Starting phenix.real_space_refine on Mon Nov 18 05:05:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctt_45918/11_2024/9ctt_45918.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctt_45918/11_2024/9ctt_45918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctt_45918/11_2024/9ctt_45918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctt_45918/11_2024/9ctt_45918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctt_45918/11_2024/9ctt_45918.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctt_45918/11_2024/9ctt_45918.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 80 5.16 5 C 10260 2.51 5 N 2550 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15595 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "E" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.65, per 1000 atoms: 0.62 Number of scatterers: 15595 At special positions: 0 Unit cell: (107.07, 108.73, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 80 16.00 O 2700 8.00 N 2550 7.00 C 10260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.19 Conformation dependent library (CDL) restraints added in 1.9 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 3 sheets defined 70.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.735A pdb=" N LEU D 22 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.817A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 removed outlier: 3.954A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.689A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.779A pdb=" N LEU D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 264 through 268 removed outlier: 4.107A pdb=" N GLU D 268 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.775A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 348 through 355 removed outlier: 3.685A pdb=" N ALA D 352 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLN D 353 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.704A pdb=" N LEU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.686A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 70 Processing helix chain 'B' and resid 75 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 175 Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.695A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.941A pdb=" N LEU B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.784A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.714A pdb=" N LEU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 52 removed outlier: 5.713A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.668A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 4.524A pdb=" N ILE E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.679A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.761A pdb=" N LEU E 252 " --> pdb=" O PHE E 248 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.579A pdb=" N LYS E 262 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.774A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.650A pdb=" N ARG E 355 " --> pdb=" O ALA E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 374 removed outlier: 3.527A pdb=" N GLU E 374 " --> pdb=" O GLU E 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.576A pdb=" N LEU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.789A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 4.003A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.676A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.898A pdb=" N LEU A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.789A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.552A pdb=" N ARG A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 373 Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.672A pdb=" N LEU C 22 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 52 removed outlier: 5.771A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 removed outlier: 3.818A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.707A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.523A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.793A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'D' and resid 375 through 376 removed outlier: 4.453A pdb=" N TYR C 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.396A pdb=" N TYR B 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 347 through 348 removed outlier: 4.398A pdb=" N TYR E 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4827 1.34 - 1.46: 4122 1.46 - 1.58: 6981 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 16065 Sorted by residual: bond pdb=" N LYS B 64 " pdb=" CA LYS B 64 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 7.98e+00 bond pdb=" N TYR C 50 " pdb=" CA TYR C 50 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.55e+00 bond pdb=" N ASP B 303 " pdb=" CA ASP B 303 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.35e+00 bond pdb=" N LYS C 262 " pdb=" CA LYS C 262 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.35e-02 5.49e+03 7.18e+00 bond pdb=" CA LYS B 64 " pdb=" C LYS B 64 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.32e-02 5.74e+03 6.76e+00 ... (remaining 16060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 21354 1.57 - 3.14: 431 3.14 - 4.70: 70 4.70 - 6.27: 23 6.27 - 7.84: 7 Bond angle restraints: 21885 Sorted by residual: angle pdb=" C LEU D 75 " pdb=" N ILE D 76 " pdb=" CA ILE D 76 " ideal model delta sigma weight residual 120.33 123.51 -3.18 8.00e-01 1.56e+00 1.58e+01 angle pdb=" N LEU B 52 " pdb=" CA LEU B 52 " pdb=" CB LEU B 52 " ideal model delta sigma weight residual 110.49 115.58 -5.09 1.48e+00 4.57e-01 1.18e+01 angle pdb=" CA MET B 214 " pdb=" C MET B 214 " pdb=" O MET B 214 " ideal model delta sigma weight residual 120.55 117.14 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" O PHE B 62 " pdb=" C PHE B 62 " pdb=" N GLU B 63 " ideal model delta sigma weight residual 122.12 125.38 -3.26 1.06e+00 8.90e-01 9.43e+00 angle pdb=" CA TYR C 50 " pdb=" C TYR C 50 " pdb=" O TYR C 50 " ideal model delta sigma weight residual 120.55 117.30 3.25 1.06e+00 8.90e-01 9.40e+00 ... (remaining 21880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8217 17.90 - 35.81: 869 35.81 - 53.71: 222 53.71 - 71.62: 43 71.62 - 89.52: 24 Dihedral angle restraints: 9375 sinusoidal: 3810 harmonic: 5565 Sorted by residual: dihedral pdb=" CA LEU E 52 " pdb=" C LEU E 52 " pdb=" N ALA E 53 " pdb=" CA ALA E 53 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CG ARG D 13 " pdb=" CD ARG D 13 " pdb=" NE ARG D 13 " pdb=" CZ ARG D 13 " ideal model delta sinusoidal sigma weight residual -90.00 -41.94 -48.06 2 1.50e+01 4.44e-03 1.18e+01 dihedral pdb=" CB GLU C 119 " pdb=" CG GLU C 119 " pdb=" CD GLU C 119 " pdb=" OE1 GLU C 119 " ideal model delta sinusoidal sigma weight residual 0.00 88.76 -88.76 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 9372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1780 0.040 - 0.080: 472 0.080 - 0.120: 109 0.120 - 0.160: 12 0.160 - 0.200: 2 Chirality restraints: 2375 Sorted by residual: chirality pdb=" CA LEU B 52 " pdb=" N LEU B 52 " pdb=" C LEU B 52 " pdb=" CB LEU B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 2372 not shown) Planarity restraints: 2750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 80 " 0.013 2.00e-02 2.50e+03 1.57e-02 4.29e+00 pdb=" CG PHE E 80 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE E 80 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE E 80 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 80 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 80 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 80 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 164 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO B 165 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 164 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 165 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.027 5.00e-02 4.00e+02 ... (remaining 2747 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 175 2.63 - 3.20: 13753 3.20 - 3.76: 26577 3.76 - 4.33: 37133 4.33 - 4.90: 60170 Nonbonded interactions: 137808 Sorted by model distance: nonbonded pdb=" O LEU C 52 " pdb=" CD1 LEU C 52 " model vdw 2.059 3.460 nonbonded pdb=" NH2 ARG B 51 " pdb=" O PHE B 257 " model vdw 2.163 3.120 nonbonded pdb=" OE1 GLU D 292 " pdb=" OG SER E 16 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR E 43 " pdb=" O ARG E 255 " model vdw 2.213 3.040 nonbonded pdb=" O GLN A 353 " pdb=" NH1 ARG A 356 " model vdw 2.236 3.120 ... (remaining 137803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.730 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.003 0.036 16065 Z= 0.203 Angle : 0.564 7.838 21885 Z= 0.319 Chirality : 0.039 0.200 2375 Planarity : 0.004 0.048 2750 Dihedral : 16.167 89.523 5785 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.66 % Favored : 98.29 % Rotamer: Outliers : 1.53 % Allowed : 15.63 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.18), residues: 1870 helix: 1.47 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.39 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.002 0.001 HIS B 267 PHE 0.036 0.001 PHE E 80 TYR 0.024 0.001 TYR D 97 ARG 0.010 0.000 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.6529 (mtm-85) REVERT: D 374 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7286 (tm-30) REVERT: B 13 ARG cc_start: 0.7923 (ptt180) cc_final: 0.7683 (ptt90) REVERT: E 169 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8083 (tptp) REVERT: A 25 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.6909 (mtm-85) REVERT: A 374 GLU cc_start: 0.7949 (mp0) cc_final: 0.7451 (mp0) REVERT: C 119 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: C 169 LYS cc_start: 0.8334 (mttp) cc_final: 0.8056 (mmmt) outliers start: 26 outliers final: 17 residues processed: 222 average time/residue: 1.5089 time to fit residues: 366.6327 Evaluate side-chains 207 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 GLN A 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16065 Z= 0.217 Angle : 0.521 7.691 21885 Z= 0.272 Chirality : 0.039 0.152 2375 Planarity : 0.004 0.050 2750 Dihedral : 5.652 80.529 2119 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.60 % Allowed : 15.10 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 1870 helix: 1.45 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.40 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 309 HIS 0.003 0.001 HIS A 326 PHE 0.025 0.001 PHE E 80 TYR 0.022 0.001 TYR D 97 ARG 0.008 0.001 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 1.910 Fit side-chains REVERT: D 25 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.6646 (mtm-85) REVERT: D 374 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7130 (tm-30) REVERT: B 13 ARG cc_start: 0.7923 (ptt180) cc_final: 0.7589 (ptt90) REVERT: B 376 GLN cc_start: 0.7414 (mt0) cc_final: 0.7168 (mt0) REVERT: E 119 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: A 25 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.6931 (mtm-85) REVERT: C 169 LYS cc_start: 0.8349 (mttp) cc_final: 0.8103 (mmmt) REVERT: C 331 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7164 (ttp-170) REVERT: C 333 GLU cc_start: 0.8315 (pt0) cc_final: 0.7865 (pt0) outliers start: 44 outliers final: 19 residues processed: 233 average time/residue: 1.4641 time to fit residues: 373.4190 Evaluate side-chains 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 181 optimal weight: 0.2980 chunk 149 optimal weight: 0.0980 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16065 Z= 0.152 Angle : 0.477 6.996 21885 Z= 0.250 Chirality : 0.037 0.151 2375 Planarity : 0.004 0.050 2750 Dihedral : 4.557 46.892 2092 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.36 % Allowed : 15.69 % Favored : 81.95 % 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: 1.30 (0.18), residues: 1870 helix: 1.54 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.40 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.002 0.001 HIS A 326 PHE 0.015 0.001 PHE D 80 TYR 0.018 0.001 TYR A 97 ARG 0.006 0.000 ARG C 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.874 Fit side-chains revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.6462 (mpt180) REVERT: D 374 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7033 (tm-30) REVERT: B 13 ARG cc_start: 0.7909 (ptt180) cc_final: 0.7505 (ptt90) REVERT: B 67 LEU cc_start: 0.7906 (mp) cc_final: 0.7698 (mm) REVERT: B 203 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8337 (t70) REVERT: E 119 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: E 374 GLU cc_start: 0.8264 (mp0) cc_final: 0.8014 (mp0) REVERT: A 25 ARG cc_start: 0.8094 (mtp-110) cc_final: 0.6873 (mtm-85) REVERT: C 169 LYS cc_start: 0.8369 (mttp) cc_final: 0.8156 (mmmt) outliers start: 40 outliers final: 16 residues processed: 236 average time/residue: 1.4696 time to fit residues: 381.5535 Evaluate side-chains 204 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 GLN E 376 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16065 Z= 0.185 Angle : 0.488 7.127 21885 Z= 0.256 Chirality : 0.038 0.151 2375 Planarity : 0.004 0.049 2750 Dihedral : 4.351 46.603 2089 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.60 % Allowed : 15.81 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 1870 helix: 1.51 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.36 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 309 HIS 0.003 0.001 HIS A 326 PHE 0.022 0.001 PHE E 80 TYR 0.021 0.001 TYR C 68 ARG 0.006 0.000 ARG C 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 1.600 Fit side-chains REVERT: D 25 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.6598 (mtm-85) REVERT: D 374 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: E 119 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: E 374 GLU cc_start: 0.8242 (mp0) cc_final: 0.7964 (mp0) REVERT: A 25 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.6839 (mtm-85) REVERT: C 119 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: C 169 LYS cc_start: 0.8348 (mttp) cc_final: 0.8128 (mmmt) REVERT: C 331 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7457 (ttp-170) REVERT: C 373 MET cc_start: 0.8719 (mtm) cc_final: 0.8479 (mtt) outliers start: 44 outliers final: 21 residues processed: 225 average time/residue: 1.4010 time to fit residues: 346.6257 Evaluate side-chains 210 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 0.0270 chunk 160 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16065 Z= 0.404 Angle : 0.600 7.951 21885 Z= 0.315 Chirality : 0.044 0.165 2375 Planarity : 0.005 0.051 2750 Dihedral : 4.788 45.804 2089 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.95 % Allowed : 15.34 % Favored : 81.71 % 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: 0.68 (0.18), residues: 1870 helix: 1.03 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.65 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 309 HIS 0.004 0.001 HIS B 267 PHE 0.030 0.002 PHE E 248 TYR 0.030 0.002 TYR C 44 ARG 0.007 0.001 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 1.949 Fit side-chains REVERT: D 25 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.6702 (mtm-85) REVERT: D 374 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: B 29 TYR cc_start: 0.8973 (m-80) cc_final: 0.8744 (m-80) REVERT: B 203 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8436 (t70) REVERT: E 119 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7316 (tp30) REVERT: E 374 GLU cc_start: 0.8248 (mp0) cc_final: 0.7907 (mp0) REVERT: A 25 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.6824 (mtm-85) REVERT: A 374 GLU cc_start: 0.7910 (mp0) cc_final: 0.7351 (mp0) REVERT: C 119 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: C 169 LYS cc_start: 0.8313 (mttp) cc_final: 0.8054 (mmmt) REVERT: C 331 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7229 (ttp-170) outliers start: 50 outliers final: 24 residues processed: 226 average time/residue: 1.4422 time to fit residues: 358.3064 Evaluate side-chains 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 178 optimal weight: 0.0970 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16065 Z= 0.181 Angle : 0.505 7.722 21885 Z= 0.264 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.480 46.329 2089 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.65 % Allowed : 15.75 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 1870 helix: 1.32 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.47 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 309 HIS 0.003 0.001 HIS A 326 PHE 0.019 0.001 PHE D 80 TYR 0.020 0.001 TYR A 97 ARG 0.007 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 1.852 Fit side-chains REVERT: D 25 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.6651 (mtm-85) REVERT: D 374 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: B 203 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8282 (t70) REVERT: E 119 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7202 (tp30) REVERT: E 374 GLU cc_start: 0.8245 (mp0) cc_final: 0.7916 (mp0) REVERT: A 25 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.6871 (mtm-85) REVERT: A 374 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: C 119 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: C 169 LYS cc_start: 0.8309 (mttp) cc_final: 0.8077 (mmmt) REVERT: C 331 ARG cc_start: 0.7732 (ttp-110) cc_final: 0.7296 (ttp-170) REVERT: C 373 MET cc_start: 0.8682 (mtm) cc_final: 0.8411 (mtm) outliers start: 45 outliers final: 26 residues processed: 219 average time/residue: 1.3815 time to fit residues: 333.4578 Evaluate side-chains 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 178 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16065 Z= 0.157 Angle : 0.479 6.844 21885 Z= 0.250 Chirality : 0.037 0.150 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.324 46.175 2089 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.48 % Allowed : 16.17 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 1870 helix: 1.46 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.38 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.002 0.001 HIS A 326 PHE 0.020 0.001 PHE D 80 TYR 0.018 0.001 TYR D 97 ARG 0.007 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 1.851 Fit side-chains REVERT: D 25 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.6647 (mtm-85) REVERT: D 374 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: B 203 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8286 (t70) REVERT: E 119 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7181 (tp30) REVERT: E 374 GLU cc_start: 0.8302 (mp0) cc_final: 0.7915 (mp0) REVERT: A 25 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.6862 (mtm-85) REVERT: A 271 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6429 (mp) REVERT: A 374 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: C 119 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7187 (tp30) REVERT: C 123 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8291 (tt) REVERT: C 169 LYS cc_start: 0.8331 (mttp) cc_final: 0.8102 (mmmt) REVERT: C 331 ARG cc_start: 0.7719 (ttp-110) cc_final: 0.7307 (ttp-170) outliers start: 42 outliers final: 23 residues processed: 224 average time/residue: 1.3426 time to fit residues: 331.8422 Evaluate side-chains 212 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN E 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16065 Z= 0.173 Angle : 0.492 6.974 21885 Z= 0.256 Chirality : 0.037 0.151 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.337 46.526 2089 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.12 % Allowed : 16.46 % Favored : 81.42 % 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: 1.25 (0.19), residues: 1870 helix: 1.47 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.35 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 309 HIS 0.002 0.001 HIS A 326 PHE 0.024 0.001 PHE B 80 TYR 0.027 0.001 TYR A 33 ARG 0.006 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 1.728 Fit side-chains REVERT: D 25 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.6645 (mtm-85) REVERT: D 374 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: B 203 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8291 (t70) REVERT: E 119 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: E 374 GLU cc_start: 0.8307 (mp0) cc_final: 0.7916 (mp0) REVERT: A 25 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.6871 (mtm-85) REVERT: A 374 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: C 119 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: C 123 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8318 (tt) REVERT: C 169 LYS cc_start: 0.8340 (mttp) cc_final: 0.8119 (mmmt) REVERT: C 331 ARG cc_start: 0.7736 (ttp-110) cc_final: 0.7291 (ttp-170) outliers start: 36 outliers final: 23 residues processed: 214 average time/residue: 1.4350 time to fit residues: 338.2338 Evaluate side-chains 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN E 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16065 Z= 0.155 Angle : 0.483 7.698 21885 Z= 0.250 Chirality : 0.037 0.150 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.277 46.630 2089 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % Rotamer: Outliers : 2.06 % Allowed : 16.28 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 1870 helix: 1.52 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.33 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.002 0.001 HIS A 326 PHE 0.023 0.001 PHE B 80 TYR 0.025 0.001 TYR A 33 ARG 0.006 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.898 Fit side-chains REVERT: D 25 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.6638 (mtm-85) REVERT: D 374 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: B 203 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8302 (t70) REVERT: E 119 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: E 374 GLU cc_start: 0.8334 (mp0) cc_final: 0.8022 (mp0) REVERT: A 25 ARG cc_start: 0.8115 (mtp-110) cc_final: 0.6860 (mtm-85) REVERT: A 374 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: C 119 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7163 (tp30) REVERT: C 123 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8340 (tt) REVERT: C 169 LYS cc_start: 0.8328 (mttp) cc_final: 0.8105 (mmmt) REVERT: C 331 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7354 (ttp-170) outliers start: 35 outliers final: 23 residues processed: 221 average time/residue: 1.3813 time to fit residues: 336.9929 Evaluate side-chains 216 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN E 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16065 Z= 0.176 Angle : 0.496 7.662 21885 Z= 0.258 Chirality : 0.038 0.157 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.314 46.677 2089 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 1.83 % Allowed : 16.81 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 1870 helix: 1.50 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.32 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 309 HIS 0.002 0.001 HIS A 326 PHE 0.031 0.001 PHE B 80 TYR 0.024 0.001 TYR A 33 ARG 0.006 0.000 ARG E 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.829 Fit side-chains REVERT: D 25 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.6661 (mtm-85) REVERT: D 374 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: B 203 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8331 (t70) REVERT: E 119 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7155 (tp30) REVERT: E 374 GLU cc_start: 0.8332 (mp0) cc_final: 0.8014 (mp0) REVERT: A 25 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.6873 (mtm-85) REVERT: A 374 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: C 119 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7179 (tp30) REVERT: C 123 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8350 (tt) REVERT: C 169 LYS cc_start: 0.8329 (mttp) cc_final: 0.8107 (mmmt) REVERT: C 331 ARG cc_start: 0.7731 (ttp-110) cc_final: 0.7358 (ttp-170) outliers start: 31 outliers final: 21 residues processed: 214 average time/residue: 1.4254 time to fit residues: 335.3373 Evaluate side-chains 210 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN D 376 GLN B 369 ASN E 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094524 restraints weight = 19231.205| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.45 r_work: 0.2997 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16065 Z= 0.233 Angle : 0.527 7.824 21885 Z= 0.276 Chirality : 0.039 0.157 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.456 46.935 2089 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.83 % Allowed : 16.76 % Favored : 81.42 % 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: 1.00 (0.19), residues: 1870 helix: 1.28 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.54 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 309 HIS 0.003 0.001 HIS A 326 PHE 0.032 0.002 PHE B 80 TYR 0.026 0.001 TYR A 97 ARG 0.005 0.000 ARG E 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5831.11 seconds wall clock time: 105 minutes 31.73 seconds (6331.73 seconds total)