Starting phenix.real_space_refine on Thu Mar 13 02:09:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xow_33361/03_2025/7xow_33361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xow_33361/03_2025/7xow_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_33361/03_2025/7xow_33361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xow_33361/03_2025/7xow_33361.map" model { file = "/net/cci-nas-00/data/ceres_data/7xow_33361/03_2025/7xow_33361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xow_33361/03_2025/7xow_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-5624/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: 5.26, 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: 2.46 Conformation dependent library (CDL) restraints added in 986.2 milliseconds 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: 0.96 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: 2.52 Time building geometry restraints manager: 2.84 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: 0.800 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- 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 : 0.905 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: 0.2532 time to fit residues: 56.1962 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 : 0.900 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.191900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.153676 restraints weight = 8953.151| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.86 r_work: 0.3664 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.944 Fit side-chains REVERT: R 207 HIS cc_start: 0.6624 (OUTLIER) cc_final: 0.5070 (m-70) REVERT: R 213 ARG cc_start: 0.5970 (mmt180) cc_final: 0.3491 (ptt-90) REVERT: R 333 ARG cc_start: 0.6641 (ttm170) cc_final: 0.5674 (ttm-80) REVERT: R 380 TYR cc_start: 0.7328 (m-80) cc_final: 0.6961 (m-80) REVERT: R 398 ARG cc_start: 0.6817 (mmt90) cc_final: 0.6525 (mmp80) REVERT: B 258 ASP cc_start: 0.8414 (t0) cc_final: 0.7531 (t0) REVERT: B 325 MET cc_start: 0.8215 (tpp) cc_final: 0.7710 (tpp) REVERT: A 242 MET cc_start: 0.7324 (tpp) cc_final: 0.6309 (tpp) REVERT: A 305 LYS cc_start: 0.6738 (ttpp) cc_final: 0.6458 (tppt) REVERT: A 339 LYS cc_start: 0.7149 (tttt) cc_final: 0.6935 (tttp) outliers start: 16 outliers final: 8 residues processed: 162 average time/residue: 0.2157 time to fit residues: 47.8915 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 : 1.001 ------------------------------------------------------------------------------- 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 32 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.184935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146465 restraints weight = 9234.422| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.91 r_work: 0.3624 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1696 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= 0.207 Angle : 0.603 8.529 11882 Z= 0.305 Chirality : 0.044 0.181 1374 Planarity : 0.004 0.082 1495 Dihedral : 4.667 38.643 1219 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 2.91 % Allowed : 12.32 % Favored : 84.77 % 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: -1.03 (0.25), residues: 1097 helix: 1.36 (0.28), residues: 367 sheet: -1.06 (0.30), residues: 285 loop : -2.20 (0.27), residues: 445 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 0.014 0.001 PHE E 27 TYR 0.018 0.001 TYR A 285 ARG 0.005 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 164 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.026 Fit side-chains REVERT: R 184 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7144 (mp) REVERT: R 196 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.6056 (mp10) REVERT: R 213 ARG cc_start: 0.6226 (mmt180) cc_final: 0.3613 (ptt-90) REVERT: R 244 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5420 (mp0) REVERT: R 333 ARG cc_start: 0.6798 (ttm170) cc_final: 0.5763 (ttm-80) REVERT: R 380 TYR cc_start: 0.7366 (m-80) cc_final: 0.6993 (m-80) REVERT: R 398 ARG cc_start: 0.6779 (mmt90) cc_final: 0.6436 (mmp80) REVERT: B 67 SER cc_start: 0.8341 (t) cc_final: 0.8060 (m) REVERT: B 137 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7515 (tpp-160) REVERT: B 258 ASP cc_start: 0.8488 (t0) cc_final: 0.7740 (t0) REVERT: B 325 MET cc_start: 0.8226 (tpp) cc_final: 0.7763 (tpp) REVERT: E 30 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8256 (t) REVERT: E 146 SER cc_start: 0.8537 (t) cc_final: 0.8220 (p) REVERT: E 177 ILE cc_start: 0.8521 (pt) cc_final: 0.8291 (pt) REVERT: A 305 LYS cc_start: 0.6749 (ttpp) cc_final: 0.6508 (tppt) REVERT: A 327 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5449 (m-30) REVERT: L 15 MET cc_start: 0.6931 (ptp) cc_final: 0.6453 (mtp) outliers start: 26 outliers final: 13 residues processed: 150 average time/residue: 0.2132 time to fit residues: 44.1218 Evaluate side-chains 150 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 40.0000 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** 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 = 0.4212 r_free = 0.4212 target = 0.190980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.152855 restraints weight = 9041.299| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.88 r_work: 0.3659 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8746 Z= 0.155 Angle : 0.568 7.679 11882 Z= 0.288 Chirality : 0.043 0.191 1374 Planarity : 0.004 0.075 1495 Dihedral : 4.421 36.421 1217 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.69 % Allowed : 14.22 % 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: -0.66 (0.26), residues: 1097 helix: 1.75 (0.28), residues: 361 sheet: -0.92 (0.30), residues: 285 loop : -1.96 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 49 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG E 18 *********************** 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 158 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.984 Fit side-chains REVERT: R 184 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7137 (mp) REVERT: R 186 MET cc_start: 0.7590 (mmt) cc_final: 0.7387 (mmt) REVERT: R 333 ARG cc_start: 0.6561 (ttm170) cc_final: 0.5510 (ttm-80) REVERT: R 380 TYR cc_start: 0.7419 (m-80) cc_final: 0.7147 (m-80) REVERT: R 398 ARG cc_start: 0.6791 (mmt90) cc_final: 0.6457 (mmp80) REVERT: B 137 ARG cc_start: 0.8246 (mmm160) cc_final: 0.7513 (tpp-160) REVERT: B 258 ASP cc_start: 0.8416 (t0) cc_final: 0.7785 (t0) REVERT: B 325 MET cc_start: 0.8244 (tpp) cc_final: 0.7715 (tpp) REVERT: E 30 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8262 (t) REVERT: E 116 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6606 (t) REVERT: E 126 ILE cc_start: 0.8004 (mp) cc_final: 0.7713 (mt) REVERT: E 146 SER cc_start: 0.8549 (t) cc_final: 0.8256 (p) REVERT: E 177 ILE cc_start: 0.8415 (pt) cc_final: 0.8167 (pt) REVERT: A 327 ASP cc_start: 0.5695 (OUTLIER) cc_final: 0.5377 (m-30) outliers start: 24 outliers final: 15 residues processed: 146 average time/residue: 0.2066 time to fit residues: 42.0225 Evaluate side-chains 145 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 30 SER 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 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 53 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN B 259 GLN A 321 HIS A 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.173365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.137979 restraints weight = 9416.455| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.65 r_work: 0.3565 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 8746 Z= 0.457 Angle : 0.746 9.767 11882 Z= 0.377 Chirality : 0.048 0.206 1374 Planarity : 0.005 0.095 1495 Dihedral : 5.167 43.567 1217 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.70 % Allowed : 14.56 % 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: -0.98 (0.26), residues: 1097 helix: 1.32 (0.28), residues: 359 sheet: -0.87 (0.30), residues: 296 loop : -2.17 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.006 0.002 HIS R 364 PHE 0.023 0.002 PHE E 27 TYR 0.013 0.002 TYR E 178 ARG 0.006 0.001 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 163 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.832 Fit side-chains REVERT: R 204 GLN cc_start: 0.6845 (mt0) cc_final: 0.5826 (pt0) REVERT: R 207 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.6003 (m-70) REVERT: R 213 ARG cc_start: 0.6643 (mmt180) cc_final: 0.4118 (ptt-90) REVERT: R 333 ARG cc_start: 0.6920 (ttm170) cc_final: 0.5942 (ttm-80) REVERT: R 380 TYR cc_start: 0.7688 (m-80) cc_final: 0.7384 (m-80) REVERT: R 398 ARG cc_start: 0.6879 (mmt90) cc_final: 0.6416 (mmp80) REVERT: B 118 ASP cc_start: 0.8286 (p0) cc_final: 0.7845 (p0) REVERT: B 137 ARG cc_start: 0.8321 (mmm160) cc_final: 0.7661 (tpp-160) REVERT: B 205 ASP cc_start: 0.8233 (p0) cc_final: 0.8022 (p0) REVERT: B 258 ASP cc_start: 0.8638 (t0) cc_final: 0.8423 (t0) REVERT: B 325 MET cc_start: 0.8225 (tpp) cc_final: 0.7858 (tpp) REVERT: A 20 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: A 306 MET cc_start: 0.6967 (mtm) cc_final: 0.6712 (mtp) REVERT: A 327 ASP cc_start: 0.5742 (OUTLIER) cc_final: 0.5530 (m-30) outliers start: 33 outliers final: 21 residues processed: 147 average time/residue: 0.2074 time to fit residues: 41.9028 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 : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP 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 30 SER 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 193 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.174510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139217 restraints weight = 9357.147| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.66 r_work: 0.3574 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8746 Z= 0.352 Angle : 0.683 9.477 11882 Z= 0.344 Chirality : 0.046 0.227 1374 Planarity : 0.005 0.086 1495 Dihedral : 5.110 42.970 1217 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.47 % Allowed : 15.79 % 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: -0.88 (0.26), residues: 1097 helix: 1.46 (0.28), residues: 359 sheet: -0.85 (0.30), residues: 296 loop : -2.14 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.004 0.001 HIS R 364 PHE 0.019 0.002 PHE E 27 TYR 0.014 0.002 TYR E 178 ARG 0.003 0.000 ARG R 57 *********************** 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 158 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.931 Fit side-chains REVERT: R 186 MET cc_start: 0.7832 (mmt) cc_final: 0.7587 (mmt) REVERT: R 204 GLN cc_start: 0.6615 (mt0) cc_final: 0.5570 (pt0) REVERT: R 213 ARG cc_start: 0.6562 (mmt180) cc_final: 0.4069 (ptt-90) REVERT: R 333 ARG cc_start: 0.6920 (ttm170) cc_final: 0.5969 (ttm-80) REVERT: R 380 TYR cc_start: 0.7662 (m-80) cc_final: 0.7375 (m-80) REVERT: R 398 ARG cc_start: 0.6864 (mmt90) cc_final: 0.6409 (mmp80) REVERT: B 67 SER cc_start: 0.8672 (t) cc_final: 0.8431 (m) REVERT: B 118 ASP cc_start: 0.8268 (p0) cc_final: 0.7811 (p0) REVERT: B 137 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7674 (tpp-160) REVERT: B 258 ASP cc_start: 0.8601 (t0) cc_final: 0.8057 (t0) REVERT: B 325 MET cc_start: 0.8403 (tpp) cc_final: 0.8030 (tpp) REVERT: E 30 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8080 (t) REVERT: A 20 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: A 306 MET cc_start: 0.6821 (mtm) cc_final: 0.6564 (mtp) REVERT: A 327 ASP cc_start: 0.5903 (OUTLIER) cc_final: 0.5670 (m-30) outliers start: 31 outliers final: 19 residues processed: 143 average time/residue: 0.2103 time to fit residues: 41.9342 Evaluate side-chains 141 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP 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 116 THR Chi-restraints excluded: chain E residue 157 ASN 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 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142543 restraints weight = 9368.780| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.53 r_work: 0.3596 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2503 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= 0.264 Angle : 0.646 9.372 11882 Z= 0.323 Chirality : 0.045 0.248 1374 Planarity : 0.004 0.084 1495 Dihedral : 4.886 40.242 1217 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.58 % Allowed : 15.90 % Favored : 80.52 % 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: -0.69 (0.26), residues: 1097 helix: 1.65 (0.28), residues: 360 sheet: -0.86 (0.30), residues: 298 loop : -1.99 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS R 364 PHE 0.017 0.002 PHE E 27 TYR 0.014 0.001 TYR E 178 ARG 0.010 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 156 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.909 Fit side-chains REVERT: R 134 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6680 (mtm) REVERT: R 204 GLN cc_start: 0.6529 (mt0) cc_final: 0.6237 (mm-40) REVERT: R 213 ARG cc_start: 0.6455 (mmt180) cc_final: 0.3861 (ptt-90) REVERT: R 333 ARG cc_start: 0.6875 (ttm170) cc_final: 0.5940 (ttm-80) REVERT: R 380 TYR cc_start: 0.7631 (m-80) cc_final: 0.7411 (m-80) REVERT: B 118 ASP cc_start: 0.8223 (p0) cc_final: 0.7748 (p0) REVERT: B 137 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7667 (tpp-160) REVERT: B 164 THR cc_start: 0.8749 (p) cc_final: 0.8376 (m) REVERT: B 325 MET cc_start: 0.8401 (tpp) cc_final: 0.8007 (tpp) REVERT: E 30 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8086 (t) REVERT: A 20 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7435 (m-30) outliers start: 32 outliers final: 23 residues processed: 143 average time/residue: 0.2006 time to fit residues: 39.7822 Evaluate side-chains 145 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 134 MET Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 225 LEU 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 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN 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 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.177886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139639 restraints weight = 9386.200| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.92 r_work: 0.3570 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8746 Z= 0.289 Angle : 0.661 8.849 11882 Z= 0.333 Chirality : 0.045 0.259 1374 Planarity : 0.004 0.083 1495 Dihedral : 4.925 40.919 1217 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.58 % Allowed : 16.13 % 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: -0.66 (0.26), residues: 1097 helix: 1.67 (0.28), residues: 361 sheet: -0.83 (0.30), residues: 298 loop : -1.97 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS R 364 PHE 0.018 0.002 PHE E 27 TYR 0.014 0.001 TYR E 178 ARG 0.008 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 146 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.404 Fit side-chains REVERT: R 184 LEU cc_start: 0.7636 (tt) cc_final: 0.7060 (mp) REVERT: R 186 MET cc_start: 0.7761 (mmt) cc_final: 0.7492 (mmt) REVERT: R 204 GLN cc_start: 0.6498 (mt0) cc_final: 0.6167 (mm-40) REVERT: R 213 ARG cc_start: 0.6424 (mmt180) cc_final: 0.3767 (ptt-90) REVERT: R 333 ARG cc_start: 0.6854 (ttm170) cc_final: 0.5851 (ttm-80) REVERT: R 380 TYR cc_start: 0.7533 (m-80) cc_final: 0.7271 (m-80) REVERT: R 402 LEU cc_start: 0.5071 (tt) cc_final: 0.4241 (mp) REVERT: B 118 ASP cc_start: 0.8196 (p0) cc_final: 0.7740 (p0) REVERT: B 137 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7505 (tpp-160) REVERT: B 325 MET cc_start: 0.8336 (tpp) cc_final: 0.7933 (tpp) REVERT: E 30 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.8034 (t) REVERT: A 20 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7336 (m-30) outliers start: 32 outliers final: 26 residues processed: 134 average time/residue: 0.2927 time to fit residues: 54.2075 Evaluate side-chains 141 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 225 LEU 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 C residue 41 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN 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 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 193 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.177527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140267 restraints weight = 9367.601| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.85 r_work: 0.3611 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8746 Z= 0.164 Angle : 0.598 8.544 11882 Z= 0.304 Chirality : 0.043 0.251 1374 Planarity : 0.004 0.074 1495 Dihedral : 4.535 35.708 1217 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.58 % Allowed : 17.47 % 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: -0.34 (0.26), residues: 1097 helix: 2.01 (0.28), residues: 362 sheet: -0.80 (0.31), residues: 287 loop : -1.74 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 321 PHE 0.016 0.001 PHE A 49 TYR 0.012 0.001 TYR E 178 ARG 0.007 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: 23 poor density : 119 time to evaluate : 0.950 Fit side-chains REVERT: R 184 LEU cc_start: 0.7616 (tt) cc_final: 0.7145 (mp) REVERT: R 333 ARG cc_start: 0.6549 (ttm170) cc_final: 0.5481 (ttm-80) REVERT: R 398 ARG cc_start: 0.6158 (mmt-90) cc_final: 0.5810 (mmp80) REVERT: R 402 LEU cc_start: 0.5478 (tt) cc_final: 0.4685 (mp) REVERT: B 118 ASP cc_start: 0.7883 (p0) cc_final: 0.7390 (p0) REVERT: B 137 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7457 (tpp-160) REVERT: B 164 THR cc_start: 0.8531 (p) cc_final: 0.8173 (m) REVERT: B 205 ASP cc_start: 0.7791 (p0) cc_final: 0.7455 (t0) REVERT: B 325 MET cc_start: 0.8300 (tpp) cc_final: 0.8006 (tpp) REVERT: E 30 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7992 (t) REVERT: E 116 THR cc_start: 0.6886 (OUTLIER) cc_final: 0.6582 (t) outliers start: 23 outliers final: 18 residues processed: 133 average time/residue: 0.1994 time to fit residues: 37.0219 Evaluate side-chains 135 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU 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 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN 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 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.175165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136713 restraints weight = 9506.828| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.96 r_work: 0.3564 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8746 Z= 0.236 Angle : 0.636 9.172 11882 Z= 0.317 Chirality : 0.044 0.220 1374 Planarity : 0.004 0.080 1495 Dihedral : 4.686 37.876 1217 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.46 % Allowed : 17.36 % Favored : 80.18 % 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: 1.97 (0.28), residues: 360 sheet: -0.76 (0.30), residues: 298 loop : -1.81 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS C 44 PHE 0.016 0.001 PHE A 49 TYR 0.034 0.001 TYR R 380 ARG 0.007 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 136 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.914 Fit side-chains REVERT: R 333 ARG cc_start: 0.6632 (ttm170) cc_final: 0.5601 (ttm-80) REVERT: R 402 LEU cc_start: 0.5390 (tt) cc_final: 0.4575 (mp) REVERT: B 118 ASP cc_start: 0.7926 (p0) cc_final: 0.7453 (p0) REVERT: B 137 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7461 (tpp-160) REVERT: B 205 ASP cc_start: 0.7825 (p0) cc_final: 0.7515 (t0) REVERT: B 325 MET cc_start: 0.8319 (tpp) cc_final: 0.7932 (tpp) REVERT: E 30 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8008 (t) REVERT: E 116 THR cc_start: 0.6917 (OUTLIER) cc_final: 0.6614 (t) outliers start: 22 outliers final: 20 residues processed: 128 average time/residue: 0.2028 time to fit residues: 36.4188 Evaluate side-chains 138 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU 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 30 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN 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 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.180652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142547 restraints weight = 9391.856| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.91 r_work: 0.3606 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2984 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= 0.172 Angle : 0.601 10.548 11882 Z= 0.299 Chirality : 0.043 0.236 1374 Planarity : 0.004 0.074 1495 Dihedral : 4.498 35.603 1217 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.69 % Allowed : 17.36 % 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: -0.22 (0.26), residues: 1097 helix: 2.17 (0.28), residues: 360 sheet: -0.77 (0.31), residues: 291 loop : -1.67 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 321 PHE 0.017 0.001 PHE A 49 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4776.44 seconds wall clock time: 85 minutes 4.38 seconds (5104.38 seconds total)