Starting phenix.real_space_refine (version: dev) on Sun Dec 11 23:13:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/12_2022/7p6e_13227.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/12_2022/7p6e_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_13227/12_2022/7p6e_13227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/12_2022/7p6e_13227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/12_2022/7p6e_13227.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6e_13227/12_2022/7p6e_13227.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 5.08, per 1000 atoms: 0.63 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: 2.86 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: 0.47 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: 2.06 Time building geometry restraints manager: 3.13 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 7.790 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.080 Process input model: 24.900 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 % 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 *********************** 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 : 1.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1931 time to fit residues: 74.8058 Evaluate side-chains 121 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4466 ------------------------------------------------------------------------------- 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: 9.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 HIS D 381 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 336 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2492 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= 0.271 Angle : 0.634 7.849 10940 Z= 0.313 Chirality : 0.050 0.141 1250 Planarity : 0.005 0.045 1390 Dihedral : 4.944 12.829 1060 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 2.21 % 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: -4.55 (0.19), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.15), residues: 1010 *********************** 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 189 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.089 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 188 average time/residue: 0.1781 time to fit residues: 46.5510 Evaluate side-chains 115 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0740 time to fit residues: 3.5446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 B 351 GLN C 286 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN ** D 374 HIS ** 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.057 8190 Z= 0.511 Angle : 0.755 7.802 10940 Z= 0.387 Chirality : 0.053 0.159 1250 Planarity : 0.004 0.035 1390 Dihedral : 5.364 14.989 1060 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.44 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.15), residues: 1010 *********************** 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 144 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 1.131 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 138 average time/residue: 0.1742 time to fit residues: 34.2274 Evaluate side-chains 125 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1169 time to fit residues: 4.8951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** C 362 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** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3444 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= 0.341 Angle : 0.641 6.020 10940 Z= 0.326 Chirality : 0.051 0.148 1250 Planarity : 0.003 0.031 1390 Dihedral : 4.912 14.326 1060 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.37 % 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: -4.27 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.16), residues: 1010 *********************** 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 136 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.110 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.1671 time to fit residues: 31.7108 Evaluate side-chains 125 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1076 time to fit residues: 2.9447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- 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** ** C 362 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 8190 Z= 0.261 Angle : 0.589 7.078 10940 Z= 0.297 Chirality : 0.050 0.143 1250 Planarity : 0.003 0.029 1390 Dihedral : 4.673 14.895 1060 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.47 % 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 : -3.17 (0.16), residues: 1010 *********************** 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 148 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.109 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 0.1591 time to fit residues: 32.6120 Evaluate side-chains 125 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1004 time to fit residues: 3.1223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.0270 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 overall best weight: 3.5442 ------------------------------------------------------------------------------- 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** ** C 362 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 8190 Z= 0.292 Angle : 0.617 7.438 10940 Z= 0.311 Chirality : 0.051 0.164 1250 Planarity : 0.003 0.026 1390 Dihedral : 4.642 15.718 1060 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.16), residues: 1010 *********************** 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 131 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.113 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 0.1767 time to fit residues: 31.0293 Evaluate side-chains 119 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1286 time to fit residues: 2.7022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 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 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** ** I 374 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** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4001 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= 0.489 Angle : 0.717 5.935 10940 Z= 0.375 Chirality : 0.053 0.170 1250 Planarity : 0.004 0.040 1390 Dihedral : 5.081 15.793 1060 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.16), residues: 1010 *********************** 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 128 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.967 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 122 average time/residue: 0.1886 time to fit residues: 32.1857 Evaluate side-chains 122 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0706 time to fit residues: 2.8137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS J 374 HIS ** Q 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4059 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= 0.258 Angle : 0.629 6.355 10940 Z= 0.315 Chirality : 0.051 0.139 1250 Planarity : 0.003 0.040 1390 Dihedral : 4.717 16.464 1060 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.63 % 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: -4.15 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.16), residues: 1010 *********************** 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 130 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.026 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 128 average time/residue: 0.1770 time to fit residues: 32.4331 Evaluate side-chains 115 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 0.0010 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 overall best weight: 4.3992 ------------------------------------------------------------------------------- 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** ** C 362 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 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** ** Q 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 8190 Z= 0.358 Angle : 0.667 6.567 10940 Z= 0.340 Chirality : 0.051 0.139 1250 Planarity : 0.003 0.045 1390 Dihedral : 4.833 15.833 1060 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 0.84 % 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 : -3.20 (0.16), residues: 1010 *********************** 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 126 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.143 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 123 average time/residue: 0.1764 time to fit residues: 31.3635 Evaluate side-chains 116 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0718 time to fit residues: 2.0438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.0040 chunk 99 optimal weight: 0.0770 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.6154 ------------------------------------------------------------------------------- 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** ** C 362 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4177 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= 0.252 Angle : 0.642 9.576 10940 Z= 0.317 Chirality : 0.051 0.139 1250 Planarity : 0.003 0.042 1390 Dihedral : 4.631 15.852 1060 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.16), residues: 1010 ********************** 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 129 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.100 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1923 time to fit residues: 35.5247 Evaluate side-chains 119 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 0.2980 chunk 10 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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** ** C 362 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 351 GLN ** Q 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 362 HIS ** 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 = 0.4950 r_free = 0.4950 target = 0.254252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.202740 restraints weight = 15621.347| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 1.95 r_work: 0.4443 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4332 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8190 Z= 0.299 Angle : 0.663 9.119 10940 Z= 0.333 Chirality : 0.051 0.144 1250 Planarity : 0.004 0.044 1390 Dihedral : 4.652 15.667 1060 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer Outliers : 0.42 % 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: -4.12 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.16), residues: 1010 =============================================================================== Job complete usr+sys time: 1827.85 seconds wall clock time: 34 minutes 50.92 seconds (2090.92 seconds total)