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7874 (tm-30) REVERT: J 379 ARG cc_start: 0.7904 (ttt-90) cc_final: 0.6900 (tmm160) REVERT: Q 349 ARG cc_start: 0.5450 (mmp-170) cc_final: 0.5173 (mmm160) REVERT: R 349 ARG cc_start: 0.5284 (mmp-170) cc_final: 0.4993 (mmm160) REVERT: R 379 ARG cc_start: 0.7851 (ttt-90) cc_final: 0.7454 (tpm170) outliers start: 40 outliers final: 39 residues processed: 162 average time/residue: 0.1880 time to fit residues: 42.0439 Evaluate side-chains 171 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 327 ASN 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 324 SER Chi-restraints excluded: chain J residue 327 ASN 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 287 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.254177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5360 r_free = 0.5360 target = 0.203281 restraints weight = 15592.793| |-----------------------------------------------------------------------------| r_work (start): 0.4543 rms_B_bonded: 1.96 r_work: 0.4435 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4322 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8190 Z= 0.256 Angle : 0.626 7.925 10940 Z= 0.311 Chirality : 0.051 0.137 1250 Planarity : 0.003 0.021 1390 Dihedral : 4.660 14.595 1060 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.79 % Allowed : 19.58 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.004 0.001 HIS R 299 PHE 0.027 0.003 PHE J 378 TYR 0.023 0.005 TYR R 310 ARG 0.003 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1949.77 seconds wall clock time: 36 minutes 40.99 seconds (2200.99 seconds total)