Starting phenix.real_space_refine on Thu Aug 6 14:07:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5j_66589/08_2026/9x5j_66589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5j_66589/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9x5j_66589/08_2026/9x5j_66589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5j_66589/08_2026/9x5j_66589.map" model { file = "/net/cci-nas-00/data/ceres_data/9x5j_66589/08_2026/9x5j_66589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5j_66589/08_2026/9x5j_66589.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.38, per 1000 atoms: 0.22 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: 1.25 Conformation dependent library (CDL) restraints added in 637.6 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: 0.29 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: 2.68 Time building geometry restraints manager: 1.69 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.510 Find NCS groups from input model: 0.290 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- 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 : 0.556 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: 0.1591 time to fit residues: 69.9543 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 : 0.460 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.5118 ------------------------------------------------------------------------------- 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 D 83 ASN D 334 ASN D 575 HIS A 367 HIS A 380 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.237191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179975 restraints weight = 19241.461| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 3.05 r_work: 0.3476 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1531 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 : 0.602 11.070 21016 Z= 0.308 Chirality : 0.038 0.161 2346 Planarity : 0.004 0.077 2635 Dihedral : 4.121 22.897 2082 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.38 % Allowed : 12.25 % 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: -0.49 (0.19), residues: 1860 helix: 0.30 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -2.42 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 127 TYR 0.025 0.001 TYR B 550 PHE 0.034 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 0.00304 / 0.14 (15593) covalent geometry : angle 0.60167 / 0.31 (21016) hydrogen bonds : bond 0.04493 / 2.94 ( 1098) hydrogen bonds : angle 4.48435 / 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 292 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 0.558 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 72 MET cc_start: 0.5262 (mtp) cc_final: 0.5012 (mtp) REVERT: F 90 PHE cc_start: 0.6755 (m-80) cc_final: 0.6403 (m-80) REVERT: F 139 TYR cc_start: 0.8355 (p90) cc_final: 0.8130 (p90) REVERT: H 31 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7719 (ttpp) REVERT: H 127 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6953 (ttp80) REVERT: H 145 MET cc_start: 0.7518 (ptt) cc_final: 0.7290 (ptt) REVERT: G 17 PHE cc_start: 0.7533 (t80) cc_final: 0.7082 (t80) REVERT: G 42 GLN cc_start: 0.6564 (mt0) cc_final: 0.5980 (tp40) REVERT: B 183 ARG cc_start: 0.6901 (tpm170) cc_final: 0.5811 (mtp-110) REVERT: B 227 ARG cc_start: 0.3433 (mtt-85) cc_final: 0.2707 (tmt170) REVERT: B 570 MET cc_start: 0.8090 (mtt) cc_final: 0.6975 (ttp) REVERT: C 380 GLN cc_start: 0.6933 (mt0) cc_final: 0.6698 (mt0) REVERT: C 542 ASP cc_start: 0.7981 (m-30) cc_final: 0.7556 (p0) REVERT: C 570 MET cc_start: 0.7551 (mtp) cc_final: 0.6999 (mtm) REVERT: D 170 VAL cc_start: 0.8178 (p) cc_final: 0.7932 (m) REVERT: D 322 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: A 227 ARG cc_start: 0.3268 (mtt-85) cc_final: 0.2171 (tmt-80) REVERT: A 341 VAL cc_start: 0.8688 (t) cc_final: 0.7755 (p) outliers start: 22 outliers final: 11 residues processed: 281 average time/residue: 0.1301 time to fit residues: 52.3403 Evaluate side-chains 256 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 244 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 126 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: 1.9990 chunk 181 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4661 r_free = 0.4661 target = 0.235618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.178224 restraints weight = 19583.875| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.02 r_work: 0.3420 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15593 Z= 0.194 Angle : 0.611 9.495 21016 Z= 0.315 Chirality : 0.039 0.169 2346 Planarity : 0.004 0.066 2635 Dihedral : 4.136 23.151 2082 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.25 % Allowed : 15.44 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.19), residues: 1860 helix: 0.62 (0.13), residues: 1459 sheet: None (None), residues: 0 loop : -2.10 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 541 TYR 0.034 0.002 TYR B 550 PHE 0.023 0.002 PHE G 69 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 0.00457 / 0.19 (15593) covalent geometry : angle 0.61149 / 0.32 (21016) hydrogen bonds : bond 0.04771 / 3.10 ( 1098) hydrogen bonds : angle 4.44805 / 3.11 ( 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 291 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.580 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 90 PHE cc_start: 0.6719 (m-80) cc_final: 0.6472 (m-10) REVERT: F 139 TYR cc_start: 0.8439 (p90) cc_final: 0.8162 (p90) REVERT: E 136 GLN cc_start: 0.5780 (mt0) cc_final: 0.4735 (mt0) REVERT: H 31 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7737 (ttpp) REVERT: H 145 MET cc_start: 0.7645 (ptt) cc_final: 0.7399 (ptt) REVERT: G 42 GLN cc_start: 0.6537 (mt0) cc_final: 0.5849 (tp40) REVERT: G 145 MET cc_start: 0.5889 (ptt) cc_final: 0.5507 (ttt) REVERT: B 183 ARG cc_start: 0.6825 (tpm170) cc_final: 0.5843 (mtp-110) REVERT: B 227 ARG cc_start: 0.3487 (mtt-85) cc_final: 0.2706 (tmt170) REVERT: B 380 GLN cc_start: 0.8944 (tp40) cc_final: 0.8646 (tp40) REVERT: B 531 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7715 (tmtt) REVERT: C 363 HIS cc_start: 0.5886 (m-70) cc_final: 0.5384 (m-70) REVERT: C 377 GLU cc_start: 0.5974 (tm-30) cc_final: 0.5230 (mt-10) REVERT: C 380 GLN cc_start: 0.6998 (mt0) cc_final: 0.6700 (mt0) REVERT: C 535 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8200 (mmtm) REVERT: C 542 ASP cc_start: 0.8012 (m-30) cc_final: 0.7486 (p0) REVERT: D 170 VAL cc_start: 0.8207 (p) cc_final: 0.7922 (m) REVERT: D 183 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8190 (mp) REVERT: D 322 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 204 PHE cc_start: 0.6324 (m-80) cc_final: 0.6111 (m-80) REVERT: A 227 ARG cc_start: 0.3344 (mtt-85) cc_final: 0.2214 (tmt-80) outliers start: 36 outliers final: 18 residues processed: 272 average time/residue: 0.1262 time to fit residues: 49.2855 Evaluate side-chains 262 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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 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 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: 7.9990 chunk 23 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4654 r_free = 0.4654 target = 0.234772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.177647 restraints weight = 19482.990| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.25 r_work: 0.3364 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15593 Z= 0.259 Angle : 0.659 9.985 21016 Z= 0.339 Chirality : 0.042 0.178 2346 Planarity : 0.004 0.063 2635 Dihedral : 4.237 24.181 2082 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.38 % Allowed : 17.81 % Favored : 79.81 % 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: 0.01 (0.19), residues: 1860 helix: 0.61 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.99 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 127 TYR 0.022 0.002 TYR C 280 PHE 0.027 0.002 PHE G 17 TRP 0.026 0.002 TRP D 288 HIS 0.006 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.26 (15593) covalent geometry : angle 0.65895 / 0.34 (21016) hydrogen bonds : bond 0.05130 / 3.35 ( 1098) hydrogen bonds : angle 4.55813 / 3.19 ( 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 291 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 0.532 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: E 136 GLN cc_start: 0.5835 (mt0) cc_final: 0.4725 (mt0) REVERT: H 31 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7790 (ttpp) REVERT: H 125 MET cc_start: 0.8080 (ttp) cc_final: 0.7723 (ttp) REVERT: H 145 MET cc_start: 0.7673 (ptt) cc_final: 0.7444 (ptt) REVERT: G 13 PHE cc_start: 0.5861 (m-10) cc_final: 0.5614 (m-10) REVERT: G 42 GLN cc_start: 0.6571 (mt0) cc_final: 0.5906 (tp40) REVERT: G 145 MET cc_start: 0.5979 (ptt) cc_final: 0.5506 (ttt) REVERT: B 183 ARG cc_start: 0.6856 (tpm170) cc_final: 0.5900 (mtp-110) REVERT: B 227 ARG cc_start: 0.3608 (mtt-85) cc_final: 0.2814 (tmt170) REVERT: B 531 LYS cc_start: 0.8041 (tmtt) cc_final: 0.7739 (tmtt) REVERT: B 570 MET cc_start: 0.7020 (ttp) cc_final: 0.5769 (mtt) REVERT: C 362 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6430 (mp10) REVERT: C 363 HIS cc_start: 0.6031 (m-70) cc_final: 0.5527 (m-70) REVERT: C 377 GLU cc_start: 0.6047 (tm-30) cc_final: 0.5143 (mt-10) REVERT: C 380 GLN cc_start: 0.7116 (mt0) cc_final: 0.6842 (mt0) REVERT: C 531 LYS cc_start: 0.7613 (pttp) cc_final: 0.6977 (pttp) REVERT: C 535 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8182 (mmtm) REVERT: C 542 ASP cc_start: 0.8099 (m-30) cc_final: 0.7622 (p0) REVERT: C 565 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7661 (mm-40) REVERT: C 567 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7144 (tpm170) REVERT: C 570 MET cc_start: 0.7476 (mtp) cc_final: 0.7176 (mtm) REVERT: D 170 VAL cc_start: 0.8275 (p) cc_final: 0.7924 (m) REVERT: D 322 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: D 556 LYS cc_start: 0.8628 (tppt) cc_final: 0.8274 (tppt) REVERT: A 204 PHE cc_start: 0.6509 (m-80) cc_final: 0.6272 (m-80) REVERT: A 227 ARG cc_start: 0.3474 (mtt-85) cc_final: 0.2181 (tmt-80) REVERT: A 241 ASP cc_start: 0.6072 (t70) cc_final: 0.5397 (p0) outliers start: 38 outliers final: 26 residues processed: 272 average time/residue: 0.1134 time to fit residues: 44.4318 Evaluate side-chains 275 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 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 342 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4683 r_free = 0.4683 target = 0.236004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.181373 restraints weight = 19474.901| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.96 r_work: 0.3454 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15593 Z= 0.228 Angle : 0.640 9.488 21016 Z= 0.329 Chirality : 0.041 0.175 2346 Planarity : 0.004 0.058 2635 Dihedral : 4.246 24.453 2082 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.69 % Allowed : 20.25 % Favored : 77.06 % 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: 0.20 (0.19), residues: 1860 helix: 0.73 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.85 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 567 TYR 0.035 0.002 TYR B 550 PHE 0.028 0.002 PHE G 17 TRP 0.024 0.002 TRP D 288 HIS 0.006 0.001 HIS E 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (15593) covalent geometry : angle 0.64008 / 0.33 (21016) hydrogen bonds : bond 0.04943 / 3.22 ( 1098) hydrogen bonds : angle 4.50840 / 3.16 ( 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 301 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 0.566 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: E 136 GLN cc_start: 0.5924 (mt0) cc_final: 0.4758 (mt0) REVERT: H 31 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7750 (ttpp) REVERT: H 85 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6746 (mt-10) REVERT: H 136 GLN cc_start: 0.7161 (tp40) cc_final: 0.6678 (mm110) REVERT: H 145 MET cc_start: 0.7636 (ptt) cc_final: 0.7426 (ptt) REVERT: G 42 GLN cc_start: 0.6523 (mt0) cc_final: 0.5912 (tp40) REVERT: G 69 PHE cc_start: 0.7449 (t80) cc_final: 0.7221 (t80) REVERT: G 77 MET cc_start: 0.1808 (OUTLIER) cc_final: 0.1509 (mtp) REVERT: B 227 ARG cc_start: 0.3437 (mtt-85) cc_final: 0.2718 (tmt170) REVERT: B 531 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7744 (tmtt) REVERT: B 570 MET cc_start: 0.6809 (ttp) cc_final: 0.5829 (mtp) REVERT: C 200 MET cc_start: 0.6003 (ppp) cc_final: 0.5399 (ppp) REVERT: C 299 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: C 362 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6570 (mp10) REVERT: C 377 GLU cc_start: 0.5963 (tm-30) cc_final: 0.5195 (mt-10) REVERT: C 380 GLN cc_start: 0.7150 (mt0) cc_final: 0.6850 (mt0) REVERT: C 531 LYS cc_start: 0.7507 (pttp) cc_final: 0.6907 (pttp) REVERT: C 535 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8215 (mmtm) REVERT: C 542 ASP cc_start: 0.8067 (m-30) cc_final: 0.7664 (p0) REVERT: C 567 ARG cc_start: 0.7754 (tpp-160) cc_final: 0.7121 (tpm170) REVERT: C 570 MET cc_start: 0.7489 (mtp) cc_final: 0.7251 (mtm) REVERT: D 170 VAL cc_start: 0.8365 (p) cc_final: 0.8012 (m) REVERT: D 322 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: D 556 LYS cc_start: 0.8591 (tppt) cc_final: 0.8248 (tppt) REVERT: D 570 GLN cc_start: 0.7564 (tp40) cc_final: 0.7197 (tp40) REVERT: A 204 PHE cc_start: 0.6486 (m-80) cc_final: 0.6257 (m-80) REVERT: A 227 ARG cc_start: 0.3531 (mtt-85) cc_final: 0.2176 (tmt-80) REVERT: A 241 ASP cc_start: 0.6316 (t70) cc_final: 0.5589 (p0) outliers start: 43 outliers final: 24 residues processed: 280 average time/residue: 0.1177 time to fit residues: 48.4730 Evaluate side-chains 272 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 299 GLU 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 342 SER 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: 9.9990 chunk 31 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 7 optimal weight: 0.0570 chunk 63 optimal weight: 0.5980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 144 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 = 0.4709 r_free = 0.4709 target = 0.238794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.185003 restraints weight = 19241.652| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.88 r_work: 0.3521 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15593 Z= 0.143 Angle : 0.592 9.597 21016 Z= 0.299 Chirality : 0.038 0.171 2346 Planarity : 0.004 0.055 2635 Dihedral : 4.094 24.066 2082 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.00 % Allowed : 21.25 % Favored : 76.75 % 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: 0.65 (0.19), residues: 1860 helix: 1.00 (0.13), residues: 1462 sheet: None (None), residues: 0 loop : -1.55 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 567 TYR 0.027 0.001 TYR B 550 PHE 0.018 0.001 PHE G 13 TRP 0.022 0.001 TRP D 288 HIS 0.003 0.001 HIS E 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (15593) covalent geometry : angle 0.59155 / 0.30 (21016) hydrogen bonds : bond 0.04378 / 2.84 ( 1098) hydrogen bonds : angle 4.30647 / 3.02 ( 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 285 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.475 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: 0.4650 (mmm) cc_final: 0.4437 (mmt) REVERT: F 77 MET cc_start: 0.3960 (ttp) cc_final: 0.3748 (ttp) REVERT: E 136 GLN cc_start: 0.5948 (mt0) cc_final: 0.4838 (mt0) REVERT: H 31 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7895 (ttpp) REVERT: H 85 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6630 (mt-10) REVERT: H 125 MET cc_start: 0.8078 (ttp) cc_final: 0.7673 (ttp) REVERT: H 136 GLN cc_start: 0.7128 (tp40) cc_final: 0.6622 (mm110) REVERT: H 145 MET cc_start: 0.7600 (ptt) cc_final: 0.7373 (ptt) REVERT: G 42 GLN cc_start: 0.6386 (mt0) cc_final: 0.5825 (tp40) REVERT: G 77 MET cc_start: 0.1855 (OUTLIER) cc_final: 0.1570 (mtp) REVERT: G 85 GLU cc_start: 0.7193 (tt0) cc_final: 0.6722 (tt0) REVERT: G 145 MET cc_start: 0.6298 (ptt) cc_final: 0.5696 (mtm) REVERT: B 227 ARG cc_start: 0.3219 (mtt-85) cc_final: 0.2523 (tmt170) REVERT: B 531 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7732 (tmtt) REVERT: B 570 MET cc_start: 0.6693 (ttp) cc_final: 0.5590 (mtt) REVERT: C 200 MET cc_start: 0.5896 (ppp) cc_final: 0.5374 (ppp) REVERT: C 299 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7097 (pt0) REVERT: C 362 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6579 (mp10) REVERT: C 377 GLU cc_start: 0.5741 (tm-30) cc_final: 0.5144 (mt-10) REVERT: C 380 GLN cc_start: 0.7076 (mt0) cc_final: 0.6780 (mt0) REVERT: C 542 ASP cc_start: 0.7915 (m-30) cc_final: 0.7582 (p0) REVERT: C 567 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.7196 (tpm170) REVERT: C 570 MET cc_start: 0.7495 (mtp) cc_final: 0.7190 (mtm) REVERT: D 170 VAL cc_start: 0.8305 (p) cc_final: 0.8020 (m) REVERT: D 210 ARG cc_start: 0.8348 (tmm160) cc_final: 0.8014 (tmm-80) REVERT: D 556 LYS cc_start: 0.8539 (tppt) cc_final: 0.8233 (tppt) REVERT: D 570 GLN cc_start: 0.7676 (tp40) cc_final: 0.7368 (tp40) REVERT: A 154 ASP cc_start: 0.5654 (m-30) cc_final: 0.4985 (t0) REVERT: A 204 PHE cc_start: 0.6429 (m-80) cc_final: 0.6175 (m-80) outliers start: 32 outliers final: 18 residues processed: 270 average time/residue: 0.1209 time to fit residues: 47.4403 Evaluate side-chains 266 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 147 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 286 VAL 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 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 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: 0.9980 chunk 81 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 147 optimal weight: 0.0770 chunk 154 optimal weight: 0.9990 chunk 170 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.239503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.186274 restraints weight = 19213.578| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.06 r_work: 0.3527 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2623 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= 0.133 Angle : 0.580 9.749 21016 Z= 0.293 Chirality : 0.037 0.171 2346 Planarity : 0.004 0.051 2635 Dihedral : 4.006 25.644 2082 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.75 % Allowed : 22.19 % Favored : 76.06 % 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: 0.92 (0.19), residues: 1860 helix: 1.18 (0.14), residues: 1459 sheet: None (None), residues: 0 loop : -1.39 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 567 TYR 0.025 0.001 TYR B 386 PHE 0.032 0.001 PHE A 534 TRP 0.023 0.001 TRP D 360 HIS 0.002 0.000 HIS E 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15593) covalent geometry : angle 0.58004 / 0.29 (21016) hydrogen bonds : bond 0.04230 / 2.74 ( 1098) hydrogen bonds : angle 4.24254 / 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 281 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.542 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: 0.4678 (mmm) cc_final: 0.4442 (mmt) REVERT: F 95 LYS cc_start: 0.4608 (mmtm) cc_final: 0.3833 (mttt) REVERT: F 117 LEU cc_start: 0.8154 (mt) cc_final: 0.7326 (pt) REVERT: E 136 GLN cc_start: 0.5848 (mt0) cc_final: 0.4739 (mt0) REVERT: H 85 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6671 (mt-10) REVERT: H 95 LYS cc_start: 0.7270 (pttt) cc_final: 0.7032 (ptpp) REVERT: H 136 GLN cc_start: 0.7102 (tp40) cc_final: 0.6595 (mm110) REVERT: H 145 MET cc_start: 0.7578 (ptt) cc_final: 0.7355 (ptt) REVERT: G 42 GLN cc_start: 0.6262 (mt0) cc_final: 0.5730 (tp40) REVERT: G 50 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7296 (mp10) REVERT: G 72 MET cc_start: 0.7789 (tmm) cc_final: 0.7416 (tmm) REVERT: G 73 MET cc_start: 0.7157 (mmm) cc_final: 0.6497 (mmm) REVERT: G 77 MET cc_start: 0.1553 (OUTLIER) cc_final: 0.1281 (mtp) REVERT: G 91 ARG cc_start: 0.8448 (ttm110) cc_final: 0.8047 (ttm110) REVERT: G 145 MET cc_start: 0.6211 (ptt) cc_final: 0.5680 (mtm) REVERT: B 531 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7716 (tmtt) REVERT: B 567 ARG cc_start: 0.8561 (tpt90) cc_final: 0.7573 (ptm160) REVERT: C 200 MET cc_start: 0.5859 (ppp) cc_final: 0.5359 (ppp) REVERT: C 284 LYS cc_start: 0.7776 (tttp) cc_final: 0.7413 (ttmt) REVERT: C 358 LYS cc_start: 0.8364 (ttpt) cc_final: 0.7936 (ttmt) REVERT: C 362 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6538 (mp10) REVERT: C 380 GLN cc_start: 0.7106 (mt0) cc_final: 0.6823 (mt0) REVERT: C 531 LYS cc_start: 0.7270 (ptmm) cc_final: 0.6799 (pttp) REVERT: C 535 LYS cc_start: 0.8504 (mptt) cc_final: 0.8271 (mttp) REVERT: D 170 VAL cc_start: 0.8339 (p) cc_final: 0.8066 (m) REVERT: D 210 ARG cc_start: 0.8425 (tmm160) cc_final: 0.8070 (tmm-80) REVERT: D 556 LYS cc_start: 0.8517 (tppt) cc_final: 0.8246 (tppt) REVERT: D 570 GLN cc_start: 0.7713 (tp40) cc_final: 0.7454 (tp40) REVERT: A 154 ASP cc_start: 0.5631 (m-30) cc_final: 0.4995 (t0) REVERT: A 204 PHE cc_start: 0.6472 (m-80) cc_final: 0.6228 (m-80) REVERT: A 341 VAL cc_start: 0.8644 (t) cc_final: 0.7745 (p) outliers start: 28 outliers final: 16 residues processed: 270 average time/residue: 0.1136 time to fit residues: 44.7677 Evaluate side-chains 260 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 113 LEU 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 B residue 175 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 287 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 169 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.239089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.184396 restraints weight = 19323.343| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.92 r_work: 0.3534 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15593 Z= 0.137 Angle : 0.579 10.240 21016 Z= 0.294 Chirality : 0.037 0.165 2346 Planarity : 0.003 0.050 2635 Dihedral : 3.968 25.211 2082 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.88 % Allowed : 22.69 % Favored : 75.44 % 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: 1.26 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -1.33 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 567 TYR 0.041 0.001 TYR A 550 PHE 0.026 0.001 PHE A 534 TRP 0.039 0.001 TRP D 360 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (15593) covalent geometry : angle 0.57931 / 0.29 (21016) hydrogen bonds : bond 0.04217 / 2.73 ( 1098) hydrogen bonds : angle 4.21879 / 2.95 ( 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 280 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.536 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: 0.4685 (mmm) cc_final: 0.4420 (mmt) REVERT: F 95 LYS cc_start: 0.4706 (mmtm) cc_final: 0.3981 (mttt) REVERT: F 145 MET cc_start: 0.5568 (ppp) cc_final: 0.5217 (ppp) REVERT: E 136 GLN cc_start: 0.5817 (mt0) cc_final: 0.4761 (mt0) REVERT: H 85 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6755 (mt-10) REVERT: H 95 LYS cc_start: 0.7271 (pttt) cc_final: 0.6993 (ptpp) REVERT: H 136 GLN cc_start: 0.7025 (tp40) cc_final: 0.6486 (mm110) REVERT: H 145 MET cc_start: 0.7625 (ptt) cc_final: 0.7366 (ptt) REVERT: G 42 GLN cc_start: 0.6316 (mt0) cc_final: 0.5712 (tp40) REVERT: G 50 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7233 (mp10) REVERT: G 72 MET cc_start: 0.7701 (tmm) cc_final: 0.7472 (tmm) REVERT: G 73 MET cc_start: 0.6896 (mmm) cc_final: 0.6379 (mmm) REVERT: G 77 MET cc_start: 0.1524 (OUTLIER) cc_final: 0.1257 (mtp) REVERT: G 145 MET cc_start: 0.6272 (ptt) cc_final: 0.5738 (mtm) REVERT: B 531 LYS cc_start: 0.8040 (tmtt) cc_final: 0.7733 (tmtt) REVERT: C 200 MET cc_start: 0.5784 (ppp) cc_final: 0.5277 (ppp) REVERT: C 299 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7039 (pt0) REVERT: C 358 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7847 (ttmt) REVERT: C 362 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6511 (mp10) REVERT: C 377 GLU cc_start: 0.5840 (tm-30) cc_final: 0.5086 (tm-30) REVERT: C 380 GLN cc_start: 0.7116 (mt0) cc_final: 0.6775 (mt0) REVERT: C 542 ASP cc_start: 0.7926 (m-30) cc_final: 0.7585 (p0) REVERT: D 170 VAL cc_start: 0.8273 (p) cc_final: 0.7980 (m) REVERT: D 210 ARG cc_start: 0.8440 (tmm160) cc_final: 0.8079 (tmm-80) REVERT: D 546 MET cc_start: 0.8725 (mtm) cc_final: 0.8023 (mpp) REVERT: D 556 LYS cc_start: 0.8529 (tppt) cc_final: 0.8297 (tppt) REVERT: A 154 ASP cc_start: 0.5652 (m-30) cc_final: 0.4982 (t0) REVERT: A 204 PHE cc_start: 0.6556 (m-80) cc_final: 0.6295 (m-80) REVERT: A 341 VAL cc_start: 0.8630 (t) cc_final: 0.7715 (p) outliers start: 30 outliers final: 20 residues processed: 269 average time/residue: 0.1182 time to fit residues: 45.8856 Evaluate side-chains 266 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 286 VAL 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 537 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 287 THR 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 175 ILE 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: 0.0470 chunk 160 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 42 GLN G 144 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 = 0.239157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.185573 restraints weight = 19210.677| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.01 r_work: 0.3509 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2834 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= 0.146 Angle : 0.596 10.655 21016 Z= 0.302 Chirality : 0.038 0.170 2346 Planarity : 0.004 0.069 2635 Dihedral : 3.970 25.566 2082 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.81 % Allowed : 22.31 % Favored : 75.88 % 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: 1.06 (0.19), residues: 1860 helix: 1.27 (0.14), residues: 1458 sheet: None (None), residues: 0 loop : -1.26 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 567 TYR 0.030 0.001 TYR B 386 PHE 0.027 0.001 PHE A 534 TRP 0.037 0.002 TRP D 360 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15593) covalent geometry : angle 0.59625 / 0.30 (21016) hydrogen bonds : bond 0.04283 / 2.77 ( 1098) hydrogen bonds : angle 4.21686 / 2.95 ( 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 270 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.369 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: 0.4617 (mmm) cc_final: 0.4325 (mmt) REVERT: F 95 LYS cc_start: 0.4694 (mmtm) cc_final: 0.3977 (mttt) REVERT: F 117 LEU cc_start: 0.8102 (mt) cc_final: 0.7126 (pt) REVERT: F 145 MET cc_start: 0.5729 (ppp) cc_final: 0.5437 (ppp) REVERT: E 136 GLN cc_start: 0.5757 (mt0) cc_final: 0.4740 (mt0) REVERT: H 85 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6791 (mt-10) REVERT: H 95 LYS cc_start: 0.7250 (pttt) cc_final: 0.6979 (ptpp) REVERT: H 136 GLN cc_start: 0.6945 (tp40) cc_final: 0.6401 (mm110) REVERT: H 145 MET cc_start: 0.7599 (ptt) cc_final: 0.7347 (ptt) REVERT: G 42 GLN cc_start: 0.6325 (mt0) cc_final: 0.5769 (tp40) REVERT: G 50 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7283 (mp10) REVERT: G 73 MET cc_start: 0.6725 (mmm) cc_final: 0.6350 (mmm) REVERT: G 77 MET cc_start: 0.1402 (OUTLIER) cc_final: 0.1120 (mtp) REVERT: G 145 MET cc_start: 0.6261 (ptt) cc_final: 0.5712 (mtm) REVERT: B 531 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7752 (tmtt) REVERT: B 567 ARG cc_start: 0.8513 (tpt90) cc_final: 0.7514 (ptm160) REVERT: C 200 MET cc_start: 0.5786 (ppp) cc_final: 0.5318 (ppp) REVERT: C 299 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.6934 (pt0) REVERT: C 358 LYS cc_start: 0.8346 (ttpt) cc_final: 0.7885 (ttmt) REVERT: C 362 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6588 (mp10) REVERT: C 377 GLU cc_start: 0.5907 (tm-30) cc_final: 0.5118 (tm-30) REVERT: C 380 GLN cc_start: 0.7198 (mt0) cc_final: 0.6863 (mt0) REVERT: C 542 ASP cc_start: 0.7882 (m-30) cc_final: 0.7622 (p0) REVERT: C 567 ARG cc_start: 0.7974 (tpp-160) cc_final: 0.7295 (tpm170) REVERT: C 570 MET cc_start: 0.7300 (mtp) cc_final: 0.6967 (mtm) REVERT: D 170 VAL cc_start: 0.8279 (p) cc_final: 0.7982 (m) REVERT: D 556 LYS cc_start: 0.8521 (tppt) cc_final: 0.8284 (tppt) REVERT: A 154 ASP cc_start: 0.5712 (m-30) cc_final: 0.5002 (t0) REVERT: A 204 PHE cc_start: 0.6574 (m-80) cc_final: 0.6305 (m-80) REVERT: A 341 VAL cc_start: 0.8667 (t) cc_final: 0.7754 (p) REVERT: A 558 LEU cc_start: 0.7837 (pp) cc_final: 0.7312 (pp) outliers start: 29 outliers final: 24 residues processed: 259 average time/residue: 0.1152 time to fit residues: 43.3193 Evaluate side-chains 261 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 113 LEU 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 H residue 146 MET 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 286 VAL 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 537 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 287 THR 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 175 ILE 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: 0.2980 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 104 optimal weight: 0.5980 chunk 164 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 323 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 = 0.4714 r_free = 0.4714 target = 0.239468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.185896 restraints weight = 19225.281| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 3.04 r_work: 0.3521 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2906 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= 0.137 Angle : 0.603 9.364 21016 Z= 0.307 Chirality : 0.038 0.169 2346 Planarity : 0.004 0.089 2635 Dihedral : 3.966 26.655 2082 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.88 % Allowed : 22.56 % Favored : 75.56 % 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: 1.12 (0.19), residues: 1860 helix: 1.31 (0.14), residues: 1458 sheet: None (None), residues: 0 loop : -1.23 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 567 TYR 0.018 0.001 TYR A 550 PHE 0.023 0.001 PHE G 69 TRP 0.043 0.002 TRP D 360 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (15593) covalent geometry : angle 0.60286 / 0.31 (21016) hydrogen bonds : bond 0.04216 / 2.72 ( 1098) hydrogen bonds : angle 4.23046 / 2.96 ( 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 : 0.540 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: 0.4611 (mmm) cc_final: 0.4345 (mmt) REVERT: F 95 LYS cc_start: 0.4688 (mmtm) cc_final: 0.3995 (mttt) REVERT: F 145 MET cc_start: 0.5742 (ppp) cc_final: 0.5410 (ppp) REVERT: E 136 GLN cc_start: 0.5789 (mt0) cc_final: 0.4752 (mt0) REVERT: H 95 LYS cc_start: 0.7201 (pttt) cc_final: 0.6933 (ptpp) REVERT: H 136 GLN cc_start: 0.6860 (tp40) cc_final: 0.6301 (mm110) REVERT: H 145 MET cc_start: 0.7582 (ptt) cc_final: 0.7352 (ptt) REVERT: G 42 GLN cc_start: 0.6347 (mt0) cc_final: 0.5739 (tp40) REVERT: G 50 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7269 (mp10) REVERT: G 77 MET cc_start: 0.1315 (OUTLIER) cc_final: 0.1050 (mtp) REVERT: G 91 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7780 (ttm110) REVERT: G 145 MET cc_start: 0.6314 (ptt) cc_final: 0.5778 (mtm) REVERT: B 531 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7772 (tmtt) REVERT: C 200 MET cc_start: 0.5785 (ppp) cc_final: 0.5337 (ppp) REVERT: C 299 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.6899 (pt0) REVERT: C 358 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7905 (ttmt) REVERT: C 362 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6569 (mp10) REVERT: C 377 GLU cc_start: 0.5939 (tm-30) cc_final: 0.5221 (tm-30) REVERT: C 380 GLN cc_start: 0.7189 (mt0) cc_final: 0.6838 (mt0) REVERT: C 542 ASP cc_start: 0.7904 (m-30) cc_final: 0.7583 (p0) REVERT: D 170 VAL cc_start: 0.8253 (p) cc_final: 0.7951 (m) REVERT: A 154 ASP cc_start: 0.5720 (m-30) cc_final: 0.4990 (t0) REVERT: A 204 PHE cc_start: 0.6529 (m-80) cc_final: 0.6249 (m-80) REVERT: A 341 VAL cc_start: 0.8639 (t) cc_final: 0.7718 (p) REVERT: A 558 LEU cc_start: 0.7775 (pp) cc_final: 0.7542 (pp) outliers start: 30 outliers final: 24 residues processed: 255 average time/residue: 0.1139 time to fit residues: 42.0291 Evaluate side-chains 261 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 113 LEU 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 H residue 146 MET 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 286 VAL 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 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 287 THR 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 A residue 143 THR Chi-restraints excluded: chain A residue 175 ILE 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: 0.0670 chunk 123 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 108 optimal weight: 0.0870 chunk 120 optimal weight: 0.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 144 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 = 0.4731 r_free = 0.4731 target = 0.241528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.189085 restraints weight = 19077.192| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.86 r_work: 0.3576 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15593 Z= 0.125 Angle : 0.601 9.736 21016 Z= 0.304 Chirality : 0.038 0.246 2346 Planarity : 0.004 0.060 2635 Dihedral : 3.905 26.822 2082 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.38 % Allowed : 23.06 % Favored : 75.56 % 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: 1.26 (0.19), residues: 1860 helix: 1.41 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -1.18 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 567 TYR 0.023 0.001 TYR C 280 PHE 0.031 0.001 PHE A 534 TRP 0.044 0.001 TRP D 360 HIS 0.002 0.000 HIS B 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (15593) covalent geometry : angle 0.60121 / 0.30 (21016) hydrogen bonds : bond 0.04007 / 2.58 ( 1098) hydrogen bonds : angle 4.16564 / 2.92 ( 3273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4093.12 seconds wall clock time: 70 minutes 39.08 seconds (4239.08 seconds total)