Starting phenix.real_space_refine on Sat Dec 28 12:38:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxx_36716/12_2024/8jxx_36716_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxx_36716/12_2024/8jxx_36716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxx_36716/12_2024/8jxx_36716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxx_36716/12_2024/8jxx_36716.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxx_36716/12_2024/8jxx_36716_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxx_36716/12_2024/8jxx_36716_neut.cif" } resolution = 3.06 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= -0.002 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 Cl 1 4.86 5 C 5446 2.51 5 N 1411 2.21 5 O 1577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 8493 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2107 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1717 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2518 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 385 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1746 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'VCL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.59, per 1000 atoms: 0.66 Number of scatterers: 8493 At special positions: 0 Unit cell: (90.2, 123.2, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 58 16.00 O 1577 8.00 N 1411 7.00 C 5446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.05 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 39.3% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'R' and resid 14 through 43 removed outlier: 3.750A pdb=" N LEU R 18 " --> pdb=" O THR R 14 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL R 36 " --> pdb=" O GLY R 32 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 63 removed outlier: 3.924A pdb=" N PHE R 63 " --> pdb=" O ILE R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 67 through 78 Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 removed outlier: 4.556A pdb=" N PHE R 89 " --> pdb=" O GLU R 85 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 124 removed outlier: 3.565A pdb=" N THR R 124 " --> pdb=" O VAL R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 146 Processing helix chain 'R' and resid 147 through 153 removed outlier: 3.850A pdb=" N VAL R 153 " --> pdb=" O PRO R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 170 removed outlier: 3.725A pdb=" N PHE R 169 " --> pdb=" O PRO R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 203 removed outlier: 3.799A pdb=" N LEU R 175 " --> pdb=" O GLU R 171 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix removed outlier: 3.738A pdb=" N LYS R 203 " --> pdb=" O TRP R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 330 Proline residue: R 318 - end of helix removed outlier: 3.701A pdb=" N PHE R 328 " --> pdb=" O ILE R 324 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 349 removed outlier: 3.751A pdb=" N ARG R 341 " --> pdb=" O SER R 337 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 362 removed outlier: 3.706A pdb=" N VAL R 353 " --> pdb=" O PHE R 349 " (cutoff:3.500A) Proline residue: R 355 - end of helix removed outlier: 3.542A pdb=" N TYR R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix removed outlier: 3.729A pdb=" N HIS R 362 " --> pdb=" O TYR R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 371 Processing helix chain 'B' and resid 6 through 30 removed outlier: 3.705A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.854A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.598A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.623A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 4.087A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.612A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.501A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.893A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 4.077A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.527A pdb=" N GLN C 32 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.663A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.640A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.531A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.887A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.849A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.080A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.049A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.074A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 7.130A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.093A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.702A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278 Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 6.757A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.062A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 143 Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.248A pdb=" N VAL E 148 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1128 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: 2.43 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2671 1.34 - 1.46: 2200 1.46 - 1.59: 3730 1.59 - 1.71: 0 1.71 - 1.83: 85 Bond restraints: 8686 Sorted by residual: bond pdb=" CD GLN R 366 " pdb=" OE1 GLN R 366 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.52e+01 bond pdb=" CD GLN R 366 " pdb=" NE2 GLN R 366 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.22e+01 bond pdb=" C09 VCL R 401 " pdb=" S11 VCL R 401 " ideal model delta sigma weight residual 1.805 1.714 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C GLU E 235 " pdb=" N TYR E 236 " ideal model delta sigma weight residual 1.331 1.236 0.095 2.83e-02 1.25e+03 1.12e+01 bond pdb=" C09 VCL R 401 " pdb=" N08 VCL R 401 " ideal model delta sigma weight residual 1.268 1.322 -0.054 2.00e-02 2.50e+03 7.38e+00 ... (remaining 8681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11394 1.92 - 3.85: 343 3.85 - 5.77: 51 5.77 - 7.69: 12 7.69 - 9.62: 3 Bond angle restraints: 11803 Sorted by residual: angle pdb=" C LEU C 261 " pdb=" N MET C 262 " pdb=" CA MET C 262 " ideal model delta sigma weight residual 121.75 115.11 6.64 1.73e+00 3.34e-01 1.47e+01 angle pdb=" OE1 GLN R 347 " pdb=" CD GLN R 347 " pdb=" NE2 GLN R 347 " ideal model delta sigma weight residual 122.60 118.84 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA PRO R 359 " pdb=" N PRO R 359 " pdb=" CD PRO R 359 " ideal model delta sigma weight residual 112.00 107.02 4.98 1.40e+00 5.10e-01 1.26e+01 angle pdb=" C GLU R 182 " pdb=" CA GLU R 182 " pdb=" CB GLU R 182 " ideal model delta sigma weight residual 109.29 115.72 -6.43 1.82e+00 3.02e-01 1.25e+01 angle pdb=" N GLU R 182 " pdb=" CA GLU R 182 " pdb=" CB GLU R 182 " ideal model delta sigma weight residual 110.53 105.42 5.11 1.47e+00 4.63e-01 1.21e+01 ... (remaining 11798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.58: 4972 32.58 - 65.15: 79 65.15 - 97.73: 8 97.73 - 130.31: 2 130.31 - 162.89: 1 Dihedral angle restraints: 5062 sinusoidal: 1855 harmonic: 3207 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 143.97 -50.97 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA ALA C 305 " pdb=" C ALA C 305 " pdb=" N GLY C 306 " pdb=" CA GLY C 306 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" C13 VCL R 401 " pdb=" C14 VCL R 401 " pdb=" C15 VCL R 401 " pdb=" N19 VCL R 401 " ideal model delta sinusoidal sigma weight residual 290.86 127.97 162.89 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 5059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 969 0.049 - 0.098: 297 0.098 - 0.146: 79 0.146 - 0.195: 1 0.195 - 0.244: 3 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA TRP R 316 " pdb=" N TRP R 316 " pdb=" C TRP R 316 " pdb=" CB TRP R 316 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA GLN B 306 " pdb=" N GLN B 306 " pdb=" C GLN B 306 " pdb=" CB GLN B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU R 181 " pdb=" CB LEU R 181 " pdb=" CD1 LEU R 181 " pdb=" CD2 LEU R 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 1346 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 VCL R 401 " -0.153 2.00e-02 2.50e+03 1.35e-01 2.28e+02 pdb=" C09 VCL R 401 " 0.051 2.00e-02 2.50e+03 pdb=" N08 VCL R 401 " 0.222 2.00e-02 2.50e+03 pdb=" N10 VCL R 401 " -0.125 2.00e-02 2.50e+03 pdb=" S11 VCL R 401 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 90 " 0.080 2.00e-02 2.50e+03 5.51e-02 7.60e+01 pdb=" CG TRP R 90 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP R 90 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP R 90 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 90 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TRP R 90 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP R 90 " -0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 90 " 0.082 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 90 " -0.062 2.00e-02 2.50e+03 pdb=" CH2 TRP R 90 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 316 " -0.063 2.00e-02 2.50e+03 3.95e-02 3.91e+01 pdb=" CG TRP R 316 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP R 316 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP R 316 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 316 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP R 316 " -0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP R 316 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 316 " -0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 316 " 0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP R 316 " -0.001 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 366 2.72 - 3.26: 8013 3.26 - 3.81: 12573 3.81 - 4.35: 15219 4.35 - 4.90: 27049 Nonbonded interactions: 63220 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.173 3.040 nonbonded pdb=" OE1 GLU B 33 " pdb=" NZ LYS B 197 " model vdw 2.243 3.120 nonbonded pdb=" ND2 ASN D 59 " pdb=" O ARG D 62 " model vdw 2.249 3.120 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.252 3.040 nonbonded pdb=" O GLY E 8 " pdb=" NH2 ARG E 18 " model vdw 2.269 3.120 ... (remaining 63215 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: 1.380 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.300 Find NCS groups from input model: 0.110 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.007 0.099 8686 Z= 0.425 Angle : 0.817 9.616 11803 Z= 0.468 Chirality : 0.049 0.244 1349 Planarity : 0.007 0.135 1483 Dihedral : 13.568 162.886 2984 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1081 helix: 1.35 (0.27), residues: 361 sheet: 0.43 (0.31), residues: 247 loop : -1.70 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.007 TRP R 90 HIS 0.006 0.002 HIS C 62 PHE 0.041 0.003 PHE R 183 TYR 0.049 0.004 TYR R 95 ARG 0.007 0.001 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: R 165 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7866 (mm-30) REVERT: B 197 LYS cc_start: 0.8063 (mttp) cc_final: 0.7746 (mttm) REVERT: B 306 GLN cc_start: 0.6852 (mp10) cc_final: 0.6436 (mp10) REVERT: C 46 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7555 (mtp85) REVERT: C 215 GLU cc_start: 0.6978 (mp0) cc_final: 0.6684 (mp0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2127 time to fit residues: 36.8934 Evaluate side-chains 106 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 33 ASN R 366 GLN B 269 ASN C 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8686 Z= 0.174 Angle : 0.568 7.180 11803 Z= 0.304 Chirality : 0.042 0.144 1349 Planarity : 0.004 0.056 1483 Dihedral : 8.753 145.272 1189 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.57 % Allowed : 4.93 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1081 helix: 2.17 (0.28), residues: 362 sheet: 0.41 (0.29), residues: 282 loop : -1.64 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 80 HIS 0.004 0.001 HIS R 75 PHE 0.012 0.001 PHE R 168 TYR 0.016 0.001 TYR B 302 ARG 0.003 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.7964 (ptp) cc_final: 0.7690 (ptm) REVERT: R 165 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 197 LYS cc_start: 0.8139 (mttp) cc_final: 0.7779 (mttm) REVERT: C 130 GLU cc_start: 0.7841 (mp0) cc_final: 0.7566 (mp0) REVERT: C 215 GLU cc_start: 0.6606 (mp0) cc_final: 0.6309 (mp0) REVERT: C 280 LYS cc_start: 0.7228 (mttm) cc_final: 0.6962 (mttp) REVERT: E 82 GLN cc_start: 0.7693 (tp40) cc_final: 0.7460 (tp-100) REVERT: E 87 ARG cc_start: 0.7238 (ptp-170) cc_final: 0.6964 (ptp-170) outliers start: 14 outliers final: 10 residues processed: 121 average time/residue: 0.2180 time to fit residues: 36.9176 Evaluate side-chains 119 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8686 Z= 0.204 Angle : 0.566 6.732 11803 Z= 0.300 Chirality : 0.042 0.160 1349 Planarity : 0.004 0.056 1483 Dihedral : 8.191 142.574 1189 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.24 % Allowed : 7.28 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1081 helix: 2.29 (0.28), residues: 361 sheet: 0.47 (0.29), residues: 277 loop : -1.46 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 90 HIS 0.004 0.001 HIS R 75 PHE 0.013 0.002 PHE C 199 TYR 0.014 0.001 TYR R 173 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7728 (ptp) REVERT: R 165 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8068 (mm-30) REVERT: B 197 LYS cc_start: 0.8097 (mttp) cc_final: 0.7812 (mttm) REVERT: B 211 TRP cc_start: 0.6350 (OUTLIER) cc_final: 0.5136 (t60) REVERT: C 130 GLU cc_start: 0.7827 (mp0) cc_final: 0.7538 (mp0) REVERT: C 215 GLU cc_start: 0.6484 (mp0) cc_final: 0.6268 (mp0) REVERT: C 262 MET cc_start: 0.8008 (tpp) cc_final: 0.7786 (tpp) REVERT: C 280 LYS cc_start: 0.7468 (mttm) cc_final: 0.7103 (mttp) REVERT: E 87 ARG cc_start: 0.7271 (ptp-170) cc_final: 0.6995 (ptp-170) REVERT: E 220 LEU cc_start: 0.8514 (mp) cc_final: 0.8017 (pt) outliers start: 20 outliers final: 13 residues processed: 124 average time/residue: 0.2073 time to fit residues: 35.9160 Evaluate side-chains 122 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 0.0050 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 0.0570 chunk 104 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.4912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8686 Z= 0.131 Angle : 0.508 6.816 11803 Z= 0.269 Chirality : 0.041 0.157 1349 Planarity : 0.004 0.054 1483 Dihedral : 7.598 144.997 1189 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.79 % Allowed : 9.63 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1081 helix: 2.60 (0.29), residues: 359 sheet: 0.69 (0.30), residues: 267 loop : -1.38 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.004 0.001 HIS R 75 PHE 0.012 0.001 PHE B 189 TYR 0.009 0.001 TYR R 173 ARG 0.004 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7636 (ptp) REVERT: R 165 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8051 (mm-30) REVERT: B 197 LYS cc_start: 0.8101 (mttp) cc_final: 0.7880 (mttm) REVERT: B 269 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8565 (m-40) REVERT: C 260 GLU cc_start: 0.7806 (tt0) cc_final: 0.7569 (tt0) REVERT: E 87 ARG cc_start: 0.7277 (ptp-170) cc_final: 0.6966 (ptp-170) REVERT: E 220 LEU cc_start: 0.8428 (mp) cc_final: 0.7996 (pt) outliers start: 16 outliers final: 11 residues processed: 131 average time/residue: 0.2022 time to fit residues: 37.0035 Evaluate side-chains 124 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.0770 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 118 ASN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8686 Z= 0.159 Angle : 0.528 7.180 11803 Z= 0.277 Chirality : 0.041 0.145 1349 Planarity : 0.004 0.054 1483 Dihedral : 7.062 152.905 1189 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.58 % Allowed : 9.85 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1081 helix: 2.62 (0.29), residues: 360 sheet: 0.78 (0.31), residues: 256 loop : -1.31 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 90 HIS 0.004 0.001 HIS R 75 PHE 0.011 0.001 PHE B 189 TYR 0.010 0.001 TYR R 173 ARG 0.006 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7734 (ptp) REVERT: R 165 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8028 (mm-30) REVERT: B 197 LYS cc_start: 0.8121 (mttp) cc_final: 0.7892 (mttm) REVERT: B 211 TRP cc_start: 0.6421 (OUTLIER) cc_final: 0.5653 (t60) REVERT: B 269 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8592 (m-40) REVERT: E 87 ARG cc_start: 0.7281 (ptp-170) cc_final: 0.7018 (ptp-170) REVERT: E 220 LEU cc_start: 0.8383 (mp) cc_final: 0.8042 (pt) outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 0.2051 time to fit residues: 36.6152 Evaluate side-chains 131 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 118 ASN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8686 Z= 0.201 Angle : 0.553 7.172 11803 Z= 0.290 Chirality : 0.042 0.147 1349 Planarity : 0.004 0.054 1483 Dihedral : 6.928 161.627 1189 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.91 % Allowed : 10.08 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1081 helix: 2.56 (0.28), residues: 363 sheet: 0.65 (0.30), residues: 270 loop : -1.36 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 90 HIS 0.004 0.001 HIS R 75 PHE 0.013 0.001 PHE C 199 TYR 0.012 0.001 TYR R 173 ARG 0.005 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7757 (ptp) REVERT: R 165 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 197 LYS cc_start: 0.8108 (mttp) cc_final: 0.7893 (mttm) REVERT: B 211 TRP cc_start: 0.6608 (OUTLIER) cc_final: 0.5864 (t60) REVERT: B 269 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8145 (m110) REVERT: C 280 LYS cc_start: 0.7049 (mttm) cc_final: 0.6795 (mttp) REVERT: E 87 ARG cc_start: 0.7294 (ptp-170) cc_final: 0.7022 (ptp-170) REVERT: E 220 LEU cc_start: 0.8365 (mp) cc_final: 0.8057 (pt) outliers start: 26 outliers final: 17 residues processed: 123 average time/residue: 0.2126 time to fit residues: 36.4850 Evaluate side-chains 125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 118 ASN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8686 Z= 0.132 Angle : 0.514 7.398 11803 Z= 0.268 Chirality : 0.041 0.144 1349 Planarity : 0.004 0.052 1483 Dihedral : 6.739 169.709 1189 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.13 % Allowed : 11.09 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1081 helix: 2.71 (0.29), residues: 363 sheet: 0.79 (0.31), residues: 261 loop : -1.23 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.003 0.001 HIS R 75 PHE 0.011 0.001 PHE B 189 TYR 0.009 0.001 TYR R 173 ARG 0.006 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7753 (ptp) REVERT: R 165 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8087 (mm-30) REVERT: B 197 LYS cc_start: 0.8151 (mttp) cc_final: 0.7932 (mttm) REVERT: B 269 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8388 (m-40) REVERT: E 87 ARG cc_start: 0.7269 (ptp-170) cc_final: 0.7018 (ptp-170) REVERT: E 193 MET cc_start: 0.7147 (tmm) cc_final: 0.6923 (tmm) REVERT: E 220 LEU cc_start: 0.8332 (mp) cc_final: 0.8078 (pt) outliers start: 19 outliers final: 14 residues processed: 124 average time/residue: 0.2054 time to fit residues: 35.6212 Evaluate side-chains 129 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 118 ASN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8686 Z= 0.158 Angle : 0.521 7.496 11803 Z= 0.274 Chirality : 0.041 0.141 1349 Planarity : 0.004 0.053 1483 Dihedral : 6.770 175.130 1189 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.35 % Allowed : 11.65 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1081 helix: 2.67 (0.29), residues: 363 sheet: 0.78 (0.31), residues: 261 loop : -1.19 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.005 0.001 HIS R 75 PHE 0.016 0.001 PHE R 82 TYR 0.010 0.001 TYR R 173 ARG 0.006 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7789 (ptp) REVERT: R 165 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 197 LYS cc_start: 0.8141 (mttp) cc_final: 0.7796 (mtmt) REVERT: B 269 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8343 (m-40) REVERT: C 254 ASP cc_start: 0.8616 (t70) cc_final: 0.8298 (t0) REVERT: C 280 LYS cc_start: 0.7225 (mttm) cc_final: 0.6899 (mttp) REVERT: E 87 ARG cc_start: 0.7246 (ptp-170) cc_final: 0.6986 (ptp-170) REVERT: E 220 LEU cc_start: 0.8312 (mp) cc_final: 0.8080 (pt) outliers start: 21 outliers final: 18 residues processed: 122 average time/residue: 0.2093 time to fit residues: 35.7159 Evaluate side-chains 131 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 118 ASN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8686 Z= 0.152 Angle : 0.525 7.807 11803 Z= 0.276 Chirality : 0.041 0.140 1349 Planarity : 0.004 0.052 1483 Dihedral : 6.797 179.709 1189 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.46 % Allowed : 11.65 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1081 helix: 2.77 (0.29), residues: 358 sheet: 0.80 (0.31), residues: 261 loop : -1.19 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.004 0.001 HIS R 75 PHE 0.011 0.001 PHE B 189 TYR 0.008 0.001 TYR R 173 ARG 0.006 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7786 (ptp) REVERT: R 165 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8077 (mm-30) REVERT: R 322 PHE cc_start: 0.8160 (t80) cc_final: 0.7929 (t80) REVERT: B 197 LYS cc_start: 0.8136 (mttp) cc_final: 0.7795 (mtmt) REVERT: B 269 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8440 (m-40) REVERT: C 280 LYS cc_start: 0.7130 (mttm) cc_final: 0.6780 (mttp) REVERT: E 87 ARG cc_start: 0.7241 (ptp-170) cc_final: 0.6981 (ptp-170) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 0.2022 time to fit residues: 34.6423 Evaluate side-chains 130 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 118 ASN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8686 Z= 0.134 Angle : 0.518 7.914 11803 Z= 0.271 Chirality : 0.040 0.138 1349 Planarity : 0.004 0.052 1483 Dihedral : 6.613 175.509 1189 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.79 % Allowed : 12.77 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1081 helix: 2.81 (0.29), residues: 358 sheet: 0.87 (0.32), residues: 252 loop : -1.12 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 90 HIS 0.003 0.001 HIS R 75 PHE 0.012 0.001 PHE B 189 TYR 0.008 0.001 TYR R 72 ARG 0.007 0.000 ARG E 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.091 Fit side-chains REVERT: R 30 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7780 (ptp) REVERT: R 165 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 306 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: C 254 ASP cc_start: 0.8621 (t70) cc_final: 0.8283 (t0) REVERT: C 280 LYS cc_start: 0.7079 (mttm) cc_final: 0.6734 (mttp) REVERT: E 219 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7072 (mtm-85) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 0.2174 time to fit residues: 36.6155 Evaluate side-chains 125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 0.0040 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 118 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.165459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117550 restraints weight = 11323.622| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.89 r_work: 0.3318 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8686 Z= 0.155 Angle : 0.526 7.876 11803 Z= 0.277 Chirality : 0.041 0.138 1349 Planarity : 0.004 0.052 1483 Dihedral : 6.492 170.315 1189 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.02 % Allowed : 12.65 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1081 helix: 2.80 (0.29), residues: 359 sheet: 0.87 (0.32), residues: 251 loop : -1.07 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.004 0.001 HIS R 75 PHE 0.011 0.001 PHE C 199 TYR 0.009 0.001 TYR R 173 ARG 0.006 0.000 ARG E 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.57 seconds wall clock time: 38 minutes 35.11 seconds (2315.11 seconds total)