Starting phenix.real_space_refine on Wed Aug 5 05:03:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzz_36755/08_2026/8jzz_36755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzz_36755/08_2026/8jzz_36755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jzz_36755/08_2026/8jzz_36755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzz_36755/08_2026/8jzz_36755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jzz_36755/08_2026/8jzz_36755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzz_36755/08_2026/8jzz_36755.map" } resolution = 3.31 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5542 2.51 5 N 1485 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 8680 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2410 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 11, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 106 Chain: "C" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1555 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 395 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2204 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 8, 'PHE:plan': 2, 'ASP:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "D" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 458 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 1.48, per 1000 atoms: 0.17 Number of scatterers: 8680 At special positions: 0 Unit cell: (85.56, 121.44, 142.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1601 8.00 N 1485 7.00 C 5542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 47 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 54 " distance=2.04 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 55 " distance=2.03 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: 0.63 Conformation dependent library (CDL) restraints added in 418.7 milliseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 37.8% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.542A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 8 through 31 removed outlier: 3.630A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.561A pdb=" N CYS C 215 " --> pdb=" O TRP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.580A pdb=" N ASN C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 removed outlier: 4.098A pdb=" N ILE C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 296 through 310 removed outlier: 3.608A pdb=" N ALA C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'A' and resid 34 through 53 removed outlier: 3.884A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 88 removed outlier: 3.804A pdb=" N ALA A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.626A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 140 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 149 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 198 through 212 Processing helix chain 'A' and resid 212 through 230 Processing helix chain 'A' and resid 239 through 268 removed outlier: 4.105A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 272 through 303 removed outlier: 4.521A pdb=" N SER A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.817A pdb=" N TYR A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 removed outlier: 3.794A pdb=" N GLY A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.958A pdb=" N ARG D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 66 removed outlier: 4.128A pdb=" N SER D 66 " --> pdb=" O ARG D 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.075A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.511A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.748A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.538A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.986A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.715A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 288 removed outlier: 4.193A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 186 through 191 removed outlier: 6.255A pdb=" N VAL C 34 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE C 200 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU C 36 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 223 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 37 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N CYS C 225 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 39 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASP C 227 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE C 222 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE C 268 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE C 224 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN C 270 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 226 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.610A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.864A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'H' and resid 194 through 195 removed outlier: 5.632A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 175 through 179 removed outlier: 3.710A pdb=" N VAL A 176 " --> pdb=" O GLY A 189 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1224 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: 1.24 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2824 1.35 - 1.47: 2239 1.47 - 1.59: 3734 1.59 - 1.72: 0 1.72 - 1.84: 65 Bond restraints: 8862 Sorted by residual: bond pdb=" N ARG H 67 " pdb=" CA ARG H 67 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.32e-02 5.74e+03 6.17e+00 bond pdb=" N PHE A 307 " pdb=" CA PHE A 307 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.30e-02 5.92e+03 5.09e+00 bond pdb=" N ARG A 200 " pdb=" CA ARG A 200 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.90e+00 bond pdb=" N LYS A 313 " pdb=" CA LYS A 313 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.31e-02 5.83e+03 4.12e+00 bond pdb=" N ARG A 310 " pdb=" CA ARG A 310 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.02e+00 ... (remaining 8857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11714 1.31 - 2.62: 286 2.62 - 3.93: 71 3.93 - 5.24: 17 5.24 - 6.55: 3 Bond angle restraints: 12091 Sorted by residual: angle pdb=" N GLN A 305 " pdb=" CA GLN A 305 " pdb=" C GLN A 305 " ideal model delta sigma weight residual 112.38 105.83 6.55 1.22e+00 6.72e-01 2.89e+01 angle pdb=" N GLN A 308 " pdb=" CA GLN A 308 " pdb=" C GLN A 308 " ideal model delta sigma weight residual 111.28 106.96 4.32 1.09e+00 8.42e-01 1.57e+01 angle pdb=" N GLY A 306 " pdb=" CA GLY A 306 " pdb=" C GLY A 306 " ideal model delta sigma weight residual 114.67 111.17 3.50 1.10e+00 8.26e-01 1.01e+01 angle pdb=" CA GLY A 309 " pdb=" C GLY A 309 " pdb=" O GLY A 309 " ideal model delta sigma weight residual 120.75 117.48 3.27 1.03e+00 9.43e-01 1.01e+01 angle pdb=" N PHE A 307 " pdb=" CA PHE A 307 " pdb=" C PHE A 307 " ideal model delta sigma weight residual 112.23 108.24 3.99 1.26e+00 6.30e-01 1.00e+01 ... (remaining 12086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 4669 16.04 - 32.08: 386 32.08 - 48.12: 100 48.12 - 64.16: 16 64.16 - 80.20: 7 Dihedral angle restraints: 5178 sinusoidal: 1715 harmonic: 3463 Sorted by residual: dihedral pdb=" CB CYS D 34 " pdb=" SG CYS D 34 " pdb=" SG CYS D 55 " pdb=" CB CYS D 55 " ideal model delta sinusoidal sigma weight residual -86.00 -152.58 66.58 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 56.76 36.24 1 1.00e+01 1.00e-02 1.86e+01 dihedral pdb=" CA CYS A 144 " pdb=" C CYS A 144 " pdb=" N GLN A 145 " pdb=" CA GLN A 145 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1110 0.046 - 0.092: 252 0.092 - 0.138: 65 0.138 - 0.184: 0 0.184 - 0.229: 1 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA GLN A 305 " pdb=" N GLN A 305 " pdb=" C GLN A 305 " pdb=" CB GLN A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ARG A 200 " pdb=" N ARG A 200 " pdb=" C ARG A 200 " pdb=" CB ARG A 200 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA LEU A 311 " pdb=" N LEU A 311 " pdb=" C LEU A 311 " pdb=" CB LEU A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1425 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 89 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 90 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 102 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 103 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 183 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.70e+00 pdb=" N PRO A 184 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 184 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 184 " 0.023 5.00e-02 4.00e+02 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 741 2.74 - 3.28: 8793 3.28 - 3.82: 14339 3.82 - 4.36: 16174 4.36 - 4.90: 29086 Nonbonded interactions: 69133 Sorted by model distance: nonbonded pdb=" O THR A 229 " pdb=" OG1 THR A 235 " model vdw 2.205 3.040 nonbonded pdb=" OG SER B 161 " pdb=" O THR B 165 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU B 215 " pdb=" NH2 ARG B 219 " model vdw 2.227 3.120 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.237 3.040 nonbonded pdb=" O ARG H 67 " pdb=" OG1 THR H 84 " model vdw 2.241 3.040 ... (remaining 69128 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.520 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 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 : 0.002 0.033 8868 Z= 0.137 Angle : 0.538 6.555 12103 Z= 0.309 Chirality : 0.041 0.229 1428 Planarity : 0.004 0.051 1540 Dihedral : 13.165 80.205 2922 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.24 % Allowed : 0.72 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.38 (0.26), residues: 1178 helix: 1.56 (0.26), residues: 428 sheet: -1.33 (0.34), residues: 252 loop : -1.23 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 160 TYR 0.011 0.001 TYR H 190 PHE 0.014 0.001 PHE A 288 TRP 0.008 0.001 TRP B 211 HIS 0.001 0.000 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 ( 8862) covalent geometry : angle 0.53530 / 0.31 (12091) SS BOND : bond 0.00559 / 0.35 ( 6) SS BOND : angle 1.67211 / 1.06 ( 12) hydrogen bonds : bond 0.18311 / 12.66 ( 429) hydrogen bonds : angle 7.17202 / 5.06 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.197 Fit side-chains REVERT: B 17 GLN cc_start: 0.8154 (pt0) cc_final: 0.7733 (pt0) REVERT: B 78 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7242 (mmtt) REVERT: B 181 THR cc_start: 0.7783 (t) cc_final: 0.7575 (p) REVERT: B 284 LEU cc_start: 0.7478 (mt) cc_final: 0.7182 (tt) REVERT: B 323 ASP cc_start: 0.7694 (m-30) cc_final: 0.7462 (m-30) REVERT: C 297 TYR cc_start: 0.6714 (t80) cc_final: 0.6366 (t80) outliers start: 2 outliers final: 1 residues processed: 139 average time/residue: 0.0745 time to fit residues: 14.8001 Evaluate side-chains 114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 GLN C 330 ASN H 231 GLN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.196850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.158417 restraints weight = 10327.556| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.64 r_work: 0.3796 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8868 Z= 0.137 Angle : 0.538 6.314 12103 Z= 0.288 Chirality : 0.042 0.154 1428 Planarity : 0.004 0.049 1540 Dihedral : 4.242 39.653 1268 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.08 % Allowed : 8.17 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.45 (0.26), residues: 1178 helix: 1.49 (0.26), residues: 436 sheet: -1.61 (0.32), residues: 265 loop : -1.14 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.013 0.001 TYR H 190 PHE 0.015 0.001 PHE A 307 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8862) covalent geometry : angle 0.53487 / 0.29 (12091) SS BOND : bond 0.00570 / 0.36 ( 6) SS BOND : angle 1.91955 / 1.19 ( 12) hydrogen bonds : bond 0.03899 / 2.75 ( 429) hydrogen bonds : angle 5.20856 / 3.65 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.230 Fit side-chains REVERT: B 170 ASP cc_start: 0.8355 (t0) cc_final: 0.8125 (t0) REVERT: B 284 LEU cc_start: 0.7791 (mt) cc_final: 0.7194 (tt) REVERT: C 14 GLU cc_start: 0.8050 (tt0) cc_final: 0.7508 (tm-30) REVERT: C 297 TYR cc_start: 0.7041 (t80) cc_final: 0.6740 (t80) REVERT: A 228 ARG cc_start: 0.8023 (tpt-90) cc_final: 0.7688 (tpp80) outliers start: 9 outliers final: 8 residues processed: 129 average time/residue: 0.0713 time to fit residues: 13.2331 Evaluate side-chains 121 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 231 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 293 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 14 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 78 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 231 GLN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.196071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.157756 restraints weight = 10202.038| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.61 r_work: 0.3787 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8868 Z= 0.129 Angle : 0.518 5.767 12103 Z= 0.276 Chirality : 0.042 0.136 1428 Planarity : 0.004 0.048 1540 Dihedral : 4.034 28.030 1266 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.44 % Allowed : 12.98 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.43 (0.25), residues: 1178 helix: 1.53 (0.26), residues: 430 sheet: -1.50 (0.32), residues: 276 loop : -1.15 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 160 TYR 0.011 0.001 TYR H 190 PHE 0.010 0.001 PHE H 68 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8862) covalent geometry : angle 0.51425 / 0.27 (12091) SS BOND : bond 0.00557 / 0.36 ( 6) SS BOND : angle 1.97254 / 1.22 ( 12) hydrogen bonds : bond 0.03639 / 2.57 ( 429) hydrogen bonds : angle 4.90029 / 3.43 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.331 Fit side-chains REVERT: B 170 ASP cc_start: 0.8353 (t0) cc_final: 0.8098 (t0) REVERT: B 284 LEU cc_start: 0.7778 (mt) cc_final: 0.7176 (tt) REVERT: C 14 GLU cc_start: 0.8017 (tt0) cc_final: 0.7490 (tm-30) REVERT: C 297 TYR cc_start: 0.7081 (t80) cc_final: 0.6849 (t80) REVERT: A 228 ARG cc_start: 0.8017 (tpt-90) cc_final: 0.7682 (tpp80) outliers start: 12 outliers final: 10 residues processed: 129 average time/residue: 0.0868 time to fit residues: 16.1273 Evaluate side-chains 129 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 293 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 0.0470 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 GLN C 205 GLN H 231 GLN A 101 HIS A 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.193003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.155068 restraints weight = 10457.096| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.53 r_work: 0.3747 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8868 Z= 0.159 Angle : 0.549 9.077 12103 Z= 0.290 Chirality : 0.042 0.138 1428 Planarity : 0.004 0.048 1540 Dihedral : 4.198 26.779 1266 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.00 % Allowed : 14.30 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.54 (0.25), residues: 1178 helix: 1.47 (0.26), residues: 431 sheet: -1.68 (0.31), residues: 274 loop : -1.17 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 160 TYR 0.015 0.002 TYR H 190 PHE 0.014 0.002 PHE H 68 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 8862) covalent geometry : angle 0.54580 / 0.29 (12091) SS BOND : bond 0.00551 / 0.35 ( 6) SS BOND : angle 2.04703 / 1.26 ( 12) hydrogen bonds : bond 0.03613 / 2.55 ( 429) hydrogen bonds : angle 4.88827 / 3.42 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.390 Fit side-chains REVERT: B 170 ASP cc_start: 0.8409 (t0) cc_final: 0.8148 (t0) REVERT: B 234 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: A 228 ARG cc_start: 0.8031 (tpt-90) cc_final: 0.7706 (tpp80) outliers start: 25 outliers final: 16 residues processed: 133 average time/residue: 0.0757 time to fit residues: 14.4897 Evaluate side-chains 131 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 220 GLU Chi-restraints excluded: chain H residue 231 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.193384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155696 restraints weight = 10385.028| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.44 r_work: 0.3766 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8868 Z= 0.139 Angle : 0.532 9.558 12103 Z= 0.281 Chirality : 0.042 0.133 1428 Planarity : 0.004 0.048 1540 Dihedral : 4.141 28.459 1266 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.76 % Allowed : 17.07 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.53 (0.25), residues: 1178 helix: 1.51 (0.26), residues: 430 sheet: -1.70 (0.31), residues: 274 loop : -1.18 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 160 TYR 0.014 0.001 TYR H 190 PHE 0.010 0.001 PHE H 27 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8862) covalent geometry : angle 0.52875 / 0.28 (12091) SS BOND : bond 0.00550 / 0.35 ( 6) SS BOND : angle 2.00925 / 1.24 ( 12) hydrogen bonds : bond 0.03443 / 2.43 ( 429) hydrogen bonds : angle 4.76329 / 3.33 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.309 Fit side-chains REVERT: B 170 ASP cc_start: 0.8391 (t0) cc_final: 0.8131 (t0) REVERT: B 234 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: A 77 ASN cc_start: 0.7711 (m110) cc_final: 0.7462 (m110) REVERT: A 228 ARG cc_start: 0.8049 (tpt-90) cc_final: 0.7724 (tpp80) outliers start: 23 outliers final: 19 residues processed: 127 average time/residue: 0.0896 time to fit residues: 16.2980 Evaluate side-chains 132 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 220 GLU Chi-restraints excluded: chain H residue 231 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 293 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 0.0770 chunk 40 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.195600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.158289 restraints weight = 10294.748| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.40 r_work: 0.3782 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8868 Z= 0.111 Angle : 0.504 7.540 12103 Z= 0.266 Chirality : 0.041 0.131 1428 Planarity : 0.004 0.048 1540 Dihedral : 3.968 29.202 1266 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.28 % Allowed : 18.27 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.33 (0.26), residues: 1178 helix: 1.63 (0.26), residues: 430 sheet: -1.40 (0.31), residues: 279 loop : -1.15 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 160 TYR 0.012 0.001 TYR H 190 PHE 0.009 0.001 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8862) covalent geometry : angle 0.50002 / 0.26 (12091) SS BOND : bond 0.00548 / 0.35 ( 6) SS BOND : angle 2.01886 / 1.24 ( 12) hydrogen bonds : bond 0.03213 / 2.27 ( 429) hydrogen bonds : angle 4.56227 / 3.19 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.306 Fit side-chains REVERT: B 124 TYR cc_start: 0.5750 (m-80) cc_final: 0.5128 (m-80) REVERT: B 170 ASP cc_start: 0.8354 (t0) cc_final: 0.8120 (t0) REVERT: B 234 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: A 228 ARG cc_start: 0.8022 (tpt-90) cc_final: 0.7645 (tpp80) outliers start: 19 outliers final: 15 residues processed: 138 average time/residue: 0.0753 time to fit residues: 15.0301 Evaluate side-chains 133 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 231 GLN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 41 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.0616 > 50:) chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 196 HIS ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.193542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.156008 restraints weight = 10419.813| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.72 r_work: 0.3745 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8868 Z= 0.139 Angle : 0.530 6.254 12103 Z= 0.280 Chirality : 0.042 0.137 1428 Planarity : 0.004 0.048 1540 Dihedral : 4.039 27.823 1266 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.37 % Allowed : 17.91 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.38 (0.26), residues: 1178 helix: 1.62 (0.26), residues: 430 sheet: -1.56 (0.32), residues: 273 loop : -1.12 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.017 0.001 TYR B 85 PHE 0.011 0.001 PHE B 241 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8862) covalent geometry : angle 0.52606 / 0.28 (12091) SS BOND : bond 0.00553 / 0.35 ( 6) SS BOND : angle 2.04580 / 1.26 ( 12) hydrogen bonds : bond 0.03317 / 2.35 ( 429) hydrogen bonds : angle 4.61336 / 3.23 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.303 Fit side-chains REVERT: B 170 ASP cc_start: 0.8367 (t0) cc_final: 0.8113 (t0) REVERT: B 234 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: A 228 ARG cc_start: 0.8021 (tpt-90) cc_final: 0.7629 (tpp80) outliers start: 28 outliers final: 23 residues processed: 134 average time/residue: 0.0822 time to fit residues: 16.0416 Evaluate side-chains 135 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 220 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 102 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 142 GLN H 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.195789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157916 restraints weight = 10181.237| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.47 r_work: 0.3784 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8868 Z= 0.111 Angle : 0.518 6.129 12103 Z= 0.272 Chirality : 0.041 0.142 1428 Planarity : 0.004 0.047 1540 Dihedral : 3.945 27.959 1266 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.49 % Allowed : 17.91 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.25 (0.26), residues: 1178 helix: 1.69 (0.26), residues: 430 sheet: -1.37 (0.31), residues: 289 loop : -1.08 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.029 0.001 TYR B 85 PHE 0.009 0.001 PHE H 68 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8862) covalent geometry : angle 0.51445 / 0.27 (12091) SS BOND : bond 0.00557 / 0.36 ( 6) SS BOND : angle 2.02004 / 1.25 ( 12) hydrogen bonds : bond 0.03161 / 2.24 ( 429) hydrogen bonds : angle 4.47530 / 3.13 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.190 Fit side-chains REVERT: B 124 TYR cc_start: 0.5687 (m-80) cc_final: 0.5062 (m-80) REVERT: B 163 ASP cc_start: 0.7361 (p0) cc_final: 0.7120 (p0) REVERT: B 170 ASP cc_start: 0.8324 (t0) cc_final: 0.8080 (t0) REVERT: B 219 ARG cc_start: 0.8002 (mpt180) cc_final: 0.6645 (ttm-80) REVERT: B 234 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: A 228 ARG cc_start: 0.7972 (tpt-90) cc_final: 0.7597 (tpp80) outliers start: 29 outliers final: 23 residues processed: 140 average time/residue: 0.0833 time to fit residues: 16.6316 Evaluate side-chains 140 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 220 GLU Chi-restraints excluded: chain H residue 231 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN H 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.194119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.156303 restraints weight = 10291.216| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.55 r_work: 0.3767 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8868 Z= 0.137 Angle : 0.541 8.242 12103 Z= 0.284 Chirality : 0.042 0.195 1428 Planarity : 0.004 0.047 1540 Dihedral : 4.020 26.535 1266 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.37 % Allowed : 18.63 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.33 (0.26), residues: 1178 helix: 1.66 (0.26), residues: 430 sheet: -1.53 (0.31), residues: 277 loop : -1.08 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.029 0.001 TYR B 85 PHE 0.010 0.001 PHE H 27 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8862) covalent geometry : angle 0.53714 / 0.28 (12091) SS BOND : bond 0.00558 / 0.36 ( 6) SS BOND : angle 2.04197 / 1.26 ( 12) hydrogen bonds : bond 0.03320 / 2.34 ( 429) hydrogen bonds : angle 4.57189 / 3.20 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.312 Fit side-chains REVERT: B 124 TYR cc_start: 0.5800 (m-80) cc_final: 0.5092 (m-80) REVERT: B 170 ASP cc_start: 0.8344 (t0) cc_final: 0.8107 (t0) REVERT: B 219 ARG cc_start: 0.8036 (mpt180) cc_final: 0.6688 (ttm-80) REVERT: B 234 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8393 (m-80) outliers start: 28 outliers final: 26 residues processed: 135 average time/residue: 0.0833 time to fit residues: 16.1542 Evaluate side-chains 139 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 220 GLU Chi-restraints excluded: chain H residue 231 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 0.1980 chunk 97 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 113 optimal weight: 0.0010 overall best weight: 0.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.197770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.160049 restraints weight = 10279.406| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.55 r_work: 0.3822 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8868 Z= 0.101 Angle : 0.515 7.623 12103 Z= 0.270 Chirality : 0.041 0.169 1428 Planarity : 0.004 0.047 1540 Dihedral : 3.848 27.078 1266 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.88 % Allowed : 19.23 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.18 (0.26), residues: 1178 helix: 1.78 (0.26), residues: 430 sheet: -1.36 (0.31), residues: 285 loop : -1.06 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.023 0.001 TYR B 85 PHE 0.008 0.001 PHE H 68 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 8862) covalent geometry : angle 0.51099 / 0.27 (12091) SS BOND : bond 0.00565 / 0.36 ( 6) SS BOND : angle 2.01023 / 1.25 ( 12) hydrogen bonds : bond 0.03043 / 2.15 ( 429) hydrogen bonds : angle 4.36027 / 3.05 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.315 Fit side-chains REVERT: B 124 TYR cc_start: 0.5647 (m-80) cc_final: 0.5066 (m-80) REVERT: B 170 ASP cc_start: 0.8272 (t0) cc_final: 0.8039 (t0) REVERT: B 219 ARG cc_start: 0.7985 (mpt180) cc_final: 0.6827 (ttm-80) REVERT: B 234 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: B 284 LEU cc_start: 0.8070 (mt) cc_final: 0.7356 (tt) REVERT: A 228 ARG cc_start: 0.7961 (tpt-90) cc_final: 0.7623 (tpp80) outliers start: 24 outliers final: 22 residues processed: 131 average time/residue: 0.0860 time to fit residues: 16.0099 Evaluate side-chains 138 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 220 GLU Chi-restraints excluded: chain H residue 231 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 0.0980 chunk 106 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.195113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.156849 restraints weight = 10340.557| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.58 r_work: 0.3781 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8868 Z= 0.127 Angle : 0.536 10.061 12103 Z= 0.281 Chirality : 0.042 0.224 1428 Planarity : 0.004 0.047 1540 Dihedral : 3.916 25.183 1266 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.25 % Allowed : 19.59 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.26), residues: 1178 helix: 1.76 (0.26), residues: 430 sheet: -1.34 (0.31), residues: 285 loop : -1.08 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.025 0.001 TYR B 85 PHE 0.017 0.001 PHE H 68 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS H 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8862) covalent geometry : angle 0.53224 / 0.28 (12091) SS BOND : bond 0.00566 / 0.36 ( 6) SS BOND : angle 2.02916 / 1.25 ( 12) hydrogen bonds : bond 0.03214 / 2.26 ( 429) hydrogen bonds : angle 4.43701 / 3.10 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.18 seconds wall clock time: 33 minutes 33.39 seconds (2013.39 seconds total)