Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 22:40:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/04_2023/7ek3_31167.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/04_2023/7ek3_31167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/04_2023/7ek3_31167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/04_2023/7ek3_31167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/04_2023/7ek3_31167.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/04_2023/7ek3_31167.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8700 2.51 5 N 2360 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ASP 231": "OD1" <-> "OD2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ASP 354": "OD1" <-> "OD2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 390": "OD1" <-> "OD2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ASP 231": "OD1" <-> "OD2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E ASP 231": "OD1" <-> "OD2" Residue "E ASP 262": "OD1" <-> "OD2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E ASP 354": "OD1" <-> "OD2" Residue "E PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 390": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13505 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2701 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain: "B" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2701 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2701 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain: "D" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2701 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain: "E" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2701 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Time building chain proxies: 7.17, per 1000 atoms: 0.53 Number of scatterers: 13505 At special positions: 0 Unit cell: (108.896, 111.552, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2390 8.00 N 2360 7.00 C 8700 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: 5.46 Conformation dependent library (CDL) restraints added in 1.9 seconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 88.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.708A pdb=" N ILE A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 162 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 176 through 226 Proline residue: A 184 - end of helix Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 254 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.603A pdb=" N VAL A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 310 through 326 Processing helix chain 'A' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASP A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 388 through 406 removed outlier: 3.751A pdb=" N VAL A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 397 " --> pdb=" O CYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 removed outlier: 3.577A pdb=" N GLY A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.709A pdb=" N ILE B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 133 through 162 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 176 through 226 Proline residue: B 184 - end of helix Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 231 through 254 Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.603A pdb=" N VAL B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'B' and resid 310 through 326 Processing helix chain 'B' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.751A pdb=" N VAL B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 397 " --> pdb=" O CYS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 418 removed outlier: 3.577A pdb=" N GLY B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.709A pdb=" N ILE C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 103 Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 162 Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 176 through 226 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 254 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 268 through 277 removed outlier: 3.603A pdb=" N VAL C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'C' and resid 310 through 326 Processing helix chain 'C' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 388 through 406 removed outlier: 3.751A pdb=" N VAL C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 397 " --> pdb=" O CYS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.576A pdb=" N GLY C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 removed outlier: 3.708A pdb=" N ILE D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 162 Proline residue: D 141 - end of helix Processing helix chain 'D' and resid 176 through 226 Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 231 through 254 Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 268 through 277 removed outlier: 3.603A pdb=" N VAL D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'D' and resid 310 through 326 Processing helix chain 'D' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASP D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 388 through 406 removed outlier: 3.751A pdb=" N VAL D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG D 397 " --> pdb=" O CYS D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 418 removed outlier: 3.577A pdb=" N GLY D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.708A pdb=" N ILE E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 162 Proline residue: E 141 - end of helix Processing helix chain 'E' and resid 176 through 226 Proline residue: E 184 - end of helix Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 254 Proline residue: E 246 - end of helix Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 268 through 277 removed outlier: 3.604A pdb=" N VAL E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'E' and resid 310 through 326 Processing helix chain 'E' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASP E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE E 373 " --> pdb=" O SER E 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 374 " --> pdb=" O LEU E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 388 through 406 removed outlier: 3.752A pdb=" N VAL E 396 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 397 " --> pdb=" O CYS E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 418 removed outlier: 3.577A pdb=" N GLY E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 3030 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: 4.14 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1843 1.26 - 1.40: 3443 1.40 - 1.54: 7665 1.54 - 1.68: 764 1.68 - 1.81: 75 Bond restraints: 13790 Sorted by residual: bond pdb=" C PRO B 385 " pdb=" O PRO B 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.20e+01 bond pdb=" C PRO A 385 " pdb=" O PRO A 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.16e+01 bond pdb=" C PRO C 385 " pdb=" O PRO C 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.13e+01 bond pdb=" C PRO D 385 " pdb=" O PRO D 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.13e+01 bond pdb=" C PRO E 385 " pdb=" O PRO E 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.12e+01 ... (remaining 13785 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.92: 617 106.92 - 113.84: 7664 113.84 - 120.76: 6219 120.76 - 127.67: 4030 127.67 - 134.59: 225 Bond angle restraints: 18755 Sorted by residual: angle pdb=" CA ILE A 140 " pdb=" C ILE A 140 " pdb=" N PRO A 141 " ideal model delta sigma weight residual 120.83 130.60 -9.77 5.90e-01 2.87e+00 2.74e+02 angle pdb=" CA ILE D 140 " pdb=" C ILE D 140 " pdb=" N PRO D 141 " ideal model delta sigma weight residual 120.83 130.59 -9.76 5.90e-01 2.87e+00 2.74e+02 angle pdb=" CA ILE C 140 " pdb=" C ILE C 140 " pdb=" N PRO C 141 " ideal model delta sigma weight residual 120.83 130.59 -9.76 5.90e-01 2.87e+00 2.73e+02 angle pdb=" CA ILE B 140 " pdb=" C ILE B 140 " pdb=" N PRO B 141 " ideal model delta sigma weight residual 120.83 130.58 -9.75 5.90e-01 2.87e+00 2.73e+02 angle pdb=" CA ILE E 140 " pdb=" C ILE E 140 " pdb=" N PRO E 141 " ideal model delta sigma weight residual 120.83 130.58 -9.75 5.90e-01 2.87e+00 2.73e+02 ... (remaining 18750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7537 17.25 - 34.49: 633 34.49 - 51.74: 136 51.74 - 68.98: 54 68.98 - 86.23: 15 Dihedral angle restraints: 8375 sinusoidal: 3350 harmonic: 5025 Sorted by residual: dihedral pdb=" N GLN D 401 " pdb=" C GLN D 401 " pdb=" CA GLN D 401 " pdb=" CB GLN D 401 " ideal model delta harmonic sigma weight residual 122.80 112.07 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" N GLN C 401 " pdb=" C GLN C 401 " pdb=" CA GLN C 401 " pdb=" CB GLN C 401 " ideal model delta harmonic sigma weight residual 122.80 112.07 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" N GLN A 401 " pdb=" C GLN A 401 " pdb=" CA GLN A 401 " pdb=" CB GLN A 401 " ideal model delta harmonic sigma weight residual 122.80 112.08 10.72 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 8372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 946 0.048 - 0.096: 637 0.096 - 0.144: 462 0.144 - 0.192: 160 0.192 - 0.240: 40 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CB VAL C 359 " pdb=" CA VAL C 359 " pdb=" CG1 VAL C 359 " pdb=" CG2 VAL C 359 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL B 359 " pdb=" CA VAL B 359 " pdb=" CG1 VAL B 359 " pdb=" CG2 VAL B 359 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL D 359 " pdb=" CA VAL D 359 " pdb=" CG1 VAL D 359 " pdb=" CG2 VAL D 359 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2242 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 343 " 0.030 2.00e-02 2.50e+03 1.53e-02 5.86e+00 pdb=" CG TRP C 343 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP C 343 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C 343 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP C 343 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 343 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 343 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 343 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 343 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 343 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 343 " 0.030 2.00e-02 2.50e+03 1.53e-02 5.86e+00 pdb=" CG TRP E 343 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP E 343 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP E 343 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP E 343 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 343 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 343 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 343 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 343 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 343 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 343 " 0.030 2.00e-02 2.50e+03 1.53e-02 5.83e+00 pdb=" CG TRP D 343 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP D 343 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP D 343 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP D 343 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 343 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 343 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 343 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 343 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 343 " 0.009 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1144 2.76 - 3.30: 14061 3.30 - 3.83: 22548 3.83 - 4.37: 28970 4.37 - 4.90: 46596 Nonbonded interactions: 113319 Sorted by model distance: nonbonded pdb=" OH TYR D 179 " pdb=" OG1 THR D 346 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR A 179 " pdb=" OG1 THR A 346 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR C 179 " pdb=" OG1 THR C 346 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR E 179 " pdb=" OG1 THR E 346 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR B 179 " pdb=" OG1 THR B 346 " model vdw 2.232 2.440 ... (remaining 113314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.080 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: 1.710 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 35.190 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.018 0.116 13790 Z= 1.181 Angle : 1.847 11.599 18755 Z= 1.370 Chirality : 0.084 0.240 2245 Planarity : 0.006 0.022 2340 Dihedral : 14.915 86.230 5085 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.30 % 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: -0.56 (0.19), residues: 1695 helix: -0.07 (0.13), residues: 1430 sheet: None (None), residues: 0 loop : -1.31 (0.35), residues: 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 281 time to evaluate : 1.749 Fit side-chains outliers start: 25 outliers final: 3 residues processed: 299 average time/residue: 1.6785 time to fit residues: 536.8447 Evaluate side-chains 205 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 202 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.1590 time to fit residues: 3.0550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 30.0000 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 264 GLN C 104 GLN D 252 HIS D 264 GLN E 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 13790 Z= 0.243 Angle : 0.620 6.932 18755 Z= 0.322 Chirality : 0.042 0.153 2245 Planarity : 0.005 0.039 2340 Dihedral : 4.348 25.005 1855 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.21), residues: 1695 helix: 1.49 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.89 (0.38), residues: 250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 1.692 Fit side-chains outliers start: 39 outliers final: 10 residues processed: 240 average time/residue: 1.5257 time to fit residues: 394.4872 Evaluate side-chains 202 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 1.591 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 5 average time/residue: 0.4320 time to fit residues: 4.8520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 264 GLN D 401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 13790 Z= 0.287 Angle : 0.612 6.741 18755 Z= 0.314 Chirality : 0.042 0.155 2245 Planarity : 0.005 0.043 2340 Dihedral : 4.259 24.673 1855 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer Outliers : 3.31 % 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: 1.86 (0.21), residues: 1695 helix: 1.65 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -1.04 (0.36), residues: 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 1.605 Fit side-chains outliers start: 50 outliers final: 25 residues processed: 231 average time/residue: 1.4524 time to fit residues: 362.8414 Evaluate side-chains 215 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 13 average time/residue: 0.2681 time to fit residues: 7.0239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS D 264 GLN D 401 GLN E 375 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 13790 Z= 0.211 Angle : 0.539 6.644 18755 Z= 0.276 Chirality : 0.039 0.151 2245 Planarity : 0.005 0.042 2340 Dihedral : 4.027 22.236 1855 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 2.72 % 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: 2.26 (0.21), residues: 1695 helix: 1.96 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -1.13 (0.36), residues: 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 197 time to evaluate : 1.731 Fit side-chains outliers start: 41 outliers final: 21 residues processed: 220 average time/residue: 1.4810 time to fit residues: 352.0930 Evaluate side-chains 213 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 9 average time/residue: 0.5000 time to fit residues: 7.7457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 30.0000 chunk 93 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 104 GLN D 264 GLN D 401 GLN E 375 GLN E 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 13790 Z= 0.275 Angle : 0.576 6.651 18755 Z= 0.295 Chirality : 0.041 0.157 2245 Planarity : 0.005 0.044 2340 Dihedral : 4.112 23.025 1855 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 2.52 % 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: 2.29 (0.20), residues: 1695 helix: 1.96 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -1.10 (0.36), residues: 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 1.623 Fit side-chains outliers start: 38 outliers final: 25 residues processed: 208 average time/residue: 1.4747 time to fit residues: 331.1895 Evaluate side-chains 212 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 11 average time/residue: 0.5416 time to fit residues: 9.1135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 96 optimal weight: 0.0010 chunk 40 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 307 GLN C 401 GLN D 264 GLN D 401 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 13790 Z= 0.159 Angle : 0.494 6.624 18755 Z= 0.251 Chirality : 0.038 0.148 2245 Planarity : 0.004 0.042 2340 Dihedral : 3.738 19.838 1855 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 2.12 % 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: 2.79 (0.21), residues: 1695 helix: 2.33 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -1.03 (0.36), residues: 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 1.720 Fit side-chains outliers start: 32 outliers final: 17 residues processed: 222 average time/residue: 1.4640 time to fit residues: 352.4135 Evaluate side-chains 218 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 4 average time/residue: 0.5481 time to fit residues: 4.8069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 0.1980 chunk 138 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 99 optimal weight: 0.0970 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN D 264 GLN E 375 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 13790 Z= 0.202 Angle : 0.518 6.586 18755 Z= 0.263 Chirality : 0.039 0.151 2245 Planarity : 0.005 0.042 2340 Dihedral : 3.785 20.594 1855 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 2.32 % 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: 2.78 (0.21), residues: 1695 helix: 2.32 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.99 (0.36), residues: 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 1.567 Fit side-chains outliers start: 35 outliers final: 25 residues processed: 220 average time/residue: 1.4899 time to fit residues: 354.7566 Evaluate side-chains 221 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 10 average time/residue: 0.6845 time to fit residues: 10.2370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 111 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 221 GLN D 264 GLN E 375 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 13790 Z= 0.247 Angle : 0.552 6.597 18755 Z= 0.281 Chirality : 0.040 0.155 2245 Planarity : 0.005 0.043 2340 Dihedral : 3.928 21.764 1855 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 2.05 % 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: 2.74 (0.21), residues: 1695 helix: 2.26 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.90 (0.38), residues: 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 1.550 Fit side-chains outliers start: 31 outliers final: 24 residues processed: 213 average time/residue: 1.4654 time to fit residues: 337.3615 Evaluate side-chains 208 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 9 average time/residue: 0.6225 time to fit residues: 8.8868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN E 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 13790 Z= 0.247 Angle : 0.556 6.592 18755 Z= 0.282 Chirality : 0.040 0.154 2245 Planarity : 0.005 0.043 2340 Dihedral : 3.955 21.752 1855 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 2.05 % 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: 2.58 (0.21), residues: 1695 helix: 2.17 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.95 (0.36), residues: 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 1.586 Fit side-chains outliers start: 31 outliers final: 25 residues processed: 202 average time/residue: 1.5218 time to fit residues: 332.3543 Evaluate side-chains 213 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 16 residues processed: 10 average time/residue: 0.8583 time to fit residues: 11.9636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 13790 Z= 0.241 Angle : 0.549 6.582 18755 Z= 0.280 Chirality : 0.040 0.153 2245 Planarity : 0.005 0.043 2340 Dihedral : 3.942 21.628 1855 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.59 % 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: 2.60 (0.21), residues: 1695 helix: 2.18 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.91 (0.37), residues: 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.819 Fit side-chains outliers start: 24 outliers final: 21 residues processed: 207 average time/residue: 1.4296 time to fit residues: 320.5153 Evaluate side-chains 202 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 3 average time/residue: 0.1549 time to fit residues: 2.8355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 221 GLN B 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.091265 restraints weight = 14768.404| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.33 r_work: 0.2726 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 13790 Z= 0.182 Angle : 0.508 6.566 18755 Z= 0.259 Chirality : 0.038 0.150 2245 Planarity : 0.005 0.042 2340 Dihedral : 3.766 20.439 1855 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.21), residues: 1695 helix: 2.36 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 260 =============================================================================== Job complete usr+sys time: 5401.13 seconds wall clock time: 96 minutes 24.16 seconds (5784.16 seconds total)