Starting phenix.real_space_refine on Tue Apr 29 12:57:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzz_36755/04_2025/8jzz_36755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzz_36755/04_2025/8jzz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzz_36755/04_2025/8jzz_36755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzz_36755/04_2025/8jzz_36755.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzz_36755/04_2025/8jzz_36755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzz_36755/04_2025/8jzz_36755.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 11} 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: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG: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, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 8} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 6.21, per 1000 atoms: 0.72 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: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.95 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: 2.53 Time building geometry restraints manager: 2.82 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: 3.060 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.710 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 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 : 9.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (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 TRP 0.008 0.001 TRP B 211 HIS 0.001 0.000 HIS B 91 PHE 0.014 0.001 PHE A 288 TYR 0.011 0.001 TYR H 190 ARG 0.002 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.18311 ( 429) hydrogen bonds : angle 7.17202 ( 1224) SS BOND : bond 0.00559 ( 6) SS BOND : angle 1.67211 ( 12) covalent geometry : bond 0.00238 ( 8862) covalent geometry : angle 0.53530 (12091) *********************** 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 : 0.868 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: 0.2019 time to fit residues: 39.1040 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 : 0.929 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 ASN H 231 GLN ** A 101 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 = 0.4324 r_free = 0.4324 target = 0.193873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.155429 restraints weight = 10236.051| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.60 r_work: 0.3762 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8868 Z= 0.172 Angle : 0.569 5.931 12103 Z= 0.305 Chirality : 0.043 0.158 1428 Planarity : 0.004 0.049 1540 Dihedral : 4.436 40.469 1268 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.44 % Allowed : 9.01 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1178 helix: 1.40 (0.26), residues: 436 sheet: -1.70 (0.32), residues: 265 loop : -1.20 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.016 0.002 PHE A 307 TYR 0.015 0.002 TYR H 190 ARG 0.004 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 429) hydrogen bonds : angle 5.33226 ( 1224) SS BOND : bond 0.00563 ( 6) SS BOND : angle 1.94625 ( 12) covalent geometry : bond 0.00393 ( 8862) covalent geometry : angle 0.56638 (12091) *********************** 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 137 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.889 Fit side-chains REVERT: B 153 ASP cc_start: 0.8122 (p0) cc_final: 0.7908 (p0) REVERT: B 170 ASP cc_start: 0.8362 (t0) cc_final: 0.8122 (t0) REVERT: B 219 ARG cc_start: 0.7879 (mmt-90) cc_final: 0.6754 (ttm-80) REVERT: B 284 LEU cc_start: 0.7837 (mt) cc_final: 0.7154 (tt) REVERT: C 14 GLU cc_start: 0.8098 (tt0) cc_final: 0.7489 (tm-30) REVERT: C 297 TYR cc_start: 0.7064 (t80) cc_final: 0.6693 (t80) REVERT: A 228 ARG cc_start: 0.8059 (tpt-90) cc_final: 0.7700 (tpp80) REVERT: D 70 MET cc_start: 0.7638 (tpp) cc_final: 0.7350 (tpp) outliers start: 12 outliers final: 10 residues processed: 131 average time/residue: 0.1999 time to fit residues: 36.6481 Evaluate side-chains 127 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain H residue 31 SER 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 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4330 r_free = 0.4330 target = 0.194374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155905 restraints weight = 10440.854| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.61 r_work: 0.3768 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1445 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= 0.138 Angle : 0.535 8.388 12103 Z= 0.283 Chirality : 0.042 0.137 1428 Planarity : 0.004 0.048 1540 Dihedral : 4.150 28.731 1266 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.56 % Allowed : 14.18 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1178 helix: 1.42 (0.26), residues: 431 sheet: -1.67 (0.32), residues: 268 loop : -1.19 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE B 241 TYR 0.012 0.001 TYR H 190 ARG 0.004 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 429) hydrogen bonds : angle 4.98759 ( 1224) SS BOND : bond 0.00559 ( 6) SS BOND : angle 1.98163 ( 12) covalent geometry : bond 0.00311 ( 8862) covalent geometry : angle 0.53174 (12091) *********************** 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 138 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.923 Fit side-chains REVERT: B 153 ASP cc_start: 0.8052 (p0) cc_final: 0.7833 (p0) REVERT: B 170 ASP cc_start: 0.8390 (t0) cc_final: 0.8111 (t0) REVERT: B 219 ARG cc_start: 0.7894 (mmt-90) cc_final: 0.6730 (ttm-80) REVERT: B 234 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: B 284 LEU cc_start: 0.7796 (mt) cc_final: 0.7150 (tt) REVERT: C 14 GLU cc_start: 0.8115 (tt0) cc_final: 0.7528 (tm-30) REVERT: C 297 TYR cc_start: 0.7065 (t80) cc_final: 0.6779 (t80) REVERT: A 228 ARG cc_start: 0.8047 (tpt-90) cc_final: 0.7696 (tpp80) REVERT: D 70 MET cc_start: 0.7683 (tpp) cc_final: 0.7253 (tpp) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 0.1974 time to fit residues: 36.6927 Evaluate side-chains 128 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 219 VAL Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 158 SER 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 293 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 72 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 GLN H 142 GLN 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 = 0.4324 r_free = 0.4324 target = 0.193492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.155965 restraints weight = 10330.610| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.42 r_work: 0.3755 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1611 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= 0.144 Angle : 0.533 8.949 12103 Z= 0.282 Chirality : 0.042 0.134 1428 Planarity : 0.004 0.047 1540 Dihedral : 4.151 28.865 1266 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.12 % Allowed : 15.02 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1178 helix: 1.45 (0.26), residues: 431 sheet: -1.69 (0.31), residues: 274 loop : -1.20 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE H 27 TYR 0.013 0.001 TYR H 190 ARG 0.005 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 429) hydrogen bonds : angle 4.87597 ( 1224) SS BOND : bond 0.00559 ( 6) SS BOND : angle 2.00889 ( 12) covalent geometry : bond 0.00327 ( 8862) covalent geometry : angle 0.52994 (12091) *********************** 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: 26 poor density : 117 time to evaluate : 0.967 Fit side-chains REVERT: B 153 ASP cc_start: 0.8067 (p0) cc_final: 0.7852 (p0) REVERT: B 170 ASP cc_start: 0.8399 (t0) cc_final: 0.8137 (t0) REVERT: B 234 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: C 14 GLU cc_start: 0.7981 (tt0) cc_final: 0.7388 (tm-30) REVERT: A 228 ARG cc_start: 0.8041 (tpt-90) cc_final: 0.7694 (tpp80) REVERT: D 70 MET cc_start: 0.7724 (tpp) cc_final: 0.7509 (tpp) outliers start: 26 outliers final: 16 residues processed: 134 average time/residue: 0.1986 time to fit residues: 37.1794 Evaluate side-chains 130 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 331 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 168 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 HIS ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN H 231 GLN A 101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.191659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.153966 restraints weight = 10306.106| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.42 r_work: 0.3746 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1775 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= 0.169 Angle : 0.553 6.716 12103 Z= 0.294 Chirality : 0.042 0.136 1428 Planarity : 0.004 0.047 1540 Dihedral : 4.284 28.726 1266 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.49 % Allowed : 16.83 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1178 helix: 1.40 (0.26), residues: 430 sheet: -1.72 (0.32), residues: 267 loop : -1.32 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.003 0.001 HIS B 183 PHE 0.013 0.001 PHE H 27 TYR 0.015 0.002 TYR H 190 ARG 0.005 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 429) hydrogen bonds : angle 4.92840 ( 1224) SS BOND : bond 0.00555 ( 6) SS BOND : angle 2.03823 ( 12) covalent geometry : bond 0.00390 ( 8862) covalent geometry : angle 0.54943 (12091) *********************** 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 144 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.921 Fit side-chains REVERT: B 170 ASP cc_start: 0.8418 (t0) cc_final: 0.8165 (t0) REVERT: B 234 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8307 (m-80) outliers start: 29 outliers final: 20 residues processed: 134 average time/residue: 0.1884 time to fit residues: 36.0143 Evaluate side-chains 133 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 SER 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 168 SER 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 261 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4315 r_free = 0.4315 target = 0.192635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154659 restraints weight = 10277.978| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.55 r_work: 0.3755 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.1836 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= 0.144 Angle : 0.543 10.441 12103 Z= 0.286 Chirality : 0.042 0.139 1428 Planarity : 0.004 0.047 1540 Dihedral : 4.223 30.285 1266 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.73 % Allowed : 17.07 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1178 helix: 1.46 (0.26), residues: 430 sheet: -1.68 (0.32), residues: 267 loop : -1.31 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.011 0.001 PHE H 27 TYR 0.013 0.001 TYR H 190 ARG 0.006 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 429) hydrogen bonds : angle 4.85006 ( 1224) SS BOND : bond 0.00570 ( 6) SS BOND : angle 2.07101 ( 12) covalent geometry : bond 0.00330 ( 8862) covalent geometry : angle 0.53887 (12091) *********************** 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: 31 poor density : 113 time to evaluate : 1.011 Fit side-chains REVERT: B 170 ASP cc_start: 0.8380 (t0) cc_final: 0.8118 (t0) REVERT: B 234 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8343 (m-80) outliers start: 31 outliers final: 24 residues processed: 133 average time/residue: 0.2090 time to fit residues: 39.6930 Evaluate side-chains 136 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 3 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 11 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4333 r_free = 0.4333 target = 0.194410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.156858 restraints weight = 10372.154| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.71 r_work: 0.3767 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1848 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= 0.118 Angle : 0.524 8.795 12103 Z= 0.275 Chirality : 0.041 0.134 1428 Planarity : 0.004 0.048 1540 Dihedral : 4.085 30.654 1266 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.25 % Allowed : 17.91 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1178 helix: 1.55 (0.26), residues: 430 sheet: -1.52 (0.32), residues: 265 loop : -1.22 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS H 232 PHE 0.009 0.001 PHE B 151 TYR 0.016 0.001 TYR B 85 ARG 0.007 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 429) hydrogen bonds : angle 4.69415 ( 1224) SS BOND : bond 0.00574 ( 6) SS BOND : angle 2.05912 ( 12) covalent geometry : bond 0.00263 ( 8862) covalent geometry : angle 0.52071 (12091) *********************** 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 146 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.883 Fit side-chains REVERT: B 170 ASP cc_start: 0.8368 (t0) cc_final: 0.8108 (t0) REVERT: B 234 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: A 228 ARG cc_start: 0.7963 (tpt-90) cc_final: 0.7644 (tpp80) outliers start: 27 outliers final: 20 residues processed: 137 average time/residue: 0.1981 time to fit residues: 38.1707 Evaluate side-chains 137 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 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 133 ASP 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 104 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 0.0070 chunk 84 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4325 r_free = 0.4325 target = 0.193860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155997 restraints weight = 10386.527| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.51 r_work: 0.3781 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1904 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= 0.130 Angle : 0.530 5.940 12103 Z= 0.281 Chirality : 0.042 0.143 1428 Planarity : 0.004 0.048 1540 Dihedral : 4.097 29.927 1266 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.49 % Allowed : 18.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1178 helix: 1.57 (0.26), residues: 430 sheet: -1.56 (0.32), residues: 275 loop : -1.16 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS A 101 PHE 0.010 0.001 PHE B 151 TYR 0.013 0.001 TYR H 190 ARG 0.007 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 429) hydrogen bonds : angle 4.67274 ( 1224) SS BOND : bond 0.00575 ( 6) SS BOND : angle 2.06773 ( 12) covalent geometry : bond 0.00294 ( 8862) covalent geometry : angle 0.52608 (12091) *********************** 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 141 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.864 Fit side-chains REVERT: B 170 ASP cc_start: 0.8330 (t0) cc_final: 0.8057 (t0) REVERT: B 234 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8375 (m-80) outliers start: 29 outliers final: 23 residues processed: 134 average time/residue: 0.2227 time to fit residues: 41.9143 Evaluate side-chains 133 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 315 VAL 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 279 ILE 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 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 294 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4332 r_free = 0.4332 target = 0.194735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.156333 restraints weight = 10406.559| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.60 r_work: 0.3782 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.1949 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= 0.122 Angle : 0.532 8.463 12103 Z= 0.280 Chirality : 0.041 0.196 1428 Planarity : 0.004 0.048 1540 Dihedral : 4.054 29.505 1266 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.73 % Allowed : 18.63 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1178 helix: 1.60 (0.26), residues: 430 sheet: -1.49 (0.32), residues: 275 loop : -1.16 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS A 101 PHE 0.011 0.001 PHE H 68 TYR 0.012 0.001 TYR H 190 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 429) hydrogen bonds : angle 4.62802 ( 1224) SS BOND : bond 0.00575 ( 6) SS BOND : angle 2.06022 ( 12) covalent geometry : bond 0.00274 ( 8862) covalent geometry : angle 0.52811 (12091) *********************** 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 144 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.919 Fit side-chains REVERT: B 170 ASP cc_start: 0.8326 (t0) cc_final: 0.8069 (t0) REVERT: B 234 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8345 (m-80) outliers start: 31 outliers final: 27 residues processed: 135 average time/residue: 0.2008 time to fit residues: 38.5325 Evaluate side-chains 139 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL 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 279 ILE 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 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 58 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4316 r_free = 0.4316 target = 0.192666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.154633 restraints weight = 10439.894| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.54 r_work: 0.3761 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8868 Z= 0.155 Angle : 0.565 8.474 12103 Z= 0.296 Chirality : 0.042 0.186 1428 Planarity : 0.004 0.048 1540 Dihedral : 4.180 28.764 1266 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.85 % Allowed : 18.63 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1178 helix: 1.55 (0.26), residues: 430 sheet: -1.52 (0.32), residues: 272 loop : -1.20 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.001 PHE H 68 TYR 0.014 0.002 TYR H 59 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 429) hydrogen bonds : angle 4.72646 ( 1224) SS BOND : bond 0.00570 ( 6) SS BOND : angle 2.10300 ( 12) covalent geometry : bond 0.00358 ( 8862) covalent geometry : angle 0.56158 (12091) ********************** 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 148 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.778 Fit side-chains REVERT: B 170 ASP cc_start: 0.8368 (t0) cc_final: 0.8128 (t0) REVERT: B 234 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8365 (m-80) outliers start: 32 outliers final: 26 residues processed: 140 average time/residue: 0.1944 time to fit residues: 38.6614 Evaluate side-chains 141 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL 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 144 CYS 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 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 59 optimal weight: 0.0770 chunk 31 optimal weight: 0.0670 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.198456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.160296 restraints weight = 10335.485| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.60 r_work: 0.3814 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8868 Z= 0.101 Angle : 0.523 8.316 12103 Z= 0.273 Chirality : 0.041 0.202 1428 Planarity : 0.003 0.047 1540 Dihedral : 3.904 30.271 1266 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.16 % Allowed : 20.19 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1178 helix: 1.77 (0.26), residues: 429 sheet: -1.18 (0.33), residues: 273 loop : -1.21 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS H 35 PHE 0.009 0.001 PHE H 68 TYR 0.014 0.001 TYR H 103 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03079 ( 429) hydrogen bonds : angle 4.43152 ( 1224) SS BOND : bond 0.00566 ( 6) SS BOND : angle 2.02479 ( 12) covalent geometry : bond 0.00215 ( 8862) covalent geometry : angle 0.51906 (12091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4416.32 seconds wall clock time: 77 minutes 53.36 seconds (4673.36 seconds total)