Starting phenix.real_space_refine on Fri Jul 3 18:49:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5j_66589/07_2026/9x5j_66589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5j_66589/07_2026/9x5j_66589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x5j_66589/07_2026/9x5j_66589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5j_66589/07_2026/9x5j_66589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x5j_66589/07_2026/9x5j_66589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5j_66589/07_2026/9x5j_66589.map" } resolution = 3.05 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 82 5.16 5 C 9867 2.51 5 N 2582 2.21 5 O 2765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15300 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "E" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "H" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2657 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2657 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2821 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 6, 'TRANS': 340} Chain breaks: 3 Chain: "A" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2657 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Time building chain proxies: 3.51, per 1000 atoms: 0.23 Number of scatterers: 15300 At special positions: 0 Unit cell: (123.849, 120.285, 115.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 82 16.00 O 2765 8.00 N 2582 7.00 C 9867 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: 1.33 Conformation dependent library (CDL) restraints added in 702.0 milliseconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 4 sheets defined 80.7% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.606A pdb=" N LEU F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.610A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'F' and resid 103 through 111 removed outlier: 3.821A pdb=" N THR F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 39 removed outlier: 3.589A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 65 through 74 Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.553A pdb=" N THR E 80 " --> pdb=" O MET E 77 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP E 81 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.817A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 111 removed outlier: 3.767A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 38 Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.517A pdb=" N LEU H 49 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.626A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 80 Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.917A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.506A pdb=" N VAL H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 147 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 39 Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 65 through 74 Processing helix chain 'G' and resid 82 through 92 Processing helix chain 'G' and resid 103 through 111 removed outlier: 3.544A pdb=" N THR G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 138 through 147 removed outlier: 3.509A pdb=" N PHE G 142 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 124 through 144 Processing helix chain 'B' and resid 149 through 178 Processing helix chain 'B' and resid 185 through 195 removed outlier: 3.672A pdb=" N ARG B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 216 Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 225 through 239 removed outlier: 4.052A pdb=" N LEU B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 257 through 284 Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.548A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 366 removed outlier: 4.350A pdb=" N SER B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 367 through 368 No H-bonds generated for 'chain 'B' and resid 367 through 368' Processing helix chain 'B' and resid 369 through 370 No H-bonds generated for 'chain 'B' and resid 369 through 370' Processing helix chain 'B' and resid 371 through 386 removed outlier: 4.415A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 538 Processing helix chain 'B' and resid 542 through 573 removed outlier: 3.794A pdb=" N VAL B 546 " --> pdb=" O ASP B 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.528A pdb=" N PHE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 178 Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.750A pdb=" N ARG C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 216 Proline residue: C 211 - end of helix Processing helix chain 'C' and resid 225 through 239 removed outlier: 4.143A pdb=" N LEU C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 257 Processing helix chain 'C' and resid 257 through 283 Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 326 through 366 removed outlier: 4.445A pdb=" N SER C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 367 through 368 No H-bonds generated for 'chain 'C' and resid 367 through 368' Processing helix chain 'C' and resid 369 through 370 No H-bonds generated for 'chain 'C' and resid 369 through 370' Processing helix chain 'C' and resid 371 through 387 removed outlier: 4.354A pdb=" N ALA C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 538 Processing helix chain 'C' and resid 542 through 573 removed outlier: 3.510A pdb=" N VAL C 546 " --> pdb=" O ASP C 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 92 through 115 removed outlier: 3.910A pdb=" N HIS D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 148 removed outlier: 3.964A pdb=" N ALA D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.815A pdb=" N GLY D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 161 " --> pdb=" O TRP D 157 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 185 Processing helix chain 'D' and resid 194 through 210 removed outlier: 3.622A pdb=" N ILE D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 306 removed outlier: 4.265A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 325 removed outlier: 3.597A pdb=" N GLY D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 349 removed outlier: 3.675A pdb=" N ARG D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) Proline residue: D 335 - end of helix Processing helix chain 'D' and resid 356 through 364 removed outlier: 4.176A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 558 removed outlier: 3.821A pdb=" N GLU D 557 " --> pdb=" O ARG D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 594 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.916A pdb=" N PHE A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.733A pdb=" N GLY A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 244 through 257 removed outlier: 3.532A pdb=" N HIS A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 284 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 326 through 366 removed outlier: 4.623A pdb=" N SER A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 367 through 368 No H-bonds generated for 'chain 'A' and resid 367 through 368' Processing helix chain 'A' and resid 369 through 370 No H-bonds generated for 'chain 'A' and resid 369 through 370' Processing helix chain 'A' and resid 371 through 387 removed outlier: 4.580A pdb=" N ALA A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 538 Processing helix chain 'A' and resid 542 through 572 removed outlier: 3.631A pdb=" N VAL A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 101 removed outlier: 3.638A pdb=" N ILE E 101 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'G' and resid 101 through 102 1098 hydrogen bonds defined for protein. 3273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2502 1.29 - 1.42: 4067 1.42 - 1.55: 8884 1.55 - 1.68: 1 1.68 - 1.81: 139 Bond restraints: 15593 Sorted by residual: bond pdb=" C ALA C 348 " pdb=" O ALA C 348 " ideal model delta sigma weight residual 1.237 1.158 0.078 1.19e-02 7.06e+03 4.33e+01 bond pdb=" C ILE B 262 " pdb=" O ILE B 262 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.17e-02 7.31e+03 4.20e+01 bond pdb=" C MET D 565 " pdb=" N ASP D 566 " ideal model delta sigma weight residual 1.334 1.243 0.091 1.58e-02 4.01e+03 3.28e+01 bond pdb=" CA ALA C 348 " pdb=" C ALA C 348 " ideal model delta sigma weight residual 1.524 1.450 0.073 1.29e-02 6.01e+03 3.22e+01 bond pdb=" CA ALA B 264 " pdb=" C ALA B 264 " ideal model delta sigma weight residual 1.522 1.445 0.078 1.39e-02 5.18e+03 3.12e+01 ... (remaining 15588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 20210 1.43 - 2.86: 657 2.86 - 4.29: 95 4.29 - 5.72: 38 5.72 - 7.15: 16 Bond angle restraints: 21016 Sorted by residual: angle pdb=" N ALA C 348 " pdb=" CA ALA C 348 " pdb=" C ALA C 348 " ideal model delta sigma weight residual 111.36 104.72 6.64 1.09e+00 8.42e-01 3.71e+01 angle pdb=" N GLY C 354 " pdb=" CA GLY C 354 " pdb=" C GLY C 354 " ideal model delta sigma weight residual 113.24 118.90 -5.66 1.31e+00 5.83e-01 1.87e+01 angle pdb=" C THR B 263 " pdb=" CA THR B 263 " pdb=" CB THR B 263 " ideal model delta sigma weight residual 110.79 103.78 7.01 1.66e+00 3.63e-01 1.78e+01 angle pdb=" C MET D 565 " pdb=" N ASP D 566 " pdb=" CA ASP D 566 " ideal model delta sigma weight residual 121.98 128.36 -6.38 1.53e+00 4.27e-01 1.74e+01 angle pdb=" CA ILE B 262 " pdb=" C ILE B 262 " pdb=" N THR B 263 " ideal model delta sigma weight residual 117.15 121.82 -4.67 1.14e+00 7.69e-01 1.68e+01 ... (remaining 21011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 8144 17.67 - 35.34: 903 35.34 - 53.01: 172 53.01 - 70.68: 28 70.68 - 88.35: 16 Dihedral angle restraints: 9263 sinusoidal: 3774 harmonic: 5489 Sorted by residual: dihedral pdb=" CA TRP A 121 " pdb=" C TRP A 121 " pdb=" N ALA A 122 " pdb=" CA ALA A 122 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TRP B 121 " pdb=" C TRP B 121 " pdb=" N ALA B 122 " pdb=" CA ALA B 122 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LEU B 123 " pdb=" C LEU B 123 " pdb=" N LEU B 124 " pdb=" CA LEU B 124 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 9260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1889 0.049 - 0.098: 403 0.098 - 0.146: 50 0.146 - 0.195: 3 0.195 - 0.244: 1 Chirality restraints: 2346 Sorted by residual: chirality pdb=" CA LEU C 351 " pdb=" N LEU C 351 " pdb=" C LEU C 351 " pdb=" CB LEU C 351 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LEU B 261 " pdb=" N LEU B 261 " pdb=" C LEU B 261 " pdb=" CB LEU B 261 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA TRP A 265 " pdb=" N TRP A 265 " pdb=" C TRP A 265 " pdb=" CB TRP A 265 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 2343 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 560 " 0.062 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO D 561 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 561 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 561 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 350 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ILE C 350 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE C 350 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU C 351 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 30 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C THR F 30 " 0.029 2.00e-02 2.50e+03 pdb=" O THR F 30 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS F 31 " -0.010 2.00e-02 2.50e+03 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 4137 2.80 - 3.38: 18224 3.38 - 3.97: 29148 3.97 - 4.55: 41371 4.55 - 5.14: 58847 Nonbonded interactions: 151727 Sorted by model distance: nonbonded pdb=" O GLY C 553 " pdb=" OD1 ASP C 556 " model vdw 2.215 3.040 nonbonded pdb=" O LEU A 158 " pdb=" OG1 THR A 161 " model vdw 2.219 3.040 nonbonded pdb=" O MET D 208 " pdb=" OH TYR A 266 " model vdw 2.223 3.040 nonbonded pdb=" O THR D 349 " pdb=" NH1 ARG D 541 " model vdw 2.259 3.120 nonbonded pdb=" O TYR A 148 " pdb=" OG SER A 152 " model vdw 2.271 3.040 ... (remaining 151722 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' and resid 103 through 573) selection = (chain 'B' and resid 103 through 573) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.005 0.091 15593 Z= 0.302 Angle : 0.632 7.146 21016 Z= 0.364 Chirality : 0.039 0.244 2346 Planarity : 0.004 0.094 2635 Dihedral : 15.228 88.345 5725 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.17), residues: 1860 helix: -1.15 (0.12), residues: 1448 sheet: None (None), residues: 0 loop : -2.67 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.018 0.001 TYR A 550 PHE 0.016 0.001 PHE F 90 TRP 0.021 0.002 TRP D 288 HIS 0.004 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.30 (15593) covalent geometry : angle 0.63198 / 0.36 (21016) hydrogen bonds : bond 0.11139 / 7.57 ( 1098) hydrogen bonds : angle 5.40940 / 3.79 ( 3273) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 ILE cc_start: 0.6401 (mt) cc_final: 0.5952 (mt) REVERT: B 227 ARG cc_start: 0.3395 (mtt-85) cc_final: 0.3060 (tmt170) REVERT: B 570 MET cc_start: 0.6223 (mtt) cc_final: 0.5641 (ttp) REVERT: A 227 ARG cc_start: 0.3286 (mtt-85) cc_final: 0.2705 (tmt-80) REVERT: A 241 ASP cc_start: 0.6715 (t70) cc_final: 0.6424 (p0) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1599 time to fit residues: 69.8860 Evaluate side-chains 258 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 50 GLN H 54 ASN G 144 GLN B 257 HIS B 362 GLN C 126 HIS C 362 GLN C 380 GLN D 83 ASN D 334 ASN D 575 HIS A 367 HIS A 380 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.237454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.181085 restraints weight = 19313.405| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.04 r_work: 0.3485 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15593 Z= 0.143 Angle : 0.603 11.095 21016 Z= 0.308 Chirality : 0.038 0.171 2346 Planarity : 0.004 0.078 2635 Dihedral : 4.130 22.863 2082 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.19 % Allowed : 12.44 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 1860 helix: 0.30 (0.13), residues: 1455 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 127 TYR 0.024 0.001 TYR B 550 PHE 0.036 0.002 PHE G 17 TRP 0.018 0.001 TRP D 288 HIS 0.006 0.001 HIS F 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (15593) covalent geometry : angle 0.60311 / 0.31 (21016) hydrogen bonds : bond 0.04520 / 2.96 ( 1098) hydrogen bonds : angle 4.49326 / 3.13 ( 3273) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 MET cc_start: 0.5277 (mtp) cc_final: 0.5036 (mtp) REVERT: F 90 PHE cc_start: 0.6700 (m-80) cc_final: 0.6369 (m-80) REVERT: F 139 TYR cc_start: 0.8351 (p90) cc_final: 0.8113 (p90) REVERT: H 31 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7678 (ttpp) REVERT: H 127 ARG cc_start: 0.7269 (ttp-110) cc_final: 0.6958 (ttp80) REVERT: H 145 MET cc_start: 0.7535 (ptt) cc_final: 0.7312 (ptt) REVERT: G 17 PHE cc_start: 0.7476 (t80) cc_final: 0.7043 (t80) REVERT: G 42 GLN cc_start: 0.6601 (mt0) cc_final: 0.5977 (tp40) REVERT: G 110 MET cc_start: 0.7598 (tpt) cc_final: 0.7350 (tpt) REVERT: B 227 ARG cc_start: 0.3458 (mtt-85) cc_final: 0.2717 (tmt170) REVERT: B 570 MET cc_start: 0.8119 (mtt) cc_final: 0.7887 (ttp) REVERT: C 380 GLN cc_start: 0.6911 (mt0) cc_final: 0.6698 (mt0) REVERT: C 542 ASP cc_start: 0.8039 (m-30) cc_final: 0.7537 (p0) REVERT: C 567 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7970 (tpp-160) REVERT: C 570 MET cc_start: 0.7538 (mtp) cc_final: 0.6945 (mtm) REVERT: D 170 VAL cc_start: 0.8155 (p) cc_final: 0.7911 (m) REVERT: D 322 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: D 541 ARG cc_start: 0.8231 (tpt-90) cc_final: 0.8011 (tpt-90) REVERT: A 227 ARG cc_start: 0.3280 (mtt-85) cc_final: 0.2191 (tmt-80) REVERT: A 341 VAL cc_start: 0.8744 (t) cc_final: 0.7768 (p) outliers start: 19 outliers final: 8 residues processed: 285 average time/residue: 0.1319 time to fit residues: 53.3505 Evaluate side-chains 257 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 248 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 525 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 59 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 ASN A 108 GLN A 257 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.235901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179321 restraints weight = 19630.087| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.20 r_work: 0.3412 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15593 Z= 0.204 Angle : 0.619 10.083 21016 Z= 0.318 Chirality : 0.040 0.164 2346 Planarity : 0.004 0.068 2635 Dihedral : 4.148 23.271 2082 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.12 % Allowed : 15.31 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1860 helix: 0.59 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -2.04 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 91 TYR 0.038 0.002 TYR B 550 PHE 0.026 0.002 PHE F 66 TRP 0.021 0.002 TRP D 288 HIS 0.005 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (15593) covalent geometry : angle 0.61927 / 0.32 (21016) hydrogen bonds : bond 0.04820 / 3.14 ( 1098) hydrogen bonds : angle 4.47416 / 3.13 ( 3273) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 90 PHE cc_start: 0.6729 (m-80) cc_final: 0.6456 (m-10) REVERT: F 139 TYR cc_start: 0.8453 (p90) cc_final: 0.8186 (p90) REVERT: E 136 GLN cc_start: 0.5791 (mt0) cc_final: 0.4741 (mt0) REVERT: H 31 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7685 (ttpp) REVERT: H 145 MET cc_start: 0.7631 (ptt) cc_final: 0.7407 (ptt) REVERT: G 42 GLN cc_start: 0.6598 (mt0) cc_final: 0.5894 (tp40) REVERT: G 145 MET cc_start: 0.5896 (ptt) cc_final: 0.5419 (ttt) REVERT: B 227 ARG cc_start: 0.3545 (mtt-85) cc_final: 0.2717 (tmt170) REVERT: B 380 GLN cc_start: 0.8941 (tp40) cc_final: 0.8652 (tp40) REVERT: B 531 LYS cc_start: 0.8042 (tmtt) cc_final: 0.7743 (tmtt) REVERT: C 377 GLU cc_start: 0.6009 (tm-30) cc_final: 0.5123 (mt-10) REVERT: C 380 GLN cc_start: 0.6936 (mt0) cc_final: 0.6676 (mt0) REVERT: C 535 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8141 (mmtm) REVERT: C 542 ASP cc_start: 0.7992 (m-30) cc_final: 0.7523 (p0) REVERT: D 170 VAL cc_start: 0.8222 (p) cc_final: 0.7945 (m) REVERT: D 183 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8191 (mp) REVERT: D 322 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: D 541 ARG cc_start: 0.8232 (tpt-90) cc_final: 0.7973 (tpt-90) REVERT: A 204 PHE cc_start: 0.6383 (m-80) cc_final: 0.6174 (m-80) REVERT: A 227 ARG cc_start: 0.3340 (mtt-85) cc_final: 0.2200 (tmt-80) outliers start: 34 outliers final: 18 residues processed: 274 average time/residue: 0.1274 time to fit residues: 50.2885 Evaluate side-chains 265 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 525 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 44 optimal weight: 0.0270 chunk 6 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 144 GLN D 334 ASN ** D 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.239163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.185871 restraints weight = 19438.285| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 3.00 r_work: 0.3546 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15593 Z= 0.133 Angle : 0.576 10.344 21016 Z= 0.291 Chirality : 0.038 0.183 2346 Planarity : 0.004 0.058 2635 Dihedral : 4.024 22.261 2082 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.94 % Allowed : 17.00 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.19), residues: 1860 helix: 0.95 (0.13), residues: 1453 sheet: None (None), residues: 0 loop : -1.78 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 127 TYR 0.018 0.001 TYR C 104 PHE 0.029 0.001 PHE G 17 TRP 0.019 0.001 TRP D 288 HIS 0.003 0.001 HIS E 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (15593) covalent geometry : angle 0.57578 / 0.29 (21016) hydrogen bonds : bond 0.04246 / 2.76 ( 1098) hydrogen bonds : angle 4.28488 / 3.00 ( 3273) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 90 PHE cc_start: 0.6784 (m-80) cc_final: 0.6524 (m-10) REVERT: F 139 TYR cc_start: 0.8387 (p90) cc_final: 0.8158 (p90) REVERT: E 136 GLN cc_start: 0.5873 (mt0) cc_final: 0.4750 (mt0) REVERT: H 31 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7764 (ttpp) REVERT: H 136 GLN cc_start: 0.7154 (tp40) cc_final: 0.6726 (mm110) REVERT: H 145 MET cc_start: 0.7569 (ptt) cc_final: 0.7330 (ptt) REVERT: G 13 PHE cc_start: 0.5755 (m-10) cc_final: 0.5475 (m-10) REVERT: G 42 GLN cc_start: 0.6506 (mt0) cc_final: 0.5924 (tp40) REVERT: G 48 GLU cc_start: 0.7035 (pp20) cc_final: 0.6793 (pp20) REVERT: G 145 MET cc_start: 0.5723 (ptt) cc_final: 0.5379 (ttt) REVERT: B 227 ARG cc_start: 0.3225 (mtt-85) cc_final: 0.2562 (tmt170) REVERT: B 380 GLN cc_start: 0.8986 (tp40) cc_final: 0.8677 (tp40) REVERT: B 531 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7801 (tmtt) REVERT: B 567 ARG cc_start: 0.8355 (ptm160) cc_final: 0.7588 (tpt90) REVERT: C 200 MET cc_start: 0.5682 (ppp) cc_final: 0.5051 (ppp) REVERT: C 362 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: C 380 GLN cc_start: 0.6974 (mt0) cc_final: 0.6696 (mt0) REVERT: C 529 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7589 (mt) REVERT: C 531 LYS cc_start: 0.7621 (pttp) cc_final: 0.7052 (pttp) REVERT: C 535 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8171 (mmtm) REVERT: C 542 ASP cc_start: 0.7967 (m-30) cc_final: 0.7557 (p0) REVERT: D 170 VAL cc_start: 0.8294 (p) cc_final: 0.8016 (m) REVERT: D 322 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: A 204 PHE cc_start: 0.6504 (m-80) cc_final: 0.6282 (m-80) REVERT: A 557 MET cc_start: 0.7890 (mmt) cc_final: 0.7640 (mmt) outliers start: 31 outliers final: 14 residues processed: 279 average time/residue: 0.1183 time to fit residues: 47.2154 Evaluate side-chains 260 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 525 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 144 GLN B 554 HIS D 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.235959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.181724 restraints weight = 19584.500| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.91 r_work: 0.3463 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15593 Z= 0.259 Angle : 0.654 9.272 21016 Z= 0.335 Chirality : 0.041 0.167 2346 Planarity : 0.004 0.056 2635 Dihedral : 4.162 23.352 2082 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.25 % Allowed : 19.25 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1860 helix: 0.78 (0.13), residues: 1458 sheet: None (None), residues: 0 loop : -1.65 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 91 TYR 0.028 0.002 TYR B 550 PHE 0.029 0.002 PHE G 17 TRP 0.025 0.002 TRP D 288 HIS 0.007 0.001 HIS B 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.26 (15593) covalent geometry : angle 0.65382 / 0.34 (21016) hydrogen bonds : bond 0.05019 / 3.28 ( 1098) hydrogen bonds : angle 4.47466 / 3.14 ( 3273) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 LEU cc_start: 0.8181 (mt) cc_final: 0.7257 (pt) REVERT: E 110 MET cc_start: 0.6692 (mmp) cc_final: 0.6370 (mpp) REVERT: E 136 GLN cc_start: 0.5890 (mt0) cc_final: 0.4772 (mt0) REVERT: H 31 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7777 (ttpp) REVERT: H 136 GLN cc_start: 0.7176 (tp40) cc_final: 0.6719 (mm110) REVERT: H 145 MET cc_start: 0.7639 (ptt) cc_final: 0.7437 (ptt) REVERT: G 42 GLN cc_start: 0.6462 (mt0) cc_final: 0.5841 (tp40) REVERT: G 77 MET cc_start: 0.1678 (OUTLIER) cc_final: 0.1374 (mtp) REVERT: G 145 MET cc_start: 0.6266 (ptt) cc_final: 0.5547 (mtm) REVERT: B 227 ARG cc_start: 0.3435 (mtt-85) cc_final: 0.2742 (tmt170) REVERT: B 531 LYS cc_start: 0.8039 (tmtt) cc_final: 0.7836 (tmtt) REVERT: C 200 MET cc_start: 0.5753 (ppp) cc_final: 0.4898 (ppp) REVERT: C 362 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6662 (mp10) REVERT: C 363 HIS cc_start: 0.5952 (m-70) cc_final: 0.5448 (m-70) REVERT: C 380 GLN cc_start: 0.7086 (mt0) cc_final: 0.6875 (mt0) REVERT: C 531 LYS cc_start: 0.7610 (pttp) cc_final: 0.7001 (pttp) REVERT: C 535 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8168 (mmtm) REVERT: C 542 ASP cc_start: 0.8015 (m-30) cc_final: 0.7653 (p0) REVERT: D 170 VAL cc_start: 0.8373 (p) cc_final: 0.8028 (m) REVERT: D 322 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: D 570 GLN cc_start: 0.7650 (tp40) cc_final: 0.7314 (tp40) REVERT: A 204 PHE cc_start: 0.6542 (m-80) cc_final: 0.6305 (m-80) REVERT: A 227 ARG cc_start: 0.3441 (mtt-85) cc_final: 0.2179 (tmt-80) REVERT: A 241 ASP cc_start: 0.6160 (t70) cc_final: 0.5509 (p0) outliers start: 36 outliers final: 24 residues processed: 269 average time/residue: 0.1228 time to fit residues: 47.5127 Evaluate side-chains 269 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 525 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 151 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 10 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 144 GLN B 367 HIS D 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.239179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.186159 restraints weight = 19425.436| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.94 r_work: 0.3535 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15593 Z= 0.139 Angle : 0.584 9.678 21016 Z= 0.294 Chirality : 0.037 0.174 2346 Planarity : 0.004 0.052 2635 Dihedral : 4.046 22.535 2082 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.19 % Allowed : 19.75 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1860 helix: 1.07 (0.13), residues: 1459 sheet: None (None), residues: 0 loop : -1.55 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 91 TYR 0.022 0.001 TYR B 550 PHE 0.027 0.001 PHE A 534 TRP 0.020 0.001 TRP D 360 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (15593) covalent geometry : angle 0.58449 / 0.29 (21016) hydrogen bonds : bond 0.04279 / 2.78 ( 1098) hydrogen bonds : angle 4.26367 / 2.99 ( 3273) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: 0.4644 (mmm) cc_final: 0.4395 (mmt) REVERT: F 77 MET cc_start: 0.4096 (ttp) cc_final: 0.3877 (ttp) REVERT: F 117 LEU cc_start: 0.8106 (mt) cc_final: 0.7178 (pt) REVERT: E 110 MET cc_start: 0.6772 (mmp) cc_final: 0.6393 (mpp) REVERT: E 136 GLN cc_start: 0.5951 (mt0) cc_final: 0.4848 (mt0) REVERT: H 31 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7870 (ttpp) REVERT: H 136 GLN cc_start: 0.7087 (tp40) cc_final: 0.6551 (mm110) REVERT: H 145 MET cc_start: 0.7574 (ptt) cc_final: 0.7346 (ptt) REVERT: G 42 GLN cc_start: 0.6397 (mt0) cc_final: 0.5833 (tp40) REVERT: G 69 PHE cc_start: 0.7329 (t80) cc_final: 0.6966 (m-80) REVERT: G 77 MET cc_start: 0.1616 (OUTLIER) cc_final: 0.1338 (mtp) REVERT: G 145 MET cc_start: 0.6277 (ptt) cc_final: 0.5716 (mtm) REVERT: B 227 ARG cc_start: 0.3136 (mtt-85) cc_final: 0.2476 (tmt170) REVERT: B 531 LYS cc_start: 0.8019 (tmtt) cc_final: 0.7810 (tmtt) REVERT: C 200 MET cc_start: 0.5726 (ppp) cc_final: 0.5070 (ppp) REVERT: C 299 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: C 362 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: C 380 GLN cc_start: 0.6982 (mt0) cc_final: 0.6756 (mt0) REVERT: C 531 LYS cc_start: 0.7438 (pttp) cc_final: 0.7230 (ptmm) REVERT: C 535 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8191 (mmtm) REVERT: D 170 VAL cc_start: 0.8265 (p) cc_final: 0.7987 (m) REVERT: D 210 ARG cc_start: 0.8346 (tmm160) cc_final: 0.8017 (tmm-80) REVERT: D 322 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: D 570 GLN cc_start: 0.7641 (tp40) cc_final: 0.7335 (tp40) REVERT: A 154 ASP cc_start: 0.5622 (m-30) cc_final: 0.4978 (t0) REVERT: A 204 PHE cc_start: 0.6447 (m-80) cc_final: 0.6199 (m-80) REVERT: A 227 ARG cc_start: 0.3306 (mtt-85) cc_final: 0.1968 (tmt-80) REVERT: A 557 MET cc_start: 0.7803 (mmt) cc_final: 0.7550 (mmt) outliers start: 35 outliers final: 16 residues processed: 280 average time/residue: 0.1203 time to fit residues: 48.6374 Evaluate side-chains 263 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 525 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 144 GLN B 549 GLN D 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.239046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.185973 restraints weight = 19174.789| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 3.07 r_work: 0.3525 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15593 Z= 0.147 Angle : 0.594 9.950 21016 Z= 0.299 Chirality : 0.038 0.166 2346 Planarity : 0.004 0.051 2635 Dihedral : 4.019 25.525 2082 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.69 % Allowed : 21.06 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1860 helix: 1.17 (0.13), residues: 1459 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 91 TYR 0.025 0.001 TYR B 386 PHE 0.024 0.001 PHE D 548 TRP 0.023 0.001 TRP D 360 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15593) covalent geometry : angle 0.59372 / 0.30 (21016) hydrogen bonds : bond 0.04281 / 2.78 ( 1098) hydrogen bonds : angle 4.23545 / 2.97 ( 3273) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: 0.4605 (mmm) cc_final: 0.4370 (mmt) REVERT: F 95 LYS cc_start: 0.4603 (mmtm) cc_final: 0.3881 (mttt) REVERT: F 117 LEU cc_start: 0.8000 (mt) cc_final: 0.7098 (pt) REVERT: E 110 MET cc_start: 0.6755 (mmp) cc_final: 0.6402 (mpp) REVERT: E 136 GLN cc_start: 0.5867 (mt0) cc_final: 0.4793 (mt0) REVERT: H 31 LYS cc_start: 0.8260 (mmmt) cc_final: 0.8019 (ttpp) REVERT: H 136 GLN cc_start: 0.7049 (tp40) cc_final: 0.6496 (mm110) REVERT: H 145 MET cc_start: 0.7590 (ptt) cc_final: 0.7380 (ptt) REVERT: G 42 GLN cc_start: 0.6270 (mt0) cc_final: 0.5722 (tp40) REVERT: G 50 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7314 (mp10) REVERT: G 69 PHE cc_start: 0.7291 (t80) cc_final: 0.6996 (t80) REVERT: G 72 MET cc_start: 0.7695 (tmm) cc_final: 0.7268 (tmm) REVERT: G 73 MET cc_start: 0.7273 (mmm) cc_final: 0.6672 (mmm) REVERT: G 77 MET cc_start: 0.1506 (OUTLIER) cc_final: 0.1219 (mtp) REVERT: G 91 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8077 (ttm110) REVERT: G 145 MET cc_start: 0.6359 (ptt) cc_final: 0.5783 (mtm) REVERT: B 531 LYS cc_start: 0.8029 (tmtt) cc_final: 0.7816 (tmtt) REVERT: C 200 MET cc_start: 0.5729 (ppp) cc_final: 0.5055 (ppp) REVERT: C 284 LYS cc_start: 0.7809 (tttp) cc_final: 0.7406 (ttmt) REVERT: C 299 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.6977 (pt0) REVERT: C 362 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: C 377 GLU cc_start: 0.5882 (tm-30) cc_final: 0.5131 (tm-30) REVERT: C 380 GLN cc_start: 0.7052 (mt0) cc_final: 0.6787 (mt0) REVERT: C 535 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8215 (mmtm) REVERT: D 170 VAL cc_start: 0.8282 (p) cc_final: 0.7998 (m) REVERT: D 570 GLN cc_start: 0.7705 (tp40) cc_final: 0.7445 (tp40) REVERT: A 154 ASP cc_start: 0.5671 (m-30) cc_final: 0.4985 (t0) REVERT: A 204 PHE cc_start: 0.6479 (m-80) cc_final: 0.6222 (m-80) REVERT: A 557 MET cc_start: 0.7786 (mmt) cc_final: 0.7437 (mmt) outliers start: 27 outliers final: 17 residues processed: 266 average time/residue: 0.1188 time to fit residues: 45.8850 Evaluate side-chains 261 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 525 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 549 GLN D 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.238750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.185612 restraints weight = 19438.744| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.02 r_work: 0.3524 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15593 Z= 0.151 Angle : 0.590 10.410 21016 Z= 0.298 Chirality : 0.038 0.165 2346 Planarity : 0.004 0.048 2635 Dihedral : 3.989 24.795 2082 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.75 % Allowed : 21.75 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 1860 helix: 1.22 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -1.31 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 560 TYR 0.027 0.001 TYR B 386 PHE 0.020 0.001 PHE D 548 TRP 0.035 0.002 TRP D 360 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (15593) covalent geometry : angle 0.59005 / 0.30 (21016) hydrogen bonds : bond 0.04292 / 2.78 ( 1098) hydrogen bonds : angle 4.23687 / 2.98 ( 3273) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: 0.4682 (mmm) cc_final: 0.4381 (mmt) REVERT: F 95 LYS cc_start: 0.4612 (mmtm) cc_final: 0.3902 (mttt) REVERT: F 117 LEU cc_start: 0.7954 (mt) cc_final: 0.7040 (pt) REVERT: E 110 MET cc_start: 0.6741 (mmp) cc_final: 0.6398 (mpp) REVERT: E 136 GLN cc_start: 0.5819 (mt0) cc_final: 0.4723 (mt0) REVERT: H 85 GLU cc_start: 0.6421 (mt-10) cc_final: 0.5948 (mt-10) REVERT: H 95 LYS cc_start: 0.7292 (pttt) cc_final: 0.7016 (ptpp) REVERT: H 136 GLN cc_start: 0.7060 (tp40) cc_final: 0.6508 (mm110) REVERT: H 145 MET cc_start: 0.7548 (ptt) cc_final: 0.7324 (ptt) REVERT: G 42 GLN cc_start: 0.6337 (mt0) cc_final: 0.5727 (tp40) REVERT: G 50 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7313 (mp10) REVERT: G 72 MET cc_start: 0.7685 (tmm) cc_final: 0.7379 (tmm) REVERT: G 73 MET cc_start: 0.7213 (mmm) cc_final: 0.6643 (mmm) REVERT: G 77 MET cc_start: 0.1302 (OUTLIER) cc_final: 0.1015 (mtp) REVERT: G 145 MET cc_start: 0.6294 (ptt) cc_final: 0.5778 (mtm) REVERT: B 531 LYS cc_start: 0.8060 (tmtt) cc_final: 0.7750 (tmtt) REVERT: B 567 ARG cc_start: 0.8460 (ptm160) cc_final: 0.7441 (tpt90) REVERT: C 174 ARG cc_start: 0.3969 (mmm-85) cc_final: 0.3318 (mmm160) REVERT: C 200 MET cc_start: 0.5585 (ppp) cc_final: 0.4941 (ppp) REVERT: C 284 LYS cc_start: 0.7645 (tttp) cc_final: 0.7428 (ttmt) REVERT: C 298 GLU cc_start: 0.6668 (pt0) cc_final: 0.6454 (pt0) REVERT: C 299 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.6947 (pt0) REVERT: C 362 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: C 363 HIS cc_start: 0.5842 (m-70) cc_final: 0.5330 (m-70) REVERT: C 377 GLU cc_start: 0.5822 (tm-30) cc_final: 0.5160 (tm-30) REVERT: C 380 GLN cc_start: 0.7052 (mt0) cc_final: 0.6786 (mt0) REVERT: C 535 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8153 (mmtm) REVERT: C 567 ARG cc_start: 0.8170 (mmm160) cc_final: 0.7947 (tpm170) REVERT: D 170 VAL cc_start: 0.8267 (p) cc_final: 0.7974 (m) REVERT: D 570 GLN cc_start: 0.7764 (tp40) cc_final: 0.7516 (tp40) REVERT: A 154 ASP cc_start: 0.5702 (m-30) cc_final: 0.4996 (t0) REVERT: A 204 PHE cc_start: 0.6476 (m-80) cc_final: 0.6212 (m-80) REVERT: A 227 ARG cc_start: 0.3340 (mtt-85) cc_final: 0.1920 (tmt170) REVERT: A 240 MET cc_start: 0.7340 (mmm) cc_final: 0.7064 (mmm) outliers start: 28 outliers final: 19 residues processed: 263 average time/residue: 0.1312 time to fit residues: 49.6072 Evaluate side-chains 263 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 525 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 124 optimal weight: 0.4980 chunk 160 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 549 GLN D 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.238339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.184859 restraints weight = 19284.045| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.98 r_work: 0.3524 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15593 Z= 0.156 Angle : 0.598 10.586 21016 Z= 0.303 Chirality : 0.038 0.289 2346 Planarity : 0.004 0.049 2635 Dihedral : 3.991 25.694 2082 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.62 % Allowed : 21.88 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 1860 helix: 1.23 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -1.20 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 91 TYR 0.028 0.001 TYR B 386 PHE 0.023 0.001 PHE G 69 TRP 0.039 0.002 TRP D 360 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (15593) covalent geometry : angle 0.59811 / 0.30 (21016) hydrogen bonds : bond 0.04353 / 2.82 ( 1098) hydrogen bonds : angle 4.24518 / 2.98 ( 3273) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: 0.4654 (mmm) cc_final: 0.4369 (mmt) REVERT: F 95 LYS cc_start: 0.4681 (mmtm) cc_final: 0.3977 (mttt) REVERT: F 117 LEU cc_start: 0.7922 (mt) cc_final: 0.7141 (pt) REVERT: F 145 MET cc_start: 0.5394 (ppp) cc_final: 0.4859 (ppp) REVERT: E 110 MET cc_start: 0.6788 (mmp) cc_final: 0.6396 (mpp) REVERT: E 136 GLN cc_start: 0.5825 (mt0) cc_final: 0.4720 (mt0) REVERT: H 95 LYS cc_start: 0.7215 (pttt) cc_final: 0.6982 (ptpp) REVERT: H 136 GLN cc_start: 0.6992 (tp40) cc_final: 0.6452 (mm110) REVERT: G 42 GLN cc_start: 0.6283 (mt0) cc_final: 0.5716 (tp40) REVERT: G 50 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7320 (mp10) REVERT: G 73 MET cc_start: 0.6835 (mmm) cc_final: 0.6482 (mmm) REVERT: G 77 MET cc_start: 0.1286 (OUTLIER) cc_final: 0.1003 (mtp) REVERT: G 91 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8055 (ttm110) REVERT: G 145 MET cc_start: 0.6257 (ptt) cc_final: 0.5694 (mtm) REVERT: B 531 LYS cc_start: 0.8086 (tmtt) cc_final: 0.7773 (tmtt) REVERT: B 567 ARG cc_start: 0.8497 (ptm160) cc_final: 0.7855 (tpt90) REVERT: B 570 MET cc_start: 0.7341 (ptp) cc_final: 0.6035 (ptm) REVERT: C 105 ARG cc_start: 0.4422 (OUTLIER) cc_final: 0.4201 (ptp90) REVERT: C 200 MET cc_start: 0.5440 (ppp) cc_final: 0.4871 (ppp) REVERT: C 284 LYS cc_start: 0.7655 (tttp) cc_final: 0.7447 (ttmt) REVERT: C 299 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7059 (pt0) REVERT: C 362 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: C 363 HIS cc_start: 0.5893 (m-70) cc_final: 0.5375 (m-70) REVERT: C 377 GLU cc_start: 0.6015 (tm-30) cc_final: 0.5377 (tm-30) REVERT: C 380 GLN cc_start: 0.7087 (mt0) cc_final: 0.6817 (mt0) REVERT: C 535 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8177 (mmtm) REVERT: C 567 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7971 (tpm170) REVERT: D 170 VAL cc_start: 0.8292 (p) cc_final: 0.7996 (m) REVERT: D 560 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7251 (mmm160) REVERT: A 154 ASP cc_start: 0.5736 (m-30) cc_final: 0.5015 (t0) REVERT: A 204 PHE cc_start: 0.6559 (m-80) cc_final: 0.6288 (m-80) outliers start: 26 outliers final: 20 residues processed: 260 average time/residue: 0.1254 time to fit residues: 47.2345 Evaluate side-chains 257 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 525 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 70 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 161 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 42 GLN G 144 GLN B 549 GLN D 323 GLN D 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.238884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.184735 restraints weight = 19338.181| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.03 r_work: 0.3542 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15593 Z= 0.141 Angle : 0.604 10.033 21016 Z= 0.305 Chirality : 0.038 0.295 2346 Planarity : 0.004 0.053 2635 Dihedral : 3.954 24.606 2082 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.88 % Allowed : 21.88 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1860 helix: 1.29 (0.13), residues: 1457 sheet: None (None), residues: 0 loop : -1.15 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 91 TYR 0.021 0.001 TYR C 280 PHE 0.022 0.001 PHE G 69 TRP 0.040 0.002 TRP D 360 HIS 0.003 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15593) covalent geometry : angle 0.60415 / 0.30 (21016) hydrogen bonds : bond 0.04210 / 2.72 ( 1098) hydrogen bonds : angle 4.22719 / 2.97 ( 3273) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: 0.4596 (mmm) cc_final: 0.4322 (mmt) REVERT: F 95 LYS cc_start: 0.4646 (mmtm) cc_final: 0.3963 (mttt) REVERT: F 116 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8257 (mtmt) REVERT: F 117 LEU cc_start: 0.7978 (mt) cc_final: 0.7104 (pt) REVERT: F 145 MET cc_start: 0.5263 (ppp) cc_final: 0.4798 (ppp) REVERT: E 110 MET cc_start: 0.6802 (mmp) cc_final: 0.6421 (mpp) REVERT: E 136 GLN cc_start: 0.5792 (mt0) cc_final: 0.4713 (mt0) REVERT: H 95 LYS cc_start: 0.7207 (pttt) cc_final: 0.6976 (ptpp) REVERT: H 136 GLN cc_start: 0.6918 (tp40) cc_final: 0.6369 (mm110) REVERT: G 42 GLN cc_start: 0.6299 (mt0) cc_final: 0.5709 (tp40) REVERT: G 50 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7243 (mp10) REVERT: G 72 MET cc_start: 0.7432 (tmm) cc_final: 0.6364 (mmt) REVERT: G 77 MET cc_start: 0.1376 (OUTLIER) cc_final: 0.1111 (mtp) REVERT: G 91 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8087 (ttm110) REVERT: G 145 MET cc_start: 0.6259 (ptt) cc_final: 0.5728 (mtm) REVERT: B 531 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7775 (tmtt) REVERT: B 567 ARG cc_start: 0.8523 (ptm160) cc_final: 0.7780 (tpt90) REVERT: B 570 MET cc_start: 0.7426 (ptp) cc_final: 0.6222 (ptm) REVERT: C 200 MET cc_start: 0.5630 (ppp) cc_final: 0.5081 (ppp) REVERT: C 299 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.6948 (pt0) REVERT: C 362 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7266 (mp10) REVERT: C 363 HIS cc_start: 0.5824 (m-70) cc_final: 0.5308 (m-70) REVERT: C 380 GLN cc_start: 0.7173 (mt0) cc_final: 0.6929 (mt0) REVERT: C 535 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8210 (mmtm) REVERT: C 565 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7415 (mm-40) REVERT: C 567 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7940 (tpm170) REVERT: D 170 VAL cc_start: 0.8321 (p) cc_final: 0.8036 (m) REVERT: A 154 ASP cc_start: 0.5632 (m-30) cc_final: 0.4969 (t0) REVERT: A 204 PHE cc_start: 0.6594 (m-80) cc_final: 0.6323 (m-80) outliers start: 30 outliers final: 23 residues processed: 256 average time/residue: 0.1229 time to fit residues: 45.5736 Evaluate side-chains 260 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 525 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 175 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 122 optimal weight: 0.0980 chunk 108 optimal weight: 0.0170 chunk 120 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 42 GLN B 549 GLN D 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.239236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.185705 restraints weight = 19137.857| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.93 r_work: 0.3545 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 15593 Z= 0.199 Angle : 0.830 59.195 21016 Z= 0.459 Chirality : 0.041 0.848 2346 Planarity : 0.004 0.050 2635 Dihedral : 3.940 24.182 2082 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.75 % Allowed : 21.94 % Favored : 76.31 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 1860 helix: 1.29 (0.13), residues: 1457 sheet: None (None), residues: 0 loop : -1.14 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 91 TYR 0.019 0.001 TYR C 280 PHE 0.022 0.001 PHE G 69 TRP 0.035 0.002 TRP D 360 HIS 0.003 0.000 HIS E 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (15593) covalent geometry : angle 0.83027 / 0.46 (21016) hydrogen bonds : bond 0.04204 / 2.72 ( 1098) hydrogen bonds : angle 4.23134 / 2.98 ( 3273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4174.53 seconds wall clock time: 72 minutes 10.86 seconds (4330.86 seconds total)