Starting phenix.real_space_refine on Fri Jul 19 10:31:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xml_33300/07_2024/7xml_33300_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xml_33300/07_2024/7xml_33300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xml_33300/07_2024/7xml_33300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xml_33300/07_2024/7xml_33300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xml_33300/07_2024/7xml_33300_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xml_33300/07_2024/7xml_33300_neut.cif" } resolution = 3.2 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= 0.009 sd= 0.227 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 Mg 2 5.21 5 S 24 5.16 5 C 4794 2.51 5 N 1264 2.21 5 O 1542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7626 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3258 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain: "C" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 554 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "B" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3258 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 554 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.55, per 1000 atoms: 0.60 Number of scatterers: 7626 At special positions: 0 Unit cell: (134.48, 104.14, 77.9, 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) S 24 16.00 Mg 2 11.99 O 1542 8.00 N 1264 7.00 C 4794 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 40.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 removed outlier: 4.041A pdb=" N ASN A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.532A pdb=" N ILE A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 126 removed outlier: 3.686A pdb=" N ILE A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 122 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.750A pdb=" N ALA A 156 " --> pdb=" O GLY A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.713A pdb=" N GLY A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.566A pdb=" N VAL A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 removed outlier: 3.856A pdb=" N ASP A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.987A pdb=" N LEU A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.662A pdb=" N VAL A 318 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 4.191A pdb=" N LYS A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.686A pdb=" N PHE A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 359 " --> pdb=" O MET A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.784A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.904A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 removed outlier: 4.000A pdb=" N SER A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'B' and resid 64 through 74 removed outlier: 4.042A pdb=" N ASN B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.532A pdb=" N ILE B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.686A pdb=" N ILE B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA B 122 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 153 through 156 removed outlier: 3.749A pdb=" N ALA B 156 " --> pdb=" O GLY B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 174 through 197 removed outlier: 3.713A pdb=" N GLY B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 230 removed outlier: 3.566A pdb=" N VAL B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 removed outlier: 3.855A pdb=" N ASP B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.987A pdb=" N LEU B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.663A pdb=" N VAL B 318 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 4.190A pdb=" N LYS B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.686A pdb=" N PHE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 359 " --> pdb=" O MET B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.784A pdb=" N VAL B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 removed outlier: 3.904A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 removed outlier: 3.999A pdb=" N SER B 424 " --> pdb=" O GLY B 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 63 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 13 removed outlier: 4.127A pdb=" N ASP A 6 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 21 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.926A pdb=" N LEU A 142 " --> pdb=" O GLN A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 151 removed outlier: 6.871A pdb=" N PHE A 165 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A 168 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 283 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU A 239 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 285 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 335 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 313 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 337 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 336 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER A 366 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 338 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN A 388 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 249 through 250 removed outlier: 3.693A pdb=" N LYS A 255 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 16 through 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 13 removed outlier: 4.127A pdb=" N ASP B 6 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 21 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.926A pdb=" N LEU B 142 " --> pdb=" O GLN B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 151 removed outlier: 6.871A pdb=" N PHE B 165 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 168 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE B 283 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU B 239 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 285 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 335 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 313 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU B 337 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 336 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER B 366 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 338 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 388 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 250 removed outlier: 3.693A pdb=" N LYS B 255 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 16 through 20 280 hydrogen bonds defined for protein. 798 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: 2.18 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2481 1.34 - 1.45: 967 1.45 - 1.57: 4252 1.57 - 1.69: 0 1.69 - 1.80: 46 Bond restraints: 7746 Sorted by residual: bond pdb=" CA SER B 139 " pdb=" CB SER B 139 " ideal model delta sigma weight residual 1.527 1.466 0.061 1.75e-02 3.27e+03 1.20e+01 bond pdb=" CA SER A 139 " pdb=" CB SER A 139 " ideal model delta sigma weight residual 1.527 1.466 0.061 1.75e-02 3.27e+03 1.20e+01 bond pdb=" CB VAL A 312 " pdb=" CG2 VAL A 312 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.77e+00 bond pdb=" CB VAL B 312 " pdb=" CG2 VAL B 312 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.77e+00 bond pdb=" CB ASP A 374 " pdb=" CG ASP A 374 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.07e+00 ... (remaining 7741 not shown) Histogram of bond angle deviations from ideal: 97.41 - 104.72: 116 104.72 - 112.02: 3516 112.02 - 119.33: 2935 119.33 - 126.63: 3865 126.63 - 133.94: 68 Bond angle restraints: 10500 Sorted by residual: angle pdb=" CA LEU A 60 " pdb=" CB LEU A 60 " pdb=" CG LEU A 60 " ideal model delta sigma weight residual 116.30 130.22 -13.92 3.50e+00 8.16e-02 1.58e+01 angle pdb=" CA LEU B 60 " pdb=" CB LEU B 60 " pdb=" CG LEU B 60 " ideal model delta sigma weight residual 116.30 130.22 -13.92 3.50e+00 8.16e-02 1.58e+01 angle pdb=" N ILE A 284 " pdb=" CA ILE A 284 " pdb=" C ILE A 284 " ideal model delta sigma weight residual 113.47 109.46 4.01 1.01e+00 9.80e-01 1.58e+01 angle pdb=" N ILE B 284 " pdb=" CA ILE B 284 " pdb=" C ILE B 284 " ideal model delta sigma weight residual 113.47 109.46 4.01 1.01e+00 9.80e-01 1.58e+01 angle pdb=" C THR B 372 " pdb=" N GLU B 373 " pdb=" CA GLU B 373 " ideal model delta sigma weight residual 121.54 128.64 -7.10 1.91e+00 2.74e-01 1.38e+01 ... (remaining 10495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.53: 4375 14.53 - 29.06: 197 29.06 - 43.59: 66 43.59 - 58.12: 8 58.12 - 72.65: 4 Dihedral angle restraints: 4650 sinusoidal: 1826 harmonic: 2824 Sorted by residual: dihedral pdb=" CA GLU A 373 " pdb=" C GLU A 373 " pdb=" N ASP A 374 " pdb=" CA ASP A 374 " ideal model delta harmonic sigma weight residual 180.00 132.21 47.79 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA GLU B 373 " pdb=" C GLU B 373 " pdb=" N ASP B 374 " pdb=" CA ASP B 374 " ideal model delta harmonic sigma weight residual 180.00 132.21 47.79 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA ASN D 24 " pdb=" C ASN D 24 " pdb=" N PRO D 25 " pdb=" CA PRO D 25 " ideal model delta harmonic sigma weight residual 180.00 -144.48 -35.52 0 5.00e+00 4.00e-02 5.05e+01 ... (remaining 4647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 816 0.056 - 0.111: 302 0.111 - 0.167: 59 0.167 - 0.222: 7 0.222 - 0.278: 4 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CB VAL D 13 " pdb=" CA VAL D 13 " pdb=" CG1 VAL D 13 " pdb=" CG2 VAL D 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL C 13 " pdb=" CA VAL C 13 " pdb=" CG1 VAL C 13 " pdb=" CG2 VAL C 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE B 149 " pdb=" CA ILE B 149 " pdb=" CG1 ILE B 149 " pdb=" CG2 ILE B 149 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1185 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 350 " 0.008 2.00e-02 2.50e+03 1.60e-02 4.50e+00 pdb=" CG PHE B 350 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 350 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 350 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 350 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 350 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 350 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 350 " 0.008 2.00e-02 2.50e+03 1.60e-02 4.50e+00 pdb=" CG PHE A 350 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 350 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 350 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 350 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 350 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 350 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 374 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" CG ASP A 374 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP A 374 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 374 " 0.012 2.00e-02 2.50e+03 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2610 2.86 - 3.37: 6815 3.37 - 3.88: 11979 3.88 - 4.39: 13484 4.39 - 4.90: 24071 Nonbonded interactions: 58959 Sorted by model distance: nonbonded pdb=" OG SER A 267 " pdb=" OD2 ASP A 294 " model vdw 2.350 2.440 nonbonded pdb=" OG SER B 267 " pdb=" OD2 ASP B 294 " model vdw 2.350 2.440 nonbonded pdb=" O SER A 139 " pdb=" OG SER A 139 " model vdw 2.368 2.440 nonbonded pdb=" O SER B 139 " pdb=" OG SER B 139 " model vdw 2.368 2.440 nonbonded pdb=" OD1 ASN B 138 " pdb=" NZ LYS B 140 " model vdw 2.369 2.520 ... (remaining 58954 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' and resid 1 through 428) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.550 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 0.073 7746 Z= 0.590 Angle : 0.932 13.919 10500 Z= 0.510 Chirality : 0.059 0.278 1188 Planarity : 0.006 0.046 1394 Dihedral : 10.107 72.648 2850 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.15 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.21 % 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: -4.61 (0.21), residues: 982 helix: -3.27 (0.17), residues: 360 sheet: -3.06 (0.34), residues: 130 loop : -2.84 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 273 HIS 0.006 0.002 HIS A 187 PHE 0.031 0.004 PHE B 350 TYR 0.014 0.002 TYR C 66 ARG 0.005 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 100 THR cc_start: 0.8098 (t) cc_final: 0.7732 (p) REVERT: A 164 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7908 (mt-10) REVERT: A 292 GLU cc_start: 0.7097 (pm20) cc_final: 0.6877 (mm-30) REVERT: A 354 GLU cc_start: 0.7240 (tp30) cc_final: 0.6906 (tp30) REVERT: B 78 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 100 THR cc_start: 0.8107 (t) cc_final: 0.7739 (p) REVERT: B 164 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7929 (mt-10) REVERT: B 292 GLU cc_start: 0.7086 (pm20) cc_final: 0.6875 (mm-30) REVERT: B 354 GLU cc_start: 0.7217 (tp30) cc_final: 0.6885 (tp30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2525 time to fit residues: 46.9500 Evaluate side-chains 89 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 257 HIS C 27 ASN B 211 ASN B 257 HIS D 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7746 Z= 0.168 Angle : 0.543 7.670 10500 Z= 0.281 Chirality : 0.042 0.150 1188 Planarity : 0.004 0.032 1394 Dihedral : 5.500 34.797 1062 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.86 % Allowed : 7.64 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.24), residues: 982 helix: -1.89 (0.23), residues: 386 sheet: -2.43 (0.40), residues: 130 loop : -2.44 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 21 HIS 0.004 0.001 HIS B 257 PHE 0.009 0.001 PHE B 248 TYR 0.014 0.001 TYR C 66 ARG 0.003 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7062 (ttp80) cc_final: 0.6838 (ttt-90) REVERT: B 34 ARG cc_start: 0.7056 (ttp80) cc_final: 0.6831 (ttt-90) REVERT: B 78 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7431 (mm-30) outliers start: 7 outliers final: 2 residues processed: 102 average time/residue: 0.1884 time to fit residues: 26.3042 Evaluate side-chains 85 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 0.0770 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.0170 chunk 87 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7746 Z= 0.132 Angle : 0.482 7.575 10500 Z= 0.250 Chirality : 0.042 0.148 1188 Planarity : 0.003 0.027 1394 Dihedral : 4.918 31.092 1062 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.74 % Allowed : 11.82 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.26), residues: 982 helix: -1.02 (0.26), residues: 386 sheet: -2.03 (0.43), residues: 134 loop : -2.17 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 21 HIS 0.005 0.001 HIS B 257 PHE 0.008 0.001 PHE B 248 TYR 0.010 0.001 TYR C 66 ARG 0.002 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7324 (tt0) cc_final: 0.6849 (tt0) REVERT: C 46 GLU cc_start: 0.7646 (pp20) cc_final: 0.6822 (pm20) REVERT: B 22 GLU cc_start: 0.7312 (tt0) cc_final: 0.6836 (tt0) REVERT: D 46 GLU cc_start: 0.7285 (pp20) cc_final: 0.6450 (pm20) outliers start: 6 outliers final: 2 residues processed: 93 average time/residue: 0.2029 time to fit residues: 26.0260 Evaluate side-chains 85 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7746 Z= 0.296 Angle : 0.552 7.185 10500 Z= 0.285 Chirality : 0.044 0.137 1188 Planarity : 0.003 0.031 1394 Dihedral : 5.185 35.376 1062 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.48 % Allowed : 14.04 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.26), residues: 982 helix: -0.79 (0.27), residues: 384 sheet: -1.82 (0.45), residues: 134 loop : -2.14 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 273 HIS 0.004 0.001 HIS A 187 PHE 0.010 0.002 PHE A 248 TYR 0.014 0.002 TYR D 66 ARG 0.002 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7582 (tt0) cc_final: 0.7336 (tt0) REVERT: C 46 GLU cc_start: 0.7605 (pp20) cc_final: 0.6802 (pm20) REVERT: B 22 GLU cc_start: 0.7578 (tt0) cc_final: 0.7330 (tt0) REVERT: D 46 GLU cc_start: 0.7614 (pp20) cc_final: 0.6752 (pm20) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.1870 time to fit residues: 23.8816 Evaluate side-chains 85 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 245 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7746 Z= 0.240 Angle : 0.513 7.721 10500 Z= 0.263 Chirality : 0.043 0.142 1188 Planarity : 0.003 0.031 1394 Dihedral : 4.987 34.599 1062 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.34 % Allowed : 14.78 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.26), residues: 982 helix: -0.60 (0.27), residues: 386 sheet: -1.73 (0.45), residues: 134 loop : -2.02 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 273 HIS 0.002 0.001 HIS A 187 PHE 0.010 0.002 PHE A 248 TYR 0.013 0.001 TYR C 66 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7451 (tt0) cc_final: 0.7055 (tt0) REVERT: C 46 GLU cc_start: 0.7525 (pp20) cc_final: 0.7303 (pm20) REVERT: B 22 GLU cc_start: 0.7448 (tt0) cc_final: 0.7047 (tt0) REVERT: D 46 GLU cc_start: 0.7495 (pp20) cc_final: 0.7265 (pm20) outliers start: 19 outliers final: 13 residues processed: 97 average time/residue: 0.2062 time to fit residues: 27.3340 Evaluate side-chains 89 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 330 ASN B 293 ASN B 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7746 Z= 0.201 Angle : 0.499 8.612 10500 Z= 0.256 Chirality : 0.042 0.131 1188 Planarity : 0.003 0.028 1394 Dihedral : 4.782 33.461 1062 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.71 % Allowed : 15.02 % Favored : 82.27 % 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: -1.94 (0.27), residues: 982 helix: -0.33 (0.28), residues: 386 sheet: -1.61 (0.42), residues: 158 loop : -1.99 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 273 HIS 0.002 0.000 HIS A 187 PHE 0.009 0.001 PHE A 425 TYR 0.011 0.001 TYR D 66 ARG 0.002 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7499 (tt0) cc_final: 0.7065 (tt0) REVERT: B 22 GLU cc_start: 0.7496 (tt0) cc_final: 0.7061 (tt0) REVERT: B 78 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7071 (tp30) REVERT: D 46 GLU cc_start: 0.7416 (pp20) cc_final: 0.7184 (pm20) outliers start: 22 outliers final: 17 residues processed: 98 average time/residue: 0.2086 time to fit residues: 28.2472 Evaluate side-chains 97 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 0.0000 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- 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: 0.7581 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7746 Z= 0.263 Angle : 0.525 9.343 10500 Z= 0.269 Chirality : 0.044 0.192 1188 Planarity : 0.003 0.031 1394 Dihedral : 4.885 33.781 1062 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.96 % Allowed : 14.90 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.87 (0.27), residues: 982 helix: -0.29 (0.28), residues: 386 sheet: -1.52 (0.43), residues: 158 loop : -1.95 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 21 HIS 0.003 0.001 HIS B 420 PHE 0.010 0.002 PHE B 248 TYR 0.012 0.001 TYR C 66 ARG 0.002 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7559 (tt0) cc_final: 0.7125 (tt0) REVERT: A 78 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7065 (tp30) REVERT: B 22 GLU cc_start: 0.7555 (tt0) cc_final: 0.7124 (tt0) REVERT: B 78 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7066 (tp30) REVERT: D 46 GLU cc_start: 0.7409 (pp20) cc_final: 0.7196 (pm20) outliers start: 24 outliers final: 19 residues processed: 95 average time/residue: 0.1988 time to fit residues: 25.9954 Evaluate side-chains 94 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 45 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.7505 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7746 Z= 0.130 Angle : 0.468 9.459 10500 Z= 0.240 Chirality : 0.042 0.199 1188 Planarity : 0.003 0.026 1394 Dihedral : 4.479 30.440 1062 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.34 % Allowed : 15.39 % Favored : 82.27 % 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: -1.42 (0.27), residues: 982 helix: 0.23 (0.28), residues: 384 sheet: -1.41 (0.43), residues: 158 loop : -1.80 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 21 HIS 0.003 0.001 HIS A 420 PHE 0.008 0.001 PHE B 248 TYR 0.009 0.001 TYR D 66 ARG 0.001 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7507 (tt0) cc_final: 0.7156 (tt0) REVERT: A 78 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7096 (tp30) REVERT: B 22 GLU cc_start: 0.7507 (tt0) cc_final: 0.7151 (tt0) REVERT: B 78 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7104 (tp30) outliers start: 19 outliers final: 15 residues processed: 93 average time/residue: 0.1925 time to fit residues: 24.8381 Evaluate side-chains 92 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 0.3980 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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: 0.7576 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7746 Z= 0.267 Angle : 0.526 9.330 10500 Z= 0.271 Chirality : 0.044 0.181 1188 Planarity : 0.003 0.030 1394 Dihedral : 4.756 32.199 1062 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.46 % Allowed : 14.78 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.51 (0.27), residues: 982 helix: 0.14 (0.28), residues: 386 sheet: -1.38 (0.43), residues: 158 loop : -1.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 21 HIS 0.004 0.001 HIS B 420 PHE 0.010 0.002 PHE B 248 TYR 0.011 0.001 TYR D 66 ARG 0.002 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7589 (tt0) cc_final: 0.7070 (tt0) REVERT: A 78 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7093 (tp30) REVERT: B 22 GLU cc_start: 0.7589 (tt0) cc_final: 0.7064 (tt0) REVERT: B 78 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7121 (tp30) REVERT: D 46 GLU cc_start: 0.7352 (pp20) cc_final: 0.7115 (tt0) outliers start: 20 outliers final: 18 residues processed: 87 average time/residue: 0.1796 time to fit residues: 22.1413 Evaluate side-chains 91 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7622 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7746 Z= 0.371 Angle : 0.583 9.658 10500 Z= 0.302 Chirality : 0.046 0.189 1188 Planarity : 0.004 0.032 1394 Dihedral : 5.170 37.180 1062 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.46 % Allowed : 14.66 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.67 (0.27), residues: 982 helix: -0.11 (0.28), residues: 386 sheet: -1.47 (0.44), residues: 158 loop : -1.83 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 21 HIS 0.004 0.001 HIS B 420 PHE 0.012 0.002 PHE B 248 TYR 0.014 0.002 TYR D 66 ARG 0.004 0.000 ARG A 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7557 (tt0) cc_final: 0.7092 (tt0) REVERT: A 78 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7058 (tp30) REVERT: C 47 TYR cc_start: 0.8140 (p90) cc_final: 0.7886 (p90) REVERT: B 22 GLU cc_start: 0.7558 (tt0) cc_final: 0.7086 (tt0) REVERT: B 78 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7084 (tp30) REVERT: D 46 GLU cc_start: 0.7435 (pp20) cc_final: 0.7233 (tt0) outliers start: 20 outliers final: 17 residues processed: 94 average time/residue: 0.1717 time to fit residues: 22.9637 Evaluate side-chains 95 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.185820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136620 restraints weight = 8309.471| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.57 r_work: 0.3287 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7746 Z= 0.191 Angle : 0.503 9.726 10500 Z= 0.260 Chirality : 0.042 0.190 1188 Planarity : 0.003 0.027 1394 Dihedral : 4.785 34.067 1062 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.46 % Allowed : 15.15 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.38 (0.28), residues: 982 helix: 0.19 (0.28), residues: 386 sheet: -1.38 (0.44), residues: 158 loop : -1.71 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 273 HIS 0.003 0.001 HIS B 420 PHE 0.009 0.001 PHE B 248 TYR 0.011 0.001 TYR C 66 ARG 0.001 0.000 ARG B 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.14 seconds wall clock time: 32 minutes 3.13 seconds (1923.13 seconds total)