Starting phenix.real_space_refine on Sat Dec 28 12:42:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xow_33361/12_2024/7xow_33361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xow_33361/12_2024/7xow_33361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xow_33361/12_2024/7xow_33361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xow_33361/12_2024/7xow_33361.map" model { file = "/net/cci-nas-00/data/ceres_data/7xow_33361/12_2024/7xow_33361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xow_33361/12_2024/7xow_33361.cif" } resolution = 3.1 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= 0.007 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 58 5.16 5 C 5479 2.51 5 N 1468 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8566 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2153 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2471 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1716 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1798 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 75 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.25, per 1000 atoms: 0.61 Number of scatterers: 8566 At special positions: 0 Unit cell: (112.554, 115.596, 124.722, 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 58 16.00 O 1561 8.00 N 1468 7.00 C 5479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 36.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'R' and resid 54 through 81 Processing helix chain 'R' and resid 87 through 108 removed outlier: 4.032A pdb=" N ALA R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 118 Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 122 through 158 removed outlier: 4.142A pdb=" N ILE R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG R 158 " --> pdb=" O SER R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 166 removed outlier: 4.291A pdb=" N VAL R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP R 165 " --> pdb=" O GLN R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 186 removed outlier: 3.711A pdb=" N ARG R 173 " --> pdb=" O SER R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 192 Processing helix chain 'R' and resid 214 through 228 Processing helix chain 'R' and resid 228 through 248 removed outlier: 3.832A pdb=" N GLY R 248 " --> pdb=" O GLU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 360 removed outlier: 4.413A pdb=" N VAL R 331 " --> pdb=" O ALA R 327 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 360 through 367 removed outlier: 3.876A pdb=" N HIS R 364 " --> pdb=" O GLY R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 370 through 391 removed outlier: 3.569A pdb=" N PHE R 374 " --> pdb=" O ALA R 370 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER R 382 " --> pdb=" O LEU R 378 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS R 384 " --> pdb=" O TYR R 380 " (cutoff:3.500A) Proline residue: R 387 - end of helix Processing helix chain 'R' and resid 396 through 403 removed outlier: 3.787A pdb=" N ALA R 400 " --> pdb=" O ARG R 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.501A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.856A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.911A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.738A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.826A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.627A pdb=" N THR A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 281 through 286 removed outlier: 4.036A pdb=" N TYR A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.710A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.813A 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: 6.888A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.704A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.974A 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 153 removed outlier: 3.583A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.534A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.737A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.916A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.557A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 134 through 136 Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AB3, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.689A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 183 through 189 removed outlier: 7.147A pdb=" N LEU A 34 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL A 198 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 36 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 200 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 38 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 35 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N MET A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 37 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 223 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 183 through 189 removed outlier: 7.147A pdb=" N LEU A 34 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL A 198 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 36 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 200 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 38 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 35 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N MET A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 37 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 223 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1188 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: 2.63 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1467 1.32 - 1.45: 2344 1.45 - 1.57: 4849 1.57 - 1.69: 1 1.69 - 1.82: 85 Bond restraints: 8746 Sorted by residual: bond pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " ideal model delta sigma weight residual 1.462 1.632 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" OH TYS L 12 " pdb=" S TYS L 12 " ideal model delta sigma weight residual 1.679 1.538 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C TYR R 189 " pdb=" O TYR R 189 " ideal model delta sigma weight residual 1.244 1.202 0.042 1.00e-02 1.00e+04 1.73e+01 bond pdb=" N LEU R 203 " pdb=" CA LEU R 203 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.64e+00 bond pdb=" N VAL A 283 " pdb=" CA VAL A 283 " ideal model delta sigma weight residual 1.458 1.482 -0.025 1.41e-02 5.03e+03 3.06e+00 ... (remaining 8741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.93: 11867 5.93 - 11.86: 10 11.86 - 17.79: 2 17.79 - 23.72: 1 23.72 - 29.64: 2 Bond angle restraints: 11882 Sorted by residual: angle pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " pdb=" O2 TYS L 12 " ideal model delta sigma weight residual 114.11 84.47 29.64 3.00e+00 1.11e-01 9.76e+01 angle pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " pdb=" O3 TYS L 12 " ideal model delta sigma weight residual 115.16 88.07 27.09 3.00e+00 1.11e-01 8.16e+01 angle pdb=" N VAL R 202 " pdb=" CA VAL R 202 " pdb=" C VAL R 202 " ideal model delta sigma weight residual 110.62 118.97 -8.35 1.02e+00 9.61e-01 6.71e+01 angle pdb=" N GLN R 204 " pdb=" CA GLN R 204 " pdb=" C GLN R 204 " ideal model delta sigma weight residual 111.17 121.67 -10.50 1.41e+00 5.03e-01 5.54e+01 angle pdb=" OH TYS L 12 " pdb=" S TYS L 12 " pdb=" O3 TYS L 12 " ideal model delta sigma weight residual 100.21 118.72 -18.51 3.00e+00 1.11e-01 3.81e+01 ... (remaining 11877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4694 17.60 - 35.19: 391 35.19 - 52.79: 60 52.79 - 70.39: 10 70.39 - 87.98: 4 Dihedral angle restraints: 5159 sinusoidal: 1913 harmonic: 3246 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 137.28 42.72 0 5.00e+00 4.00e-02 7.30e+01 dihedral pdb=" C VAL R 202 " pdb=" N VAL R 202 " pdb=" CA VAL R 202 " pdb=" CB VAL R 202 " ideal model delta harmonic sigma weight residual -122.00 -131.80 9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" CA LEU A 265 " pdb=" C LEU A 265 " pdb=" N PHE A 266 " pdb=" CA PHE A 266 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1186 0.067 - 0.134: 168 0.134 - 0.201: 10 0.201 - 0.269: 6 0.269 - 0.336: 4 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA PHE L 17 " pdb=" N PHE L 17 " pdb=" C PHE L 17 " pdb=" CB PHE L 17 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA GLN R 204 " pdb=" N GLN R 204 " pdb=" C GLN R 204 " pdb=" CB GLN R 204 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA VAL R 202 " pdb=" N VAL R 202 " pdb=" C VAL R 202 " pdb=" CB VAL R 202 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 1371 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 189 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO R 190 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO R 190 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 190 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 223 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO E 224 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 224 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 224 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 187 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO R 188 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO R 188 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 188 " -0.047 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 738 2.74 - 3.28: 8406 3.28 - 3.82: 13468 3.82 - 4.36: 16062 4.36 - 4.90: 29053 Nonbonded interactions: 67727 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP B 228 " pdb=" NZ LYS A 209 " model vdw 2.244 3.120 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASP B 254 " pdb=" N ALA B 257 " model vdw 2.268 3.120 nonbonded pdb=" N CYS A 324 " pdb=" OD2 ASP A 327 " model vdw 2.269 3.120 ... (remaining 67722 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: 0.310 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.840 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 8746 Z= 0.283 Angle : 0.857 29.645 11882 Z= 0.455 Chirality : 0.052 0.336 1374 Planarity : 0.006 0.105 1495 Dihedral : 13.161 87.985 3059 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.23), residues: 1097 helix: -0.41 (0.26), residues: 364 sheet: -1.79 (0.29), residues: 289 loop : -3.05 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 111 HIS 0.003 0.001 HIS B 54 PHE 0.022 0.002 PHE B 234 TYR 0.013 0.001 TYR R 192 ARG 0.004 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.928 Fit side-chains REVERT: R 73 MET cc_start: 0.7231 (mmt) cc_final: 0.6878 (mmt) REVERT: R 207 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.5572 (m-70) REVERT: R 213 ARG cc_start: 0.6193 (mmt180) cc_final: 0.3788 (ptt-90) REVERT: R 333 ARG cc_start: 0.6314 (ttm170) cc_final: 0.5644 (ttm-80) REVERT: R 398 ARG cc_start: 0.7054 (mmt90) cc_final: 0.6744 (mmp80) REVERT: B 67 SER cc_start: 0.8803 (m) cc_final: 0.8404 (t) REVERT: B 325 MET cc_start: 0.7886 (tpp) cc_final: 0.7674 (tpp) REVERT: E 182 ASN cc_start: 0.8736 (m110) cc_final: 0.8462 (m110) REVERT: A 242 MET cc_start: 0.7403 (tpp) cc_final: 0.6316 (tpp) REVERT: A 305 LYS cc_start: 0.7059 (ttpp) cc_final: 0.6810 (tppt) REVERT: A 339 LYS cc_start: 0.7160 (tttt) cc_final: 0.6951 (tttp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2629 time to fit residues: 58.2125 Evaluate side-chains 136 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 98 optimal weight: 0.0870 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 166 GLN R 196 GLN R 204 GLN B 17 GLN B 35 ASN B 176 GLN B 220 GLN C 44 HIS E 159 ASN E 167 GLN E 171 GLN A 231 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8746 Z= 0.149 Angle : 0.580 8.341 11882 Z= 0.296 Chirality : 0.043 0.152 1374 Planarity : 0.005 0.079 1495 Dihedral : 4.659 37.775 1219 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 1.79 % Allowed : 9.63 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1097 helix: 1.01 (0.28), residues: 366 sheet: -1.33 (0.30), residues: 289 loop : -2.45 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 49 TYR 0.023 0.001 TYR R 380 ARG 0.003 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.010 Fit side-chains REVERT: R 207 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.4967 (m-70) REVERT: R 213 ARG cc_start: 0.5969 (mmt180) cc_final: 0.3678 (ptt-90) REVERT: R 333 ARG cc_start: 0.6306 (ttm170) cc_final: 0.5622 (ttm-80) REVERT: R 380 TYR cc_start: 0.7485 (m-80) cc_final: 0.7168 (m-80) REVERT: R 398 ARG cc_start: 0.6980 (mmt90) cc_final: 0.6780 (mmp80) REVERT: B 258 ASP cc_start: 0.8346 (t0) cc_final: 0.7639 (t0) REVERT: B 325 MET cc_start: 0.7929 (tpp) cc_final: 0.7418 (tpp) REVERT: A 242 MET cc_start: 0.7451 (tpp) cc_final: 0.6589 (tpp) REVERT: A 305 LYS cc_start: 0.6937 (ttpp) cc_final: 0.6713 (tppt) REVERT: A 339 LYS cc_start: 0.7109 (tttt) cc_final: 0.6872 (tttp) outliers start: 16 outliers final: 8 residues processed: 162 average time/residue: 0.2277 time to fit residues: 50.5615 Evaluate side-chains 142 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 40.0000 chunk 99 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN R 204 GLN B 220 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8746 Z= 0.233 Angle : 0.618 8.713 11882 Z= 0.313 Chirality : 0.044 0.183 1374 Planarity : 0.004 0.085 1495 Dihedral : 4.735 39.524 1219 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 2.91 % Allowed : 12.54 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.26), residues: 1097 helix: 1.33 (0.28), residues: 367 sheet: -1.09 (0.30), residues: 297 loop : -2.24 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE E 27 TYR 0.017 0.001 TYR A 285 ARG 0.004 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.969 Fit side-chains REVERT: R 184 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7428 (mp) REVERT: R 196 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6387 (mp10) REVERT: R 213 ARG cc_start: 0.6400 (mmt180) cc_final: 0.3941 (ptt-90) REVERT: R 244 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5938 (mm-30) REVERT: R 333 ARG cc_start: 0.6431 (ttm170) cc_final: 0.5706 (ttm-80) REVERT: R 380 TYR cc_start: 0.7590 (m-80) cc_final: 0.7245 (m-80) REVERT: R 398 ARG cc_start: 0.6997 (mmt90) cc_final: 0.6735 (mmp80) REVERT: B 101 MET cc_start: 0.8510 (mtp) cc_final: 0.8303 (mtp) REVERT: B 137 ARG cc_start: 0.7922 (mmm160) cc_final: 0.7502 (tpp-160) REVERT: B 258 ASP cc_start: 0.8500 (t0) cc_final: 0.7844 (t0) REVERT: B 325 MET cc_start: 0.7965 (tpp) cc_final: 0.7482 (tpp) REVERT: E 30 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8190 (t) REVERT: E 146 SER cc_start: 0.8409 (t) cc_final: 0.8087 (p) REVERT: E 177 ILE cc_start: 0.8508 (pt) cc_final: 0.8272 (pt) REVERT: A 339 LYS cc_start: 0.7114 (tttt) cc_final: 0.6914 (tttp) REVERT: L 15 MET cc_start: 0.6576 (ptp) cc_final: 0.6123 (mtp) outliers start: 26 outliers final: 14 residues processed: 146 average time/residue: 0.2117 time to fit residues: 42.5672 Evaluate side-chains 148 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN A 321 HIS A 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8746 Z= 0.185 Angle : 0.587 8.732 11882 Z= 0.297 Chirality : 0.043 0.189 1374 Planarity : 0.004 0.079 1495 Dihedral : 4.536 38.004 1217 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.80 % Allowed : 14.11 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.73 (0.26), residues: 1097 helix: 1.71 (0.28), residues: 360 sheet: -0.95 (0.30), residues: 285 loop : -2.02 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE E 27 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.876 Fit side-chains REVERT: R 184 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7386 (mp) REVERT: R 196 GLN cc_start: 0.6336 (mp10) cc_final: 0.5950 (mp10) REVERT: R 204 GLN cc_start: 0.6409 (mt0) cc_final: 0.5605 (pt0) REVERT: R 213 ARG cc_start: 0.6321 (mmt180) cc_final: 0.3973 (ptt-90) REVERT: R 333 ARG cc_start: 0.6438 (ttm170) cc_final: 0.5710 (ttm-80) REVERT: R 380 TYR cc_start: 0.7656 (m-80) cc_final: 0.7424 (m-80) REVERT: B 137 ARG cc_start: 0.7916 (mmm160) cc_final: 0.7506 (tpp-160) REVERT: B 220 GLN cc_start: 0.7615 (mt0) cc_final: 0.7353 (mt0) REVERT: B 258 ASP cc_start: 0.8468 (t0) cc_final: 0.8122 (t0) REVERT: B 259 GLN cc_start: 0.7804 (pt0) cc_final: 0.7557 (pt0) REVERT: B 325 MET cc_start: 0.8023 (tpp) cc_final: 0.7549 (tpp) REVERT: E 116 THR cc_start: 0.6837 (OUTLIER) cc_final: 0.6542 (t) REVERT: E 146 SER cc_start: 0.8400 (t) cc_final: 0.8099 (p) REVERT: E 177 ILE cc_start: 0.8416 (pt) cc_final: 0.8151 (pt) REVERT: E 180 MET cc_start: 0.7883 (ptm) cc_final: 0.7669 (ptm) REVERT: A 327 ASP cc_start: 0.5803 (OUTLIER) cc_final: 0.5468 (m-30) outliers start: 25 outliers final: 16 residues processed: 147 average time/residue: 0.2221 time to fit residues: 44.6637 Evaluate side-chains 144 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 26 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8746 Z= 0.166 Angle : 0.566 7.759 11882 Z= 0.286 Chirality : 0.043 0.202 1374 Planarity : 0.004 0.075 1495 Dihedral : 4.389 36.314 1217 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.14 % Allowed : 14.22 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.52 (0.26), residues: 1097 helix: 1.85 (0.28), residues: 361 sheet: -0.83 (0.30), residues: 285 loop : -1.87 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 49 TYR 0.014 0.001 TYR A 285 ARG 0.005 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.029 Fit side-chains REVERT: R 184 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7558 (mp) REVERT: R 196 GLN cc_start: 0.6186 (OUTLIER) cc_final: 0.5950 (mp10) REVERT: R 204 GLN cc_start: 0.6331 (mt0) cc_final: 0.5582 (pt0) REVERT: R 333 ARG cc_start: 0.6217 (ttm170) cc_final: 0.5465 (ttm-80) REVERT: R 380 TYR cc_start: 0.7692 (m-80) cc_final: 0.7470 (m-80) REVERT: B 137 ARG cc_start: 0.7922 (mmm160) cc_final: 0.7520 (tpp-160) REVERT: B 258 ASP cc_start: 0.8371 (t0) cc_final: 0.7778 (t0) REVERT: B 325 MET cc_start: 0.8053 (tpp) cc_final: 0.7562 (tpp) REVERT: E 19 LYS cc_start: 0.8248 (tttt) cc_final: 0.7996 (tptm) REVERT: E 116 THR cc_start: 0.6860 (OUTLIER) cc_final: 0.6547 (t) REVERT: E 146 SER cc_start: 0.8407 (t) cc_final: 0.8119 (p) REVERT: E 177 ILE cc_start: 0.8334 (pt) cc_final: 0.8066 (pt) REVERT: A 20 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: A 285 TYR cc_start: 0.7454 (m-10) cc_final: 0.7166 (m-10) REVERT: A 327 ASP cc_start: 0.5723 (OUTLIER) cc_final: 0.5453 (m-30) outliers start: 28 outliers final: 16 residues processed: 139 average time/residue: 0.1897 time to fit residues: 37.6827 Evaluate side-chains 142 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8746 Z= 0.165 Angle : 0.577 12.728 11882 Z= 0.288 Chirality : 0.042 0.223 1374 Planarity : 0.004 0.078 1495 Dihedral : 4.308 33.436 1217 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.14 % Allowed : 15.12 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.33 (0.26), residues: 1097 helix: 1.98 (0.28), residues: 361 sheet: -0.77 (0.30), residues: 289 loop : -1.70 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS C 44 PHE 0.013 0.001 PHE A 49 TYR 0.011 0.001 TYR E 178 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 1.098 Fit side-chains REVERT: R 184 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7471 (mp) REVERT: R 207 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.5756 (m-70) REVERT: R 333 ARG cc_start: 0.6132 (ttm170) cc_final: 0.5336 (ttm-80) REVERT: B 137 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7520 (tpp-160) REVERT: B 325 MET cc_start: 0.8042 (tpp) cc_final: 0.7553 (tpp) REVERT: E 116 THR cc_start: 0.6919 (OUTLIER) cc_final: 0.6581 (t) REVERT: E 146 SER cc_start: 0.8371 (t) cc_final: 0.8098 (p) REVERT: E 177 ILE cc_start: 0.8317 (pt) cc_final: 0.8047 (pt) REVERT: A 20 ASP cc_start: 0.7496 (t0) cc_final: 0.7277 (m-30) REVERT: A 327 ASP cc_start: 0.5731 (OUTLIER) cc_final: 0.5481 (m-30) outliers start: 28 outliers final: 19 residues processed: 140 average time/residue: 0.1763 time to fit residues: 36.1513 Evaluate side-chains 143 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 0.0020 chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 0.0570 chunk 65 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 overall best weight: 1.6110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN R 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8746 Z= 0.247 Angle : 0.622 11.198 11882 Z= 0.311 Chirality : 0.044 0.256 1374 Planarity : 0.004 0.079 1495 Dihedral : 4.509 36.674 1217 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.25 % Allowed : 16.01 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.39 (0.26), residues: 1097 helix: 1.90 (0.28), residues: 360 sheet: -0.74 (0.31), residues: 287 loop : -1.74 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS A 212 PHE 0.016 0.001 PHE E 27 TYR 0.027 0.002 TYR R 380 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.004 Fit side-chains REVERT: R 184 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7513 (mp) REVERT: R 194 VAL cc_start: 0.6166 (OUTLIER) cc_final: 0.5937 (m) REVERT: R 333 ARG cc_start: 0.6313 (ttm170) cc_final: 0.5549 (ttm-80) REVERT: R 380 TYR cc_start: 0.7644 (m-80) cc_final: 0.7274 (m-80) REVERT: B 118 ASP cc_start: 0.7700 (p0) cc_final: 0.7165 (p0) REVERT: B 137 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7520 (tpp-160) REVERT: B 205 ASP cc_start: 0.7927 (p0) cc_final: 0.7724 (p0) REVERT: B 220 GLN cc_start: 0.7922 (mt0) cc_final: 0.7656 (mt0) REVERT: B 325 MET cc_start: 0.8049 (tpp) cc_final: 0.7553 (tpp) REVERT: E 43 LYS cc_start: 0.7648 (mmtp) cc_final: 0.7435 (mmtm) REVERT: E 116 THR cc_start: 0.6890 (OUTLIER) cc_final: 0.6552 (t) REVERT: E 146 SER cc_start: 0.8349 (t) cc_final: 0.8101 (p) REVERT: E 177 ILE cc_start: 0.8346 (pt) cc_final: 0.8078 (pt) REVERT: A 20 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: A 327 ASP cc_start: 0.5614 (OUTLIER) cc_final: 0.5245 (m-30) REVERT: L 15 MET cc_start: 0.6336 (mtm) cc_final: 0.6106 (ptp) outliers start: 29 outliers final: 19 residues processed: 136 average time/residue: 0.1724 time to fit residues: 34.4990 Evaluate side-chains 140 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8746 Z= 0.180 Angle : 0.593 10.918 11882 Z= 0.295 Chirality : 0.043 0.224 1374 Planarity : 0.004 0.073 1495 Dihedral : 4.382 34.262 1217 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.80 % Allowed : 16.80 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.25 (0.26), residues: 1097 helix: 2.01 (0.28), residues: 361 sheet: -0.72 (0.31), residues: 290 loop : -1.61 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS C 44 PHE 0.014 0.001 PHE A 49 TYR 0.025 0.001 TYR R 380 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.993 Fit side-chains REVERT: R 184 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7564 (mp) REVERT: R 333 ARG cc_start: 0.6169 (ttm170) cc_final: 0.5323 (ttm-80) REVERT: R 380 TYR cc_start: 0.7748 (m-80) cc_final: 0.7415 (m-80) REVERT: B 118 ASP cc_start: 0.7667 (p0) cc_final: 0.7089 (p0) REVERT: B 137 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7518 (tpp-160) REVERT: B 156 GLN cc_start: 0.8098 (mt0) cc_final: 0.7838 (mt0) REVERT: B 220 GLN cc_start: 0.7890 (mt0) cc_final: 0.7555 (mt0) REVERT: B 325 MET cc_start: 0.8064 (tpp) cc_final: 0.7572 (tpp) REVERT: E 116 THR cc_start: 0.6862 (OUTLIER) cc_final: 0.6523 (t) REVERT: E 146 SER cc_start: 0.8386 (t) cc_final: 0.8150 (p) REVERT: E 177 ILE cc_start: 0.8323 (pt) cc_final: 0.8051 (pt) REVERT: A 20 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: A 327 ASP cc_start: 0.5577 (OUTLIER) cc_final: 0.5198 (m-30) outliers start: 25 outliers final: 20 residues processed: 124 average time/residue: 0.1886 time to fit residues: 33.8577 Evaluate side-chains 132 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 0.0010 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8746 Z= 0.147 Angle : 0.570 10.604 11882 Z= 0.283 Chirality : 0.042 0.235 1374 Planarity : 0.004 0.070 1495 Dihedral : 4.218 31.352 1217 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.91 % Allowed : 16.80 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.09 (0.26), residues: 1097 helix: 2.14 (0.28), residues: 362 sheet: -0.65 (0.30), residues: 288 loop : -1.52 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS C 44 PHE 0.015 0.001 PHE A 49 TYR 0.023 0.001 TYR R 380 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.572 Fit side-chains REVERT: R 184 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7554 (mp) REVERT: R 333 ARG cc_start: 0.6101 (ttm170) cc_final: 0.5279 (ttm-80) REVERT: R 380 TYR cc_start: 0.7740 (m-80) cc_final: 0.7452 (m-80) REVERT: B 118 ASP cc_start: 0.7330 (p0) cc_final: 0.6770 (p0) REVERT: B 137 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7515 (tpp-160) REVERT: B 156 GLN cc_start: 0.8075 (mt0) cc_final: 0.7815 (mt0) REVERT: B 164 THR cc_start: 0.8341 (p) cc_final: 0.7984 (m) REVERT: B 325 MET cc_start: 0.8043 (tpp) cc_final: 0.7548 (tpp) REVERT: E 116 THR cc_start: 0.6875 (OUTLIER) cc_final: 0.6529 (t) REVERT: E 146 SER cc_start: 0.8382 (t) cc_final: 0.8160 (p) REVERT: E 177 ILE cc_start: 0.8375 (pt) cc_final: 0.8112 (pt) REVERT: A 20 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: A 35 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8141 (mmtm) REVERT: A 327 ASP cc_start: 0.5749 (OUTLIER) cc_final: 0.5451 (m-30) REVERT: L 15 MET cc_start: 0.6796 (ptp) cc_final: 0.6241 (mtp) outliers start: 26 outliers final: 19 residues processed: 131 average time/residue: 0.2361 time to fit residues: 44.6817 Evaluate side-chains 134 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8746 Z= 0.201 Angle : 0.611 10.921 11882 Z= 0.304 Chirality : 0.044 0.299 1374 Planarity : 0.004 0.072 1495 Dihedral : 4.351 33.466 1217 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.46 % Allowed : 17.58 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.10 (0.26), residues: 1097 helix: 2.11 (0.28), residues: 362 sheet: -0.66 (0.30), residues: 289 loop : -1.51 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.005 0.001 HIS C 44 PHE 0.015 0.001 PHE A 49 TYR 0.021 0.001 TYR R 380 ARG 0.003 0.000 ARG A 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.015 Fit side-chains REVERT: R 184 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7399 (mp) REVERT: R 333 ARG cc_start: 0.6182 (ttm170) cc_final: 0.5331 (ttm-80) REVERT: R 380 TYR cc_start: 0.7762 (m-80) cc_final: 0.7499 (m-80) REVERT: B 22 ARG cc_start: 0.6694 (ttm170) cc_final: 0.6251 (ttm170) REVERT: B 118 ASP cc_start: 0.7509 (p0) cc_final: 0.6913 (p0) REVERT: B 137 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7507 (tpp-160) REVERT: B 156 GLN cc_start: 0.8146 (mt0) cc_final: 0.7917 (mt0) REVERT: B 205 ASP cc_start: 0.7622 (p0) cc_final: 0.7251 (t0) REVERT: B 325 MET cc_start: 0.8059 (tpp) cc_final: 0.7560 (tpp) REVERT: E 146 SER cc_start: 0.8376 (t) cc_final: 0.8165 (p) REVERT: E 177 ILE cc_start: 0.8411 (pt) cc_final: 0.8147 (pt) REVERT: A 20 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: A 327 ASP cc_start: 0.5832 (OUTLIER) cc_final: 0.5487 (m-30) REVERT: L 15 MET cc_start: 0.6790 (ptp) cc_final: 0.6100 (mtp) outliers start: 22 outliers final: 18 residues processed: 133 average time/residue: 0.2012 time to fit residues: 37.9454 Evaluate side-chains 135 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.184294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146072 restraints weight = 9159.539| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.89 r_work: 0.3651 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8746 Z= 0.152 Angle : 0.587 10.282 11882 Z= 0.294 Chirality : 0.043 0.298 1374 Planarity : 0.004 0.068 1495 Dihedral : 4.238 31.448 1217 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.35 % Allowed : 17.69 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.01 (0.26), residues: 1097 helix: 2.23 (0.28), residues: 362 sheet: -0.59 (0.31), residues: 282 loop : -1.47 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS A 321 PHE 0.015 0.001 PHE A 49 TYR 0.023 0.001 TYR R 380 ARG 0.004 0.000 ARG E 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.26 seconds wall clock time: 37 minutes 50.46 seconds (2270.46 seconds total)