Starting phenix.real_space_refine on Thu Sep 26 04:31:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/09_2024/7lid_23374.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/09_2024/7lid_23374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/09_2024/7lid_23374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/09_2024/7lid_23374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/09_2024/7lid_23374.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/09_2024/7lid_23374.cif" } resolution = 2.9 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= 0.002 sd= 0.105 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 120 5.16 5 C 7992 2.51 5 N 1936 2.21 5 O 2092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12140 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'EOL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 6.14, per 1000 atoms: 0.51 Number of scatterers: 12140 At special positions: 0 Unit cell: (112.27, 112.27, 92.7, 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 120 16.00 O 2092 8.00 N 1936 7.00 C 7992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.4 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 82.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 13 through 31 removed outlier: 3.676A pdb=" N LEU A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 18 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 removed outlier: 3.674A pdb=" N LYS A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 48 through 75 removed outlier: 3.718A pdb=" N CYS A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 73 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 105 removed outlier: 3.657A pdb=" N ALA A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 3.756A pdb=" N THR A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 169 removed outlier: 3.919A pdb=" N SER A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 194 through 247 removed outlier: 4.410A pdb=" N ALA A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.943A pdb=" N GLY A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 366 removed outlier: 4.166A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 407 removed outlier: 3.771A pdb=" N LEU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.867A pdb=" N VAL A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.693A pdb=" N GLN A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 469 removed outlier: 3.677A pdb=" N ILE A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 31 removed outlier: 3.676A pdb=" N LEU B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 18 " --> pdb=" O TYR B 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.674A pdb=" N LYS B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.716A pdb=" N CYS B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 73 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 105 removed outlier: 3.658A pdb=" N ALA B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 removed outlier: 3.757A pdb=" N THR B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 169 removed outlier: 3.919A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 194 through 247 removed outlier: 4.411A pdb=" N ALA B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Proline residue: B 216 - end of helix removed outlier: 3.944A pdb=" N GLY B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 366 removed outlier: 4.166A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 407 removed outlier: 3.771A pdb=" N LEU B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.867A pdb=" N VAL B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 433 removed outlier: 3.693A pdb=" N GLN B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 469 removed outlier: 3.676A pdb=" N ILE B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 31 removed outlier: 3.676A pdb=" N LEU C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 18 " --> pdb=" O TYR C 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 47 removed outlier: 3.673A pdb=" N LYS C 47 " --> pdb=" O ASN C 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 44 through 47' Processing helix chain 'C' and resid 48 through 75 removed outlier: 3.716A pdb=" N CYS C 56 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS C 74 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 75 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 105 removed outlier: 3.658A pdb=" N ALA C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 removed outlier: 3.756A pdb=" N THR C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 169 removed outlier: 3.918A pdb=" N SER C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 194 through 247 removed outlier: 4.411A pdb=" N ALA C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 3.943A pdb=" N GLY C 247 " --> pdb=" O CYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 366 removed outlier: 4.165A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 407 removed outlier: 3.771A pdb=" N LEU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.868A pdb=" N VAL C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 433 removed outlier: 3.692A pdb=" N GLN C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 469 removed outlier: 3.677A pdb=" N ILE C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 464 " --> pdb=" O THR C 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 465 " --> pdb=" O TYR C 461 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 31 removed outlier: 3.677A pdb=" N LEU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 47 removed outlier: 3.674A pdb=" N LYS D 47 " --> pdb=" O ASN D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 44 through 47' Processing helix chain 'D' and resid 48 through 75 removed outlier: 3.716A pdb=" N CYS D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 75 " --> pdb=" O ILE D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 105 removed outlier: 3.658A pdb=" N ALA D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 116 removed outlier: 3.756A pdb=" N THR D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 169 removed outlier: 3.918A pdb=" N SER D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 194 through 247 removed outlier: 4.411A pdb=" N ALA D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.944A pdb=" N GLY D 247 " --> pdb=" O CYS D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 366 removed outlier: 4.166A pdb=" N SER D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 407 removed outlier: 3.772A pdb=" N LEU D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET D 382 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.867A pdb=" N VAL D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 433 removed outlier: 3.693A pdb=" N GLN D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 469 removed outlier: 3.676A pdb=" N ILE D 463 " --> pdb=" O LEU D 459 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 464 " --> pdb=" O THR D 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 465 " --> pdb=" O TYR D 461 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2784 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: 3.34 Time building geometry restraints manager: 3.31 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: 3354 1.34 - 1.46: 2242 1.46 - 1.57: 6648 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 12416 Sorted by residual: bond pdb=" C8 EOL B 900 " pdb=" C9 EOL B 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C8 EOL A 900 " pdb=" C9 EOL A 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C8 EOL D 900 " pdb=" C9 EOL D 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C8 EOL C 900 " pdb=" C9 EOL C 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C SER D 195 " pdb=" N PRO D 196 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.23e-02 6.61e+03 1.13e+01 ... (remaining 12411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 16486 2.55 - 5.10: 308 5.10 - 7.65: 34 7.65 - 10.20: 8 10.20 - 12.75: 4 Bond angle restraints: 16840 Sorted by residual: angle pdb=" C7 EOL D 900 " pdb=" C8 EOL D 900 " pdb=" C9 EOL D 900 " ideal model delta sigma weight residual 124.74 111.99 12.75 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C7 EOL A 900 " pdb=" C8 EOL A 900 " pdb=" C9 EOL A 900 " ideal model delta sigma weight residual 124.74 112.02 12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C7 EOL C 900 " pdb=" C8 EOL C 900 " pdb=" C9 EOL C 900 " ideal model delta sigma weight residual 124.74 112.05 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C7 EOL B 900 " pdb=" C8 EOL B 900 " pdb=" C9 EOL B 900 " ideal model delta sigma weight residual 124.74 112.05 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C THR D 194 " pdb=" N SER D 195 " pdb=" CA SER D 195 " ideal model delta sigma weight residual 120.26 125.27 -5.01 1.34e+00 5.57e-01 1.40e+01 ... (remaining 16835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6487 17.99 - 35.98: 610 35.98 - 53.97: 155 53.97 - 71.96: 28 71.96 - 89.96: 4 Dihedral angle restraints: 7284 sinusoidal: 2776 harmonic: 4508 Sorted by residual: dihedral pdb=" CA ILE C 21 " pdb=" C ILE C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE D 21 " pdb=" C ILE D 21 " pdb=" N LYS D 22 " pdb=" CA LYS D 22 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE B 21 " pdb=" C ILE B 21 " pdb=" N LYS B 22 " pdb=" CA LYS B 22 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1151 0.032 - 0.064: 593 0.064 - 0.095: 180 0.095 - 0.127: 60 0.127 - 0.159: 32 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CB VAL C 184 " pdb=" CA VAL C 184 " pdb=" CG1 VAL C 184 " pdb=" CG2 VAL C 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CB VAL D 184 " pdb=" CA VAL D 184 " pdb=" CG1 VAL D 184 " pdb=" CG2 VAL D 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 2013 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 38 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO B 39 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 38 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 39 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 38 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO C 39 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " 0.035 5.00e-02 4.00e+02 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4077 2.84 - 3.36: 11738 3.36 - 3.87: 20064 3.87 - 4.39: 21392 4.39 - 4.90: 37785 Nonbonded interactions: 95056 Sorted by model distance: nonbonded pdb=" O THR A 348 " pdb=" OG1 THR A 352 " model vdw 2.330 3.040 nonbonded pdb=" O THR C 348 " pdb=" OG1 THR C 352 " model vdw 2.330 3.040 nonbonded pdb=" O THR D 348 " pdb=" OG1 THR D 352 " model vdw 2.330 3.040 nonbonded pdb=" O THR B 348 " pdb=" OG1 THR B 352 " model vdw 2.331 3.040 nonbonded pdb=" OG SER D 78 " pdb=" OE1 GLN D 81 " model vdw 2.388 3.040 ... (remaining 95051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 26.230 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.020 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 : 0.006 0.197 12416 Z= 0.412 Angle : 0.877 12.753 16840 Z= 0.494 Chirality : 0.044 0.159 2016 Planarity : 0.007 0.062 2016 Dihedral : 15.329 89.956 4356 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.47 % Allowed : 5.90 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.19), residues: 1500 helix: -0.77 (0.13), residues: 1188 sheet: None (None), residues: 0 loop : -3.07 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 158 HIS 0.003 0.001 HIS C 46 PHE 0.021 0.002 PHE D 363 TYR 0.023 0.002 TYR A 380 ARG 0.002 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 251 time to evaluate : 1.395 Fit side-chains REVERT: A 371 PHE cc_start: 0.7433 (t80) cc_final: 0.7220 (t80) REVERT: B 371 PHE cc_start: 0.7726 (t80) cc_final: 0.7448 (t80) REVERT: C 191 ASP cc_start: 0.7574 (p0) cc_final: 0.7371 (p0) REVERT: D 191 ASP cc_start: 0.7901 (p0) cc_final: 0.7669 (p0) REVERT: D 371 PHE cc_start: 0.7493 (t80) cc_final: 0.7246 (t80) outliers start: 20 outliers final: 9 residues processed: 268 average time/residue: 0.7621 time to fit residues: 231.6337 Evaluate side-chains 165 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 0.3980 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN B 52 GLN B 105 ASN B 467 GLN C 52 GLN C 467 GLN D 52 GLN D 105 ASN D 467 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12416 Z= 0.169 Angle : 0.560 6.575 16840 Z= 0.283 Chirality : 0.037 0.133 2016 Planarity : 0.005 0.040 2016 Dihedral : 5.877 54.027 1672 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.58 % Allowed : 17.99 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1500 helix: 1.14 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : -2.52 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 158 HIS 0.003 0.001 HIS A 16 PHE 0.026 0.001 PHE C 371 TYR 0.010 0.001 TYR B 380 ARG 0.007 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 1.574 Fit side-chains REVERT: A 355 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7406 (mp) REVERT: B 355 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7519 (mp) REVERT: B 371 PHE cc_start: 0.7587 (t80) cc_final: 0.7348 (t80) REVERT: C 355 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7382 (mp) REVERT: D 191 ASP cc_start: 0.7854 (p0) cc_final: 0.7636 (p0) REVERT: D 355 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7547 (mp) REVERT: D 371 PHE cc_start: 0.7411 (t80) cc_final: 0.7193 (t80) outliers start: 35 outliers final: 12 residues processed: 227 average time/residue: 0.6964 time to fit residues: 181.4828 Evaluate side-chains 180 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN C 46 HIS D 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12416 Z= 0.280 Angle : 0.600 10.977 16840 Z= 0.298 Chirality : 0.039 0.139 2016 Planarity : 0.004 0.033 2016 Dihedral : 5.353 50.565 1666 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.13 % Allowed : 20.13 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1500 helix: 1.56 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -2.43 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 158 HIS 0.004 0.001 HIS B 407 PHE 0.026 0.001 PHE C 50 TYR 0.009 0.001 TYR D 342 ARG 0.005 0.001 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 168 time to evaluate : 1.458 Fit side-chains REVERT: A 191 ASP cc_start: 0.7948 (p0) cc_final: 0.7695 (p0) REVERT: A 355 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7606 (mp) REVERT: B 355 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7616 (mp) REVERT: B 371 PHE cc_start: 0.7761 (t80) cc_final: 0.7472 (t80) REVERT: C 355 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7496 (mp) REVERT: C 371 PHE cc_start: 0.7665 (t80) cc_final: 0.7251 (t80) REVERT: D 191 ASP cc_start: 0.7918 (p0) cc_final: 0.7693 (p0) REVERT: D 355 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7599 (mp) REVERT: D 371 PHE cc_start: 0.7485 (t80) cc_final: 0.7219 (t80) outliers start: 56 outliers final: 35 residues processed: 198 average time/residue: 0.6344 time to fit residues: 146.7594 Evaluate side-chains 192 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 146 optimal weight: 0.0470 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS B 46 HIS ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN C 467 GLN D 46 HIS ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12416 Z= 0.186 Angle : 0.540 8.286 16840 Z= 0.268 Chirality : 0.037 0.133 2016 Planarity : 0.003 0.030 2016 Dihedral : 4.405 30.577 1666 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.95 % Allowed : 22.27 % Favored : 74.78 % 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: 1.93 (0.22), residues: 1500 helix: 2.03 (0.15), residues: 1208 sheet: None (None), residues: 0 loop : -2.04 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 187 HIS 0.002 0.001 HIS B 407 PHE 0.025 0.001 PHE C 50 TYR 0.009 0.001 TYR A 115 ARG 0.004 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 1.324 Fit side-chains REVERT: A 191 ASP cc_start: 0.7994 (p0) cc_final: 0.7766 (p0) REVERT: B 355 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7433 (mp) REVERT: B 371 PHE cc_start: 0.7678 (t80) cc_final: 0.7403 (t80) REVERT: B 377 MET cc_start: 0.7340 (mtt) cc_final: 0.7079 (mtt) REVERT: C 355 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7295 (mp) REVERT: C 371 PHE cc_start: 0.7638 (t80) cc_final: 0.7265 (t80) REVERT: D 355 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7410 (mp) REVERT: D 371 PHE cc_start: 0.7539 (t80) cc_final: 0.7285 (t80) outliers start: 40 outliers final: 19 residues processed: 200 average time/residue: 0.6512 time to fit residues: 151.6959 Evaluate side-chains 183 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12416 Z= 0.208 Angle : 0.552 8.215 16840 Z= 0.273 Chirality : 0.037 0.135 2016 Planarity : 0.003 0.028 2016 Dihedral : 4.154 29.537 1666 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.65 % Allowed : 23.38 % Favored : 73.97 % 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: 2.19 (0.22), residues: 1500 helix: 2.17 (0.15), residues: 1212 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 187 HIS 0.003 0.001 HIS D 407 PHE 0.025 0.001 PHE C 50 TYR 0.014 0.001 TYR B 188 ARG 0.003 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 1.382 Fit side-chains REVERT: A 191 ASP cc_start: 0.8008 (p0) cc_final: 0.7737 (p0) REVERT: B 355 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7330 (mp) REVERT: B 371 PHE cc_start: 0.7672 (t80) cc_final: 0.7391 (t80) REVERT: C 355 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7364 (mp) REVERT: C 371 PHE cc_start: 0.7737 (t80) cc_final: 0.7342 (t80) REVERT: D 355 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7470 (mp) REVERT: D 371 PHE cc_start: 0.7528 (t80) cc_final: 0.7307 (t80) REVERT: D 377 MET cc_start: 0.7332 (mtt) cc_final: 0.7031 (mtt) outliers start: 36 outliers final: 23 residues processed: 193 average time/residue: 0.6544 time to fit residues: 146.8852 Evaluate side-chains 186 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.0870 chunk 36 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12416 Z= 0.175 Angle : 0.548 8.222 16840 Z= 0.268 Chirality : 0.037 0.141 2016 Planarity : 0.003 0.027 2016 Dihedral : 4.121 29.117 1666 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.99 % Allowed : 24.48 % Favored : 73.53 % 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: 2.38 (0.22), residues: 1500 helix: 2.32 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -1.93 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 187 HIS 0.002 0.001 HIS D 407 PHE 0.026 0.001 PHE C 50 TYR 0.012 0.001 TYR B 188 ARG 0.003 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 1.360 Fit side-chains REVERT: A 191 ASP cc_start: 0.7912 (p0) cc_final: 0.7603 (p0) REVERT: A 377 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6456 (mmt) REVERT: B 355 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7332 (mp) REVERT: B 371 PHE cc_start: 0.7641 (t80) cc_final: 0.7394 (t80) REVERT: C 355 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7179 (mp) REVERT: C 371 PHE cc_start: 0.7719 (t80) cc_final: 0.7358 (t80) REVERT: D 355 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7275 (mp) REVERT: D 371 PHE cc_start: 0.7481 (t80) cc_final: 0.7241 (t80) REVERT: D 377 MET cc_start: 0.7235 (mtt) cc_final: 0.7003 (mtt) outliers start: 27 outliers final: 17 residues processed: 188 average time/residue: 0.6500 time to fit residues: 141.8212 Evaluate side-chains 187 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 0.0270 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12416 Z= 0.195 Angle : 0.580 8.625 16840 Z= 0.278 Chirality : 0.037 0.143 2016 Planarity : 0.003 0.026 2016 Dihedral : 4.095 29.124 1666 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.21 % Allowed : 25.52 % Favored : 72.27 % 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: 2.41 (0.22), residues: 1500 helix: 2.36 (0.15), residues: 1212 sheet: None (None), residues: 0 loop : -1.92 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 187 HIS 0.003 0.001 HIS D 407 PHE 0.027 0.001 PHE C 50 TYR 0.009 0.001 TYR B 188 ARG 0.002 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 1.323 Fit side-chains REVERT: A 191 ASP cc_start: 0.7792 (p0) cc_final: 0.7455 (p0) REVERT: A 377 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6493 (mmt) REVERT: B 355 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7284 (mp) REVERT: B 371 PHE cc_start: 0.7609 (t80) cc_final: 0.7400 (t80) REVERT: C 355 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7244 (mp) REVERT: C 371 PHE cc_start: 0.7726 (t80) cc_final: 0.7382 (t80) REVERT: D 355 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7250 (mp) REVERT: D 371 PHE cc_start: 0.7504 (t80) cc_final: 0.7288 (t80) outliers start: 30 outliers final: 20 residues processed: 183 average time/residue: 0.7247 time to fit residues: 152.3760 Evaluate side-chains 188 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 0.0010 chunk 28 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN D 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12416 Z= 0.170 Angle : 0.576 9.036 16840 Z= 0.274 Chirality : 0.037 0.154 2016 Planarity : 0.003 0.052 2016 Dihedral : 4.051 28.016 1666 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.70 % Allowed : 26.77 % Favored : 71.53 % 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: 2.56 (0.22), residues: 1500 helix: 2.43 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -1.77 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 187 HIS 0.002 0.000 HIS B 407 PHE 0.027 0.001 PHE C 50 TYR 0.007 0.001 TYR C 99 ARG 0.012 0.000 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 1.340 Fit side-chains REVERT: A 191 ASP cc_start: 0.7851 (p0) cc_final: 0.7474 (p0) REVERT: A 377 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6480 (mmt) REVERT: B 197 MET cc_start: 0.6643 (tmm) cc_final: 0.6363 (tmm) REVERT: B 355 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7204 (mp) REVERT: C 355 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7134 (mp) REVERT: C 371 PHE cc_start: 0.7711 (t80) cc_final: 0.7384 (t80) REVERT: D 355 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7288 (mp) REVERT: D 371 PHE cc_start: 0.7484 (t80) cc_final: 0.7278 (t80) outliers start: 23 outliers final: 19 residues processed: 196 average time/residue: 0.6693 time to fit residues: 151.4282 Evaluate side-chains 193 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN D 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12416 Z= 0.200 Angle : 0.597 10.632 16840 Z= 0.284 Chirality : 0.037 0.150 2016 Planarity : 0.003 0.025 2016 Dihedral : 4.051 28.390 1666 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.77 % Allowed : 27.88 % Favored : 70.35 % 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: 2.55 (0.22), residues: 1500 helix: 2.39 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.66 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 187 HIS 0.003 0.001 HIS C 407 PHE 0.027 0.001 PHE D 50 TYR 0.008 0.001 TYR A 99 ARG 0.002 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.437 Fit side-chains REVERT: A 191 ASP cc_start: 0.7870 (p0) cc_final: 0.7497 (p0) REVERT: B 355 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7307 (mp) REVERT: C 197 MET cc_start: 0.6493 (tmm) cc_final: 0.6128 (tmm) REVERT: C 355 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7109 (mp) REVERT: C 371 PHE cc_start: 0.7688 (t80) cc_final: 0.7367 (t80) REVERT: D 355 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7247 (mp) outliers start: 24 outliers final: 19 residues processed: 181 average time/residue: 0.7205 time to fit residues: 149.6757 Evaluate side-chains 188 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 151 optimal weight: 0.0570 chunk 139 optimal weight: 0.6980 chunk 120 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN B 233 HIS C 467 GLN D 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12416 Z= 0.174 Angle : 0.597 10.063 16840 Z= 0.283 Chirality : 0.037 0.159 2016 Planarity : 0.003 0.056 2016 Dihedral : 4.051 27.234 1666 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.47 % Allowed : 28.69 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.22), residues: 1500 helix: 2.46 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.59 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 187 HIS 0.002 0.000 HIS C 407 PHE 0.028 0.001 PHE C 50 TYR 0.009 0.001 TYR B 115 ARG 0.020 0.000 ARG C 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 1.275 Fit side-chains REVERT: A 191 ASP cc_start: 0.7841 (p0) cc_final: 0.7451 (p0) REVERT: B 355 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7286 (mp) REVERT: C 197 MET cc_start: 0.6546 (tmm) cc_final: 0.6062 (tmm) REVERT: C 355 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7129 (mp) REVERT: C 371 PHE cc_start: 0.7646 (t80) cc_final: 0.7361 (t80) REVERT: D 191 ASP cc_start: 0.7958 (m-30) cc_final: 0.7695 (p0) REVERT: D 355 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7244 (mp) outliers start: 20 outliers final: 21 residues processed: 185 average time/residue: 0.6946 time to fit residues: 147.9344 Evaluate side-chains 191 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS C 233 HIS C 467 GLN D 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.151514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120625 restraints weight = 17653.729| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.32 r_work: 0.3395 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12416 Z= 0.165 Angle : 0.591 9.563 16840 Z= 0.279 Chirality : 0.037 0.159 2016 Planarity : 0.003 0.025 2016 Dihedral : 3.997 26.486 1666 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.47 % Allowed : 29.20 % Favored : 69.32 % 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: 2.72 (0.22), residues: 1500 helix: 2.50 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.53 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 187 HIS 0.002 0.000 HIS D 407 PHE 0.029 0.001 PHE A 50 TYR 0.010 0.001 TYR A 380 ARG 0.002 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3519.66 seconds wall clock time: 63 minutes 2.44 seconds (3782.44 seconds total)